From 13d82a88f14e71cb48c21f928d150543aeda3e81 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 2 Jul 2026 13:01:53 -0700
Subject: [PATCH 01/84] feat(score-sets): add lean whole-set variant view
 channel

  Wire the UI up to the new GET /score-sets/{urn}/variants endpoint that
  serves one pre-chewed record per variant (selection key, score,
  consequence, annotation bridge ids, and parsed DNA/protein HGVS blocks).

  - add LeanVariant/HgvsField types mirrored from the OpenAPI schema
  - add getLeanScoreSetVariants and leanScoreSetVariantsUrl to the API
    client
  - fetch the lean view alongside the legacy CSV scoresData channel in
    ScoreSetView, exposing a typed leanVariantRecords handle so consumers
    can migrate off the CSV channel slice by slice
  - regenerate openapi.d.ts for the new path and schemas
---
 src/api/mavedb/score-sets.ts            |  26 +++++-
 src/components/screens/ScoreSetView.vue |  20 ++++-
 src/lib/variants.ts                     |   9 ++
 src/schema/openapi.d.ts                 | 114 ++++++++++++++++++++++++
 4 files changed, 165 insertions(+), 4 deletions(-)

diff --git a/src/api/mavedb/score-sets.ts b/src/api/mavedb/score-sets.ts
index f2211a84..3b0cb554 100644
--- a/src/api/mavedb/score-sets.ts
+++ b/src/api/mavedb/score-sets.ts
@@ -2,6 +2,7 @@ import axios from 'axios'
 
 import config from '@/config'
 import {components} from '@/schema/openapi'
+import type {LeanVariant} from '@/lib/variants'
 
 type ScoreSetSearch = components['schemas']['ScoreSetsSearch']
 type ScoreSetsSearchResponse = components['schemas']['ScoreSetsSearchResponse']
@@ -31,6 +32,23 @@ export function histogramScoreSetVariantDataUrl(urn: string): string {
   )
 }
 
+// ---------------------------------------------------------------------------
+// Lean whole-set variant view (GET /score-sets/{urn}/variants)
+// ---------------------------------------------------------------------------
+
+export function leanScoreSetVariantsUrl(urn: string): string {
+  return `${config.apiBaseUrl}/score-sets/${encodeURIComponent(urn)}/variants`
+}
+
+/** Fetch the lean whole-set variant view for a score set. */
+export async function getLeanScoreSetVariants(urn: string, signal?: AbortSignal): Promise<LeanVariant[]> {
+  const response = await axios.get(leanScoreSetVariantsUrl(urn), {
+    headers: {accept: 'application/json'},
+    signal
+  })
+  return response.data || []
+}
+
 // ---------------------------------------------------------------------------
 // Search
 // ---------------------------------------------------------------------------
@@ -103,7 +121,9 @@ export async function publishScoreSet(urn: string) {
 }
 
 export async function getScoreSetClinicalControlOptions(urn: string) {
-  const response = await axios.get(`${config.apiBaseUrl}/score-sets/${encodeURIComponent(urn)}/clinical-controls/options`)
+  const response = await axios.get(
+    `${config.apiBaseUrl}/score-sets/${encodeURIComponent(urn)}/clinical-controls/options`
+  )
   return response.data
 }
 
@@ -138,7 +158,9 @@ export async function downloadMappedVariants(urn: string) {
   return response.data
 }
 
-export async function getRecentlyPublishedScoreSets(signal?: AbortSignal): Promise<components['schemas']['ScoreSet'][]> {
+export async function getRecentlyPublishedScoreSets(
+  signal?: AbortSignal
+): Promise<components['schemas']['ScoreSet'][]> {
   const response = await axios.get(`${config.apiBaseUrl}/score-sets/recently-published`, {
     headers: {accept: 'application/json'},
     signal
diff --git a/src/components/screens/ScoreSetView.vue b/src/components/screens/ScoreSetView.vue
index 9cd13e8a..992d34f1 100644
--- a/src/components/screens/ScoreSetView.vue
+++ b/src/components/screens/ScoreSetView.vue
@@ -503,12 +503,13 @@ import config from '@/config'
 import {hasPathogenicityCalibrations, hasFunctionalCalibrations} from '@/lib/calibrations'
 import {variantNotNullOrNA} from '@/lib/mave-hgvs'
 import {getScoreSetShortName} from '@/lib/score-sets'
-import {parseScoreSetVariantData, type Variant} from '@/lib/variants'
+import {parseScoreSetVariantData, type Variant, type LeanVariant} from '@/lib/variants'
 import {
   deleteScoreSet,
   publishScoreSet,
   getScoreSetClinicalControlOptions,
-  histogramScoreSetVariantDataUrl
+  histogramScoreSetVariantDataUrl,
+  leanScoreSetVariantsUrl
 } from '@/api/mavedb'
 import {components} from '@/schema/openapi'
 import MvLoader from '@/components/common/MvLoader.vue'
@@ -566,6 +567,9 @@ export default {
   setup(props) {
     const head = useHead()
     const scoresRemoteData = useRemoteData()
+    // Transitional: the lean whole-set view fetched alongside the legacy CSV `scoresData` channel.
+    // Consumers migrate onto `leanVariants` slice by slice; the CSV channel is removed once they have.
+    const leanVariantsRemoteData = useRemoteData()
     const variantSearchSuggestions = ref<Variant[]>([])
     const selectedCalibrations = ref<(string | null)[]>([null, null])
     const urnRef = ref(props.itemId)
@@ -593,6 +597,10 @@ export default {
       scoresDataStatus: scoresRemoteData.remoteDataStatus,
       setScoresDataUrl: scoresRemoteData.setDataUrl,
       ensureScoresDataLoaded: scoresRemoteData.ensureDataLoaded,
+      leanVariants: leanVariantsRemoteData.data,
+      leanVariantsStatus: leanVariantsRemoteData.remoteDataStatus,
+      setLeanVariantsUrl: leanVariantsRemoteData.setDataUrl,
+      ensureLeanVariantsLoaded: leanVariantsRemoteData.ensureDataLoaded,
       variantSearchSuggestions,
 
       distHistogramExportFn,
@@ -686,6 +694,10 @@ export default {
     isMetaDataEmpty() {
       return Object.keys(this.item?.extraMetadata || {}).length === 0
     },
+    // Typed handle on the lean whole-set view. Consumers migrate onto this from `variants` slice by slice.
+    leanVariantRecords(): LeanVariant[] | null {
+      return (this.leanVariants as LeanVariant[] | null) ?? null
+    },
     selectedCalibrationObjects() {
       if (this.item?.scoreCalibrations && this.selectedCalibrations) {
         return this.selectedCalibrations.map(
@@ -718,11 +730,15 @@ export default {
         if (newValue !== oldValue) {
           this.setItemId(newValue)
           let scoresUrl = null
+          let leanUrl = null
           if (this.itemType?.restCollectionName && this.itemId) {
             scoresUrl = histogramScoreSetVariantDataUrl(this.itemId)
+            leanUrl = leanScoreSetVariantsUrl(this.itemId)
           }
           this.setScoresDataUrl(scoresUrl)
           this.ensureScoresDataLoaded()
+          this.setLeanVariantsUrl(leanUrl)
+          this.ensureLeanVariantsLoaded()
         }
       },
       immediate: true
diff --git a/src/lib/variants.ts b/src/lib/variants.ts
index 1046fd77..7432d5e8 100644
--- a/src/lib/variants.ts
+++ b/src/lib/variants.ts
@@ -5,8 +5,17 @@ import {DEFAULT_CLNREVSTAT_FIELD, DEFAULT_CLNSIG_FIELD} from '@/lib/clinical-con
 import geneticCodes from '@/lib/genetic-codes'
 import {parseSimpleNtVariant, parseSimpleProVariant} from '@/lib/mave-hgvs'
 import {parseScoresOrCounts} from '@/lib/scores'
+import type {components} from '@/schema/openapi'
 import type {SimpleDnaVariation, SimpleProteinVariation} from '@/lib/mave-hgvs'
 
+/**
+ * The lean per-variant record served by `GET /score-sets/{urn}/variants`, mirrored from the API's
+ * OpenAPI schema. This is the target shape for the score-set view reshape; consumers migrate onto it
+ * slice by slice, at which point the legacy CSV-derived `Variant`/`RawVariant` types below are removed.
+ */
+export type HgvsField = components['schemas']['HgvsField']
+export type LeanVariant = components['schemas']['LeanVariant']
+
 export type HgvsReferenceSequenceType = 'c' | 'p' // | 'n'
 
 export interface SequenceRange {
diff --git a/src/schema/openapi.d.ts b/src/schema/openapi.d.ts
index d07f1dbc..43af2041 100644
--- a/src/schema/openapi.d.ts
+++ b/src/schema/openapi.d.ts
@@ -747,6 +747,20 @@ export interface paths {
      */
     delete: operations["delete_score_set_api_v1_score_sets__urn__delete"];
   };
+  "/api/v1/score-sets/{urn}/variants": {
+    /**
+     * Get the lean whole-set variant view for a score set
+     * @description Return the lean whole-set view for a score set: one pre-chewed record per variant carrying the
+     * selection key (variant URN), score, a representative consequence, the bridge identifiers into the
+     * annotation dimensions (ClinGen allele id, assay-level digest), and the DNA + protein parsed
+     * position/ref/alt blocks that drive the heatmap's level toggle.
+     *
+     * The full set is returned in one payload — the score-set page bins/sorts/filters across every
+     * variant client-side. as_of time-travels the annotation layer only (scores are immutable); the
+     * resolved value is echoed in the X-As-Of response header so the content-time is a visible fact.
+     */
+    get: operations["get_score_set_lean_variants_api_v1_score_sets__urn__variants_get"];
+  };
   "/api/v1/score-sets/{urn}/variants/data": {
     /**
      * Get score set variant data in CSV format
@@ -3362,6 +3376,23 @@ export interface components {
       /** Detail */
       detail?: components["schemas"]["ValidationError"][];
     };
+    /**
+     * HgvsField
+     * @description An HGVS expression with its parsed substitution block riding alongside when representable.
+     *
+     * ``hgvs`` is always present; ``position``/``ref``/``alt`` appear only for a placeable simple
+     * substitution (the heatmap grid) and are omitted for splice/indels/multivariants.
+     */
+    HgvsField: {
+      /** Hgvs */
+      hgvs: string;
+      /** Position */
+      position?: number | null;
+      /** Ref */
+      ref?: string | null;
+      /** Alt */
+      alt?: string | null;
+    };
     /**
      * JobRunDetail
      * @description Single-job-run detail response including the error traceback.
@@ -3489,6 +3520,34 @@ export interface components {
       /** Description */
       description?: string | null;
     };
+    /**
+     * LeanVariant
+     * @description One pre-chewed per-variant record feeding the score-set table, heatmap, and histograms.
+     *
+     * ``variantUrn`` is the universal selection key; ``assayLevelDigest`` bridges into the digest-keyed
+     * annotation dimensions. The submitted HGVS (``hgvsNt``/``hgvsPro``/``hgvsSplice``, target frame) and
+     * the mapped ``assayLevelHgvs`` (reference frame) carry both sides of the heatmap's frame toggle, each
+     * with an optional parsed block for the level toggle. ``proteinLevelHgvs`` is the mapped protein
+     * representation (distinct from the *submitted* ``hgvsPro``); for a protein assay it coincides with
+     * ``assayLevelHgvs``. Fields are omitted when null.
+     */
+    LeanVariant: {
+      /** Varianturn */
+      variantUrn: string;
+      /** Score */
+      score?: number | null;
+      /** Consequence */
+      consequence?: string | null;
+      /** Clingenalleleid */
+      clingenAlleleId?: string | null;
+      /** Assayleveldigest */
+      assayLevelDigest?: string | null;
+      hgvsNt?: components["schemas"]["HgvsField"] | null;
+      hgvsPro?: components["schemas"]["HgvsField"] | null;
+      hgvsSplice?: components["schemas"]["HgvsField"] | null;
+      assayLevelHgvs?: components["schemas"]["HgvsField"] | null;
+      proteinLevelHgvs?: components["schemas"]["HgvsField"] | null;
+    };
     /**
      * LengthExpression
      * @description A sequence expressed only by its length.
@@ -10128,6 +10187,61 @@ export interface operations {
       };
     };
   };
+  /**
+   * Get the lean whole-set variant view for a score set
+   * @description Return the lean whole-set view for a score set: one pre-chewed record per variant carrying the
+   * selection key (variant URN), score, a representative consequence, the bridge identifiers into the
+   * annotation dimensions (ClinGen allele id, assay-level digest), and the DNA + protein parsed
+   * position/ref/alt blocks that drive the heatmap's level toggle.
+   *
+   * The full set is returned in one payload — the score-set page bins/sorts/filters across every
+   * variant client-side. as_of time-travels the annotation layer only (scores are immutable); the
+   * resolved value is echoed in the X-As-Of response header so the content-time is a visible fact.
+   */
+  get_score_set_lean_variants_api_v1_score_sets__urn__variants_get: {
+    parameters: {
+      query?: {
+        /** @description Reconstruct the annotation layer (mapping, allele links, VEP consequence) as it stood at this instant, over the score set's fixed scores. ISO 8601, ideally timezone-aware. This is content valid-time only — it never re-selects a score-set version. Defaults to current. */
+        as_of?: string | null;
+      };
+      header?: {
+        "x-active-roles"?: string | null;
+      };
+      path: {
+        urn: string;
+      };
+    };
+    responses: {
+      /** @description Successful Response */
+      200: {
+        content: {
+          "application/json": components["schemas"]["LeanVariant"][];
+        };
+      };
+      /** @description Authentication required. */
+      401: {
+        content: never;
+      };
+      /** @description Forbidden. Insufficient permissions. */
+      403: {
+        content: never;
+      };
+      /** @description Resource not found. */
+      404: {
+        content: never;
+      };
+      /** @description Validation Error */
+      422: {
+        content: {
+          "application/json": components["schemas"]["HTTPValidationError"];
+        };
+      };
+      /** @description Internal server error. */
+      500: {
+        content: never;
+      };
+    };
+  };
   /**
    * Get score set variant data in CSV format
    * @description Return tabular variant data from a score set, identified by URN, in CSV format.

From 3678012c930535c2e143604d281ee62fe4461249 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Mon, 6 Jul 2026 10:38:54 -0700
Subject: [PATCH 02/84] refactor(score-set): drive visualizations from lean
 variant records
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Migrate the heatmap, histogram, score-set view, visualizer, and variant
lookup off the legacy CSV-parsed `Variant` model onto the lean
`DisplayVariant`/`LeanVariant` API record. The score-set view now fetches
a single lean whole-set channel instead of the dual histogram-CSV + lean
channels, and variant identity keys move from `accession` to `variantUrn`
throughout.

- Rework use-variant-coordinates around `coordinateFor(variant, level,
  frame)` as the single source of truth for the (level × frame)
  coordinate grid; add `resolveLevel` and `isUnmapped`, and make the
  (mapped, dna) cell null for protein assays (mavedb-api#784)
- Handle unmapped variants: labels fall back to submitted HGVS rather
  than the URN, mapped/clinical mode is disabled and annotated when a set
  has no mapped data, and the search matches both frames
- Extract VEP consequence bucketing into lib/consequences.ts, replacing
  the parsed-HGVS effect classifiers (`variantIsMissense`, etc.) in
  lib/variants.ts; `isStartOrStopLoss` stays as the block-aware heatmap
  filter
- Extract shared d3 chart tooltip builders into lib/tooltips.ts and
  rebuild the heatmap/histogram tooltips on top of them
- Add `isNucleotideHgvs` to lib/mave-hgvs.ts and
  `inferReferenceSequenceFromBlocks` to lib/variants.ts
- Heatmap UX: deferred redraw with a loading indicator, a not-shown
  breakdown (no-coordinate vs complex), a note when the selection is off
  the chart, and viewport-aware hover-tooltip positioning
- Add tests for consequences, mave-hgvs, and use-variant-coordinates
---
 .../state-management.instructions.md          |  15 +-
 src/api/mavedb/score-sets.ts                  |   2 +-
 src/components/score-set/ScoreSetHeatmap.vue  | 459 +++++++-------
 .../score-set/ScoreSetHistogram.vue           | 577 +++++++-----------
 .../score-set/ScoreSetVisualizer.vue          |   6 +-
 src/components/screens/ScoreSetView.vue       | 206 ++++---
 src/components/screens/VariantScreen.vue      |   9 +-
 .../use-variant-coordinates.test.ts           | 143 +++++
 src/composables/use-variant-coordinates.ts    | 153 +++--
 src/composables/use-variant-lookup.ts         |  41 +-
 src/lib/consequences.test.ts                  | 124 ++++
 src/lib/consequences.ts                       | 160 +++++
 src/lib/heatmap.ts                            |  34 +-
 src/lib/mave-hgvs.test.ts                     |  25 +
 src/lib/mave-hgvs.ts                          |  18 +
 src/lib/tooltips.ts                           |  97 +++
 src/lib/variants.ts                           | 207 +++----
 17 files changed, 1374 insertions(+), 902 deletions(-)
 create mode 100644 src/composables/use-variant-coordinates.test.ts
 create mode 100644 src/lib/consequences.test.ts
 create mode 100644 src/lib/consequences.ts
 create mode 100644 src/lib/mave-hgvs.test.ts
 create mode 100644 src/lib/tooltips.ts

diff --git a/.github/instructions/state-management.instructions.md b/.github/instructions/state-management.instructions.md
index a3a7db7d..dc449738 100644
--- a/.github/instructions/state-management.instructions.md
+++ b/.github/instructions/state-management.instructions.md
@@ -84,12 +84,19 @@ const {downloadFile, downloadMultipleData, customDialogVisible, dataTypeOptions}
 
 ## Variant Coordinates (`src/composables/use-variant-coordinates.ts`)
 
-Stateless utilities for resolving variant HGVS coordinates based on display mode (raw vs mapped). Shared between ScoreSetView (variant search, labels, sequence type detection) and ScoreSetHeatmap.
+Stateless resolution of a lean variant's HGVS coordinate across two orthogonal axes: sequence
+**level** (`dna` ↔ `protein`) and **frame** (`raw` = submitted/target numbering ↔ `mapped` =
+reference numbering). `coordinateFor` is the single source of truth — every derivation (heatmap
+x/y, axis availability, labels, tooltips) resolves through it, so the (level, frame) → coordinate
+mapping lives in one place. The frame axis is load-bearing: `raw` and `mapped` are genuinely
+different coordinate systems, so flipping frame reprojects the grid, it does not merely relabel it.
+Shared between ScoreSetView (search, labels, level options) and ScoreSetHeatmap (plotting).
 
 ```ts
-const {getHgvsNt, getHgvsPro, labelForVariant, sequenceTypeOptions} = useVariantCoordinates()
-const nt = getHgvsNt(variant, useMapped) // resolved NT coordinate
-const options = sequenceTypeOptions(variants, useMapped) // [{title: 'DNA', value: 'dna'}, ...]
+const {coordinateFor, sequenceTypeOptions, resolveLevel, labelForVariant} = useVariantCoordinates()
+coordinateFor(variant, 'dna', 'mapped') // → HgvsField | null (null for protein assays — no mapped coding, mavedb-api#784)
+sequenceTypeOptions(variants, 'mapped') // → [{title: 'DNA', value: 'dna'}, ...] available for that frame
+resolveLevel(variants, 'protein', 'mapped') // → the level to display, falling back when the desired one is stranded
 ```
 
 ## Entity Cache (`src/composables/entity-cache.ts`)
diff --git a/src/api/mavedb/score-sets.ts b/src/api/mavedb/score-sets.ts
index 3b0cb554..6d97bb28 100644
--- a/src/api/mavedb/score-sets.ts
+++ b/src/api/mavedb/score-sets.ts
@@ -40,7 +40,7 @@ export function leanScoreSetVariantsUrl(urn: string): string {
   return `${config.apiBaseUrl}/score-sets/${encodeURIComponent(urn)}/variants`
 }
 
-/** Fetch the lean whole-set variant view for a score set. */
+/** Fetch the lean whole-set variant view for a score set — one pre-chewed record per variant. */
 export async function getLeanScoreSetVariants(urn: string, signal?: AbortSignal): Promise<LeanVariant[]> {
   const response = await axios.get(leanScoreSetVariantsUrl(urn), {
     headers: {accept: 'application/json'},
diff --git a/src/components/score-set/ScoreSetHeatmap.vue b/src/components/score-set/ScoreSetHeatmap.vue
index e7eeed65..34f4aadc 100644
--- a/src/components/score-set/ScoreSetHeatmap.vue
+++ b/src/components/score-set/ScoreSetHeatmap.vue
@@ -1,5 +1,9 @@
 <template>
   <div class="mavedb-heatmap-wrapper">
+    <div v-if="redrawing" class="mavedb-heatmap-loading">
+      <i class="pi pi-spin pi-spinner" />
+      <span>Rendering heatmap…</span>
+    </div>
     <template v-if="heatmapVisible">
       <div style="text-align: center">Functional Score by Variant</div>
       <div id="mavedb-heatmap-container" ref="heatmapContainer" class="heatmapContainer">
@@ -16,9 +20,33 @@
           />
         </div>
       </div>
-      <!-- Controls moved to parent component header -->
-      <div class="ml-2" v-if="numComplexVariants > 0">
-        {{ numComplexVariants }} variants cannot be shown on this chart.
+      <!-- Informational notes about what the heatmap can and can't show. Controls live in the parent header. -->
+      <div
+        v-if="selectedVariantNotOnHeatmap || notShownCounts.noCoordinate > 0 || notShownCounts.complex > 0"
+        class="mt-2 flex flex-col gap-1 px-2 text-sm text-text-muted"
+      >
+        <div v-if="selectedVariantNotOnHeatmap" class="flex items-center gap-1.5">
+          <i class="pi pi-info-circle text-xs" />
+          <span
+            ><span class="font-medium text-text-secondary">{{ selectedVariantLabel }}</span> is not shown on this
+            heatmap.</span
+          >
+        </div>
+        <div v-if="notShownCounts.noCoordinate > 0" class="flex items-center gap-1.5">
+          <i class="pi pi-info-circle text-xs" />
+          <span
+            >{{ notShownCounts.noCoordinate }}
+            {{ notShownCounts.noCoordinate === 1 ? 'variant has' : 'variants have' }} no
+            {{ sequenceType === 'protein' ? 'protein' : 'DNA' }} representation in this view.</span
+          >
+        </div>
+        <div v-if="notShownCounts.complex > 0" class="flex items-center gap-1.5">
+          <i class="pi pi-info-circle text-xs" />
+          <span
+            >{{ notShownCounts.complex }} {{ notShownCounts.complex === 1 ? 'variant is' : 'variants are' }} too complex
+            to plot (indels, multivariants).</span
+          >
+        </div>
       </div>
     </template>
     <template v-else-if="scoreSet?.private">
@@ -41,22 +69,23 @@ import {saveChartAsSvg, saveChartAsPng} from '@/lib/chart-export'
 import geneticCodes from '@/lib/genetic-codes'
 import makeHeatmap from '@/lib/heatmap'
 import type {Heatmap, HeatmapDatum, HeatmapRowSpecification} from '@/lib/heatmap'
-import {parseSimpleProVariant, parseSimpleNtVariant, variantNotNullOrNA} from '@/lib/mave-hgvs'
 import {NUCLEOTIDE_BASES} from '@/lib/nucleotides'
 import {
-  PARSED_POST_MAPPED_VARIANT_PROPERTIES,
-  HgvsReferenceSequenceType,
-  inferReferenceSequenceFromVariants,
-  isStartOrStopLoss,
-  Variant
-} from '@/lib/variants'
+  tooltipKeyValue,
+  tooltipRoot,
+  tooltipSection,
+  tooltipTitle,
+  tooltipVariantDetailsLink
+} from '@/lib/tooltips'
+import {inferReferenceSequenceFromBlocks, isStartOrStopLoss, type DisplayVariant, type HgvsField} from '@/lib/variants'
+import {useVariantCoordinates} from '@/composables/use-variant-coordinates'
 import {components} from '@/schema/openapi'
 
 interface VariantHeatmapDatum {
   x: number
   y: number
   score: number | undefined
-  variant: Variant
+  variant: DisplayVariant
 }
 
 interface VariantClassHeatmapDatum {
@@ -68,7 +97,7 @@ interface VariantClassHeatmapDatum {
   scoreRank?: number
   wt?: boolean
   /** One variant in the class. All of its properties are shared by the other variants except its score, which should be ignored. */
-  instance?: Variant
+  instance?: DisplayVariant
 }
 
 const HEATMAP_AMINO_ACIDS_SORTED = _.sortBy(AMINO_ACIDS, [
@@ -152,7 +181,7 @@ export default defineComponent({
       default: 'raw'
     },
     externalSelection: {
-      type: Object as PropType<Variant | null>,
+      type: Object as PropType<DisplayVariant | null>,
       default: null
     },
     margins: {
@@ -185,7 +214,7 @@ export default defineComponent({
       default: undefined
     },
     variants: {
-      type: Array as PropType<Variant[]>,
+      type: Array as PropType<DisplayVariant[]>,
       required: true
     },
     forceBothClassificationColors: {
@@ -214,11 +243,16 @@ export default defineComponent({
     'update:layout'
   ],
 
+  setup() {
+    return {...useVariantCoordinates()}
+  },
+
   data: () => ({
     isMounted: false,
     proteinStructureVisible: false,
     heatmap: null as Heatmap | null,
-    stackedHeatmap: null as Heatmap | null
+    stackedHeatmap: null as Heatmap | null,
+    redrawing: false
   }),
 
   computed: {
@@ -226,24 +260,12 @@ export default defineComponent({
     // Choice of heatmap sequence type
     ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
 
-    dnaHeatmapAvailable: function () {
-      return this.variants.some((v) => this.getHgvsNtValue(v) != null && this.getHgvsNtValue(v) != 'NA')
-    },
-
-    proteinHeatmapAvailable: function () {
-      return this.variants.some((v) => this.getHgvsProValue(v) != null && this.getHgvsProValue(v) != 'NA')
-    },
-
-    sequenceTypeOptions: function () {
-      return [
-        ...(this.dnaHeatmapAvailable && (!this.allowedSequenceTypes || this.allowedSequenceTypes.includes('dna'))
-          ? [{title: 'DNA', value: 'dna'}]
-          : []),
-        ...(this.proteinHeatmapAvailable &&
-        (!this.allowedSequenceTypes || this.allowedSequenceTypes.includes('protein'))
-          ? [{title: 'Protein', value: 'protein'}]
-          : [])
-      ]
+    availableSequenceTypeOptions: function () {
+      const options = this.sequenceTypeOptions(this.variants, this.coordinates)
+      if (!this.allowedSequenceTypes) {
+        return options
+      }
+      return options.filter((option) => this.allowedSequenceTypes!.includes(option.value))
     },
 
     ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
@@ -262,10 +284,9 @@ export default defineComponent({
               return 'none'
           }
         case 'accession':
-          // For accession-based targets, all variants should have either hgvs_nt or hgvs_pro, but not both. They should
-          // all be of the same type (AA or NT). Use the raw data (not the mapped or translated HGVS properties) to
-          // determine which.
-          if (variantNotNullOrNA(this.variants[0].hgvs_pro)) {
+          // For accession-based targets, all variants should have either a submitted nt or protein HGVS, but not both.
+          // They are all of the same type (AA or NT); use the submitted data to determine which.
+          if (this.variants[0]?.hgvsPro != null) {
             return 'aa'
           } else {
             return 'nt'
@@ -323,9 +344,12 @@ export default defineComponent({
     ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
 
     inferredTargetSequenceAndOffset: function () {
-      const {referenceSequence, referenceSequenceRange} = inferReferenceSequenceFromVariants(
+      // Accession targets have no stored sequence; infer it from the submitted (raw) blocks.
+      const level = this.targetResidueType == 'aa' ? 'protein' : 'dna'
+      const {referenceSequence, referenceSequenceRange} = inferReferenceSequenceFromBlocks(
         this.variants,
-        this.targetResidueType == 'aa' ? 'p' : 'c'
+        (v) => this.coordinateFor(v, level, 'raw'),
+        this.targetResidueType == 'aa' ? 'aa' : 'nt'
       )
       return {
         targetSequence: referenceSequence,
@@ -350,22 +374,24 @@ export default defineComponent({
     },
 
     wtSequenceAndOffset: function () {
-      if (this.wtResidueType == this.targetResidueType) {
+      // Option A: the WT sequence is expressed in the same coordinate system as the plotted cells.
+      // In the raw frame with a target sequence of the matching residue type, that sequence is the
+      // authoritative WT in target coordinates. Otherwise (mapped frame, or a residue type the target
+      // sequence doesn't provide) infer the WT from the plotted blocks in the current (level, frame).
+      if (this.coordinates == 'raw' && this.wtResidueType == this.targetResidueType && this.targetSequence) {
         return {
           wtSequence: this.targetSequence,
           wtSequenceOffset: this.targetSequenceOffset
         }
-      } else if (this.wtResidueType == 'aa' && this.targetResidueType == 'nt') {
-        const {referenceSequence, referenceSequenceRange} = inferReferenceSequenceFromVariants(this.variants, 'p')
-        return {
-          wtSequence: referenceSequence,
-          wtSequenceOffset: referenceSequenceRange.start
-        }
-      } else {
-        return {
-          wtSequence: '',
-          wtSequenceOffset: 1
-        }
+      }
+      const {referenceSequence, referenceSequenceRange} = inferReferenceSequenceFromBlocks(
+        this.variants,
+        (v) => this.plotBlock(v),
+        this.wtResidueType
+      )
+      return {
+        wtSequence: referenceSequence,
+        wtSequenceOffset: referenceSequenceRange.start
       }
     },
 
@@ -381,80 +407,34 @@ export default defineComponent({
     // Accessing variant HGVS strings
     ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
 
-    hgvsColumn: function () {
-      switch (this.sequenceType) {
-        case 'dna':
-          return this.hgvsNtColumn
-        case 'protein':
-        default:
-          return this.hgvsProColumn
-      }
-    },
-
-    hgvsNtColumn: function () {
-      switch (this.coordinates) {
-        case 'mapped':
-          if (this.variants.some((v) => v.mavedb?.post_mapped_hgvs_c != null && v.mavedb?.post_mapped_hgvs_c != 'NA')) {
-            return 'post_mapped_hgvs_c'
-          }
-          return 'hgvs_nt'
-        case 'raw':
-        default:
-          return 'hgvs_nt'
-      }
-    },
-
-    hgvsProColumn: function () {
-      switch (this.coordinates) {
-        case 'mapped':
-          if (this.variants.some((v) => v.translated_hgvs_p != null && v.translated_hgvs_p != 'NA')) {
-            return 'translated_hgvs_p'
-          }
-          return 'post_mapped_hgvs_p'
-        case 'raw':
-        default:
-          if (this.variants.some((v) => v.hgvs_pro != null && v.hgvs_pro != 'NA')) {
-            return 'hgvs_pro'
-          } else if (this.variants.some((v) => v.translated_hgvs_p != null && v.translated_hgvs_p != 'NA')) {
-            return 'translated_hgvs_p'
-          } else {
-            return 'hgvs_pro'
-          }
-      }
-    },
-
-    parseSimpleVariant: function () {
-      return this.sequenceType == 'dna' ? parseSimpleNtVariant : parseSimpleProVariant
-    },
-
     ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
     // Variants to display
     ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
 
-    hgvsReferenceSequenceType: function (): HgvsReferenceSequenceType | undefined {
-      switch (this.sequenceType) {
-        case 'dna':
-          return 'c'
-        case 'protein':
-          return 'p'
-        default:
-          return undefined
-      }
-    },
-
     simpleVariants: function () {
-      if (this.hgvsReferenceSequenceType == null) {
-        return []
-      }
-      const parsedHgvsProperty = PARSED_POST_MAPPED_VARIANT_PROPERTIES[this.hgvsReferenceSequenceType]
-      if (!parsedHgvsProperty) {
-        return []
-      }
-      return this.variants.filter((v) => v[parsedHgvsProperty] != null)
+      // Plottable variants are those with a placeable substitution block in the current (level, frame).
+      return this.variants.filter((v) => {
+        const block = this.plotBlock(v)
+        return block != null && block.position != null
+      })
     },
 
-    numComplexVariants: function () {
-      return this.variants.length - this.simpleVariants.length
+    // The unplottable variants, split by why. `noCoordinate` resolve to no coordinate at the current
+    // level/frame (unmapped, or that level absent); `complex` carry an HGVS that is not a placeable
+    // single substitution (indels, multivariants, intronic/UTR). The two are mutually exclusive and
+    // together are every variant excluded from simpleVariants.
+    notShownCounts: function (): {noCoordinate: number; complex: number} {
+      let noCoordinate = 0
+      let complex = 0
+      for (const v of this.variants) {
+        const block = this.plotBlock(v)
+        if (block == null) {
+          noCoordinate++
+        } else if (block.position == null) {
+          complex++
+        }
+      }
+      return {noCoordinate, complex}
     },
 
     ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
@@ -550,10 +530,21 @@ export default defineComponent({
 
     selectedVariant: function () {
       return this.externalSelection
-        ? this.heatmapData.filter((variant) => variant.instance?.accession == this.externalSelection.accession)[0]
+        ? this.heatmapData.filter((variant) => variant.instance?.variantUrn == this.externalSelection!.variantUrn)[0]
         : null
     },
 
+    // A selection exists but resolves to no cell on this heatmap — a complex/unmapped variant, or one
+    // with no placeable substitution in the current level and frame. selectDatum can't highlight it
+    // either (same condition), so the note explains the absent highlight.
+    selectedVariantNotOnHeatmap: function (): boolean {
+      return !!this.externalSelection && !this.selectedVariant
+    },
+
+    selectedVariantLabel: function (): string {
+      return this.externalSelection ? this.labelForVariant(this.externalSelection, this.coordinates) : ''
+    },
+
     ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
     // Heatmap coloring based only on range of scores and baseline score from primary score calibration, if any
     ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
@@ -842,13 +833,13 @@ export default defineComponent({
   watch: {
     coordinates: {
       handler: function () {
-        this.renderOrRefreshHeatmaps()
+        this.scheduleRedraw()
       }
     },
 
     heatmapData: {
       handler: function () {
-        this.renderOrRefreshHeatmaps()
+        this.scheduleRedraw()
       },
       immediate: true
     },
@@ -866,14 +857,14 @@ export default defineComponent({
     layout: {
       handler: function (newValue, oldValue) {
         if (newValue != oldValue) {
-          this.renderOrRefreshHeatmaps()
+          this.scheduleRedraw()
         }
       }
     },
 
     sequenceType: {
       handler: function () {
-        this.renderOrRefreshHeatmaps()
+        this.scheduleRedraw()
       }
     },
 
@@ -897,10 +888,13 @@ export default defineComponent({
       immediate: true
     },
 
-    sequenceTypeOptions: {
-      handler: function (newValue, oldValue) {
+    availableSequenceTypeOptions: {
+      handler: function (
+        newValue: Array<{title: string; value: string}>,
+        oldValue: Array<{title: string; value: string}>
+      ) {
         if (!_.isEqual(newValue, oldValue)) {
-          if (!newValue.find((option) => option.value == this.sequenceType)) {
+          if (newValue.length > 0 && !newValue.find((option) => option.value == this.sequenceType)) {
             this.$emit('update:sequenceType', newValue[0].value)
           }
         }
@@ -910,6 +904,9 @@ export default defineComponent({
   },
 
   mounted: function () {
+    // Render synchronously on mount so colorScale/heatmapData are ready when a parent (e.g.
+    // ScoreSetVisualizer) reads them in its own mounted() hook. scheduleRedraw() handles later updates.
+    this.isMounted = true
     this.renderOrRefreshHeatmaps()
     this.$emit('exportChart', this.buildExportFns())
   },
@@ -927,45 +924,15 @@ export default defineComponent({
 
   methods: {
     ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
-    // HGVS value accessors
+    // Coordinate resolution
     ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
 
     /**
-     * Get the HGVS nucleotide value from a variant, handling nested properties.
+     * The HGVS block that this variant plots at, in the current sequence level and coordinate frame.
+     * The single source of truth for the heatmap's x/y derivation, WT inference, and tooltips.
      */
-    getHgvsNtValue: function (variant: Variant) {
-      switch (this.coordinates) {
-        case 'mapped':
-          if (variant.mavedb?.post_mapped_hgvs_c != null && variant.mavedb?.post_mapped_hgvs_c != 'NA') {
-            return variant.mavedb.post_mapped_hgvs_c
-          }
-          return variant.hgvs_nt
-        case 'raw':
-        default:
-          return variant.hgvs_nt
-      }
-    },
-
-    /**
-     * Get the HGVS protein value from a variant, handling nested properties.
-     */
-    getHgvsProValue: function (variant: Variant) {
-      switch (this.coordinates) {
-        case 'mapped':
-          if (variant.translated_hgvs_p != null && variant.translated_hgvs_p != 'NA') {
-            return variant.translated_hgvs_p
-          }
-          return variant.mavedb?.post_mapped_hgvs_p
-        case 'raw':
-        default:
-          if (variant.hgvs_pro != null && variant.hgvs_pro != 'NA') {
-            return variant.hgvs_pro
-          } else if (variant.translated_hgvs_p != null && variant.translated_hgvs_p != 'NA') {
-            return variant.translated_hgvs_p
-          } else {
-            return variant.hgvs_pro
-          }
-      }
+    plotBlock: function (variant: DisplayVariant): HgvsField | null {
+      return this.coordinateFor(variant, this.sequenceType, this.coordinates)
     },
 
     ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
@@ -977,57 +944,48 @@ export default defineComponent({
      *
      * @param simpleVariants
      */
-    prepareSimpleVariantHeatmapData: function (simpleVariants: Variant[]) {
-      // Count of variants that do not appear to be complex but are don't have a valid substitution
+    prepareSimpleVariantHeatmapData: function (simpleVariants: DisplayVariant[]) {
+      // Count of variants that do not appear to be complex but don't have a valid substitution
       let numIgnoredVariants = 0
 
-      const distinctAccessions = new Set()
-
-      const parsedHgvsProperty = PARSED_POST_MAPPED_VARIANT_PROPERTIES[this.hgvsReferenceSequenceType]
-      let simpleVariantHeatmapData = _.filter(
+      const simpleVariantHeatmapData = _.filter(
         simpleVariants.map((variant) => {
-          const parsedVariant = variant[parsedHgvsProperty]
-          if (parsedVariant.target) {
-            distinctAccessions.add(parsedVariant.target)
+          const block = this.plotBlock(variant)
+          if (!block || block.position == null || block.alt == null) {
+            numIgnoredVariants++
+            return null
           }
-          // Don't display variants out of range from the provided sequence. This happens occassionally with legacy data
-          // sets.
+          // Don't display variants out of range from the reference sequence. This happens occasionally with legacy
+          // data sets.
           if (
-            variant.position < this.wtSequence.offset ||
-            variant.position > this.wtSequence.length + this.wtSequence.offset
+            block.position < this.wtSequenceOffset ||
+            block.position > this.wtSequence.length + this.wtSequenceOffset
           ) {
             numIgnoredVariants++
             return null
           }
-          // If hideStartAndStopLoss is set to true, omit start- and stop-loss variants. The parent component shouuld
+          // If hideStartAndStopLoss is set to true, omit start- and stop-loss variants. The parent component should
           // set this option when viewing scores in clinical mode from an assay using a synthetic target sequence.
           if (this.hideStartAndStopLoss && isStartOrStopLoss(variant)) {
             numIgnoredVariants++
             return null
           }
-          const row = this.heatmapRowForSubstitution(
-            parsedVariant.substitution == parsedVariant.original ? '=' : parsedVariant.substitution
-          )
+          const row = this.heatmapRowForSubstitution(block.alt == block.ref ? '=' : block.alt)
           if (row == null) {
             numIgnoredVariants++
             return null
           }
-          const x = parsedVariant.position
+          const x = block.position
           const y = this.heatmapRows.length - 1 - row
           return {
             x,
             y,
-            score: variant.scores.score,
+            score: variant.score ?? undefined,
             variant
           }
         }),
         (x) => x != null
       )
-      // TODO(#237) See https://github.com/VariantEffect/mavedb-ui/issues/237.
-      if (distinctAccessions.size > 1) {
-        numIgnoredVariants += simpleVariantHeatmapData.length
-        simpleVariantHeatmapData = []
-      }
 
       return {simpleVariantHeatmapData, numIgnoredVariants}
     },
@@ -1063,8 +1021,8 @@ export default defineComponent({
     // Data property accessors for the heatmap
     ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
 
-    accession: function (d: HeatmapDatum) {
-      return (d as VariantClassHeatmapDatum)?.instance?.accession
+    variantKey: function (d: HeatmapDatum) {
+      return (d as VariantClassHeatmapDatum)?.instance?.variantUrn
     },
 
     tooltipTickLabelHtmlGetter: function (rowNumber: number) {
@@ -1072,72 +1030,56 @@ export default defineComponent({
       if (this.sequenceType == 'protein') {
         const aminoAcid = AMINO_ACIDS.find((aa) => aa.codes.single == currentRow.code)
         if (aminoAcid) {
-          return `Name: ${aminoAcid.name} (${aminoAcid.codes.triple})<br/>Hydrophobicity: ${aminoAcid.hydrophobicity?.originalValue} (Kyte-Doolittle)<br/>Class: ${aminoAcid.class}`
+          return tooltipRoot([
+            tooltipSection([
+              tooltipKeyValue('Name', `${aminoAcid.name} (${aminoAcid.codes.triple})`),
+              tooltipKeyValue('Hydrophobicity', `${aminoAcid.hydrophobicity?.originalValue} (Kyte-Doolittle)`),
+              tooltipKeyValue('Class', aminoAcid.class)
+            ])
+          ])
         }
       }
       return null
     },
 
     tooltipHtmlGetter: function (v: VariantClassHeatmapDatum) {
-      const parts = []
+      // Identity: WT flag plus the variant's identifiers, resolved in the current coordinate frame.
+      const identity = []
       if (v.wt) {
-        parts.push('WT')
+        identity.push(tooltipTitle('Wild-type'))
       }
-      const nameParts = []
-      if (this.coordinates == 'mapped') {
-        switch (this.sequenceType) {
-          case 'dna':
-            if (variantNotNullOrNA(v.instance?.mavedb?.post_mapped_hgvs_c)) {
-              nameParts.push(`Variant: ${v.instance?.mavedb?.post_mapped_hgvs_c}`)
-            }
-            if (variantNotNullOrNA(v.instance?.mavedb?.post_mapped_hgvs_p)) {
-              nameParts.push(`Protein variant: ${v.instance?.mavedb?.post_mapped_hgvs_p}`)
-            } else if (variantNotNullOrNA(v.instance?.translated_hgvs_p)) {
-              nameParts.push(`Protein variant: ${v.instance?.translated_hgvs_p}`)
-            }
-            break
-          case 'protein':
-          default:
-            if (variantNotNullOrNA(v.instance?.mavedb?.post_mapped_hgvs_p)) {
-              nameParts.push(`Variant: ${v.instance?.mavedb?.post_mapped_hgvs_p}`)
-            } else if (variantNotNullOrNA(v.instance?.translated_hgvs_p)) {
-              nameParts.push(`Variant: ${v.instance?.translated_hgvs_p}`)
-            }
-            if (variantNotNullOrNA(v.instance?.mavedb?.post_mapped_hgvs_c)) {
-              nameParts.push(`NT variant: ${v.instance?.mavedb?.post_mapped_hgvs_c}`)
-            }
-        }
-      }
-      if (nameParts.length == 0) {
-        if (variantNotNullOrNA(v.instance?.hgvs_nt)) {
-          nameParts.push(`NT variant: ${v.instance?.hgvs_nt}`)
+      const instance = v.instance
+      if (instance) {
+        const protein = this.getHgvsPro(instance, this.coordinates)
+        const nucleotide = this.getHgvsNt(instance, this.coordinates)
+        const splice = instance.hgvsSplice?.hgvs
+        if (protein) {
+          identity.push(tooltipKeyValue('Protein variant', protein))
         }
-        if (variantNotNullOrNA(v.instance?.hgvs_pro)) {
-          nameParts.push(`Protein variant: ${v.instance?.hgvs_pro}`)
-        } else if (variantNotNullOrNA(v.instance?.translated_hgvs_p)) {
-          nameParts.push(`Protein variant: ${v.instance?.translated_hgvs_p}`)
+        if (nucleotide) {
+          identity.push(tooltipKeyValue('NT variant', nucleotide))
         }
-        if (variantNotNullOrNA(v.instance?.hgvs_splice)) {
-          nameParts.push(`Splice variant: ${v.instance?.hgvs_splice}`)
+        if (!protein && !nucleotide && splice) {
+          identity.push(tooltipKeyValue('Splice variant', splice))
         }
       }
-      parts.push(...nameParts)
+      if (instance?.clingenAlleleId) {
+        identity.push(tooltipVariantDetailsLink(instance.clingenAlleleId))
+      }
+
+      // Aggregate score statistics for the cell.
+      const stats = []
       if (v.numScores != null) {
-        parts.push(`# of observations: ${v.numScores}`)
+        stats.push(tooltipKeyValue('# of observations', v.numScores))
       }
       if (v.numScores == 1) {
-        parts.push(`Score: ${v.meanScore}`)
+        stats.push(tooltipKeyValue('Score', v.meanScore))
       } else if (v.numScores != null && v.numScores > 1) {
-        parts.push(`Mean score: ${v.meanScore}`)
-        parts.push(`Score stdev: ${v.scoreStdev}`)
+        stats.push(tooltipKeyValue('Mean score', v.meanScore))
+        stats.push(tooltipKeyValue('Score stdev', v.scoreStdev))
       }
 
-      const clingenAlleleId = v.instance?.clingen?.clingen_allele_id
-      if (clingenAlleleId) {
-        parts.push(`<a href="/variants/${clingenAlleleId}" target="_blank" class="text-link">View variant details</a>`)
-      }
-
-      return parts.length > 0 ? parts.join('<br />') : null
+      return tooltipRoot([tooltipSection(identity), tooltipSection(stats)])
     },
 
     vRank: function (d: HeatmapDatum) {
@@ -1156,6 +1098,27 @@ export default defineComponent({
     // Heatmap rendering and refresh
     ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
 
+    /**
+     * Show a loading indicator, then redraw on a later frame. Rebuilding the heatmap re-creates every
+     * SVG cell, which blocks the main thread; yielding two animation frames first lets the browser
+     * paint the indicator before the freeze. Re-entrant calls coalesce — the single deferred redraw
+     * reads the latest reactive state, so rapid level/frame changes collapse into one redraw.
+     */
+    scheduleRedraw: function () {
+      // Before mount, the synchronous first render in mounted() is the sole first paint (so a parent can
+      // read colorScale/heatmapData immediately). Deferring here would double-render and flash the spinner.
+      if (!this.isMounted || this.redrawing) {
+        return
+      }
+      this.redrawing = true
+      requestAnimationFrame(() =>
+        requestAnimationFrame(() => {
+          this.renderOrRefreshHeatmaps()
+          this.redrawing = false
+        })
+      )
+    },
+
     renderOrRefreshHeatmaps: function () {
       if (!this.heatmapData) {
         return
@@ -1181,7 +1144,7 @@ export default defineComponent({
         .rows(this.heatmapRows)
         .xCoordinate(this.xCoord)
         .yCoordinate(this.yCoord)
-        .accessorField(this.accession)
+        .accessorField(this.variantKey)
         .tooltipHtml(this.tooltipHtmlGetter)
         .tooltipTickLabelHtml(this.sequenceType == 'protein' ? this.tooltipTickLabelHtmlGetter : null)
         .pivotColor('#e0e0e0')
@@ -1232,7 +1195,7 @@ export default defineComponent({
         .nodeSize({width: 20, height: 1})
         .xCoordinate(this.xCoord)
         .yCoordinate(this.vRank)
-        .accessorField(this.accession)
+        .accessorField(this.variantKey)
         .drawY(false)
         .drawLegend(false)
         .alignViaLegend(true)
@@ -1374,6 +1337,21 @@ export default defineComponent({
   background-color: #fff;
 }
 
+.mavedb-heatmap-loading {
+  position: absolute;
+  inset: 0;
+  z-index: 10;
+  display: flex;
+  flex-direction: column;
+  align-items: center;
+  justify-content: center;
+  gap: 8px;
+  min-height: 120px;
+  background-color: rgba(255, 255, 255, 0.7);
+  color: #555;
+  font-size: 13px;
+}
+
 /* .mavedb-heatmap-wrapper:hover .mavedb-heatmap-controls {
   display: flex;
   flex-direction: row;
@@ -1401,6 +1379,13 @@ export default defineComponent({
   position: relative;
 }
 
+/* The sticky y-axis/legend overlay spans the wrapper's full height, so its bottom-left otherwise
+   covers the left end of the horizontal scrollbar on wide (e.g. DNA) heatmaps. Trim it to clear the
+   scrollbar track. Overrides the inline height:100% d3 sets on the overlay svg. */
+.heatmapContainer:deep(svg.exclude-from-export) {
+  height: calc(100% - 8px) !important;
+}
+
 .heatmapContainer:deep(.heatmap-y-axis-tick-labels) {
   font-size: 10px;
   user-select: none;
diff --git a/src/components/score-set/ScoreSetHistogram.vue b/src/components/score-set/ScoreSetHistogram.vue
index e10a6dd7..4558d1ab 100644
--- a/src/components/score-set/ScoreSetHistogram.vue
+++ b/src/components/score-set/ScoreSetHistogram.vue
@@ -220,27 +220,33 @@ import {
   getClassificationColor
 } from '@/lib/calibrations'
 import type {FunctionalClassificationVariant} from '@/lib/calibrations'
-import {variantNotNullOrNA} from '@/lib/mave-hgvs'
 import {
-  DEFAULT_VARIANT_EFFECT_TYPES,
-  isStartOrStopLoss,
-  variantIsMissense,
-  variantIsNonsense,
-  variantIsOther,
-  variantIsSynonymous,
-  VARIANT_EFFECT_TYPE_OPTIONS,
-  Variant,
-  allCodingVariantsHaveProteinConsequence
-} from '@/lib/variants'
+  tooltipBadgeBlock,
+  tooltipConsequence,
+  tooltipCountRow,
+  tooltipKeyValue,
+  tooltipLink,
+  tooltipNote,
+  tooltipReviewStars,
+  tooltipRoot,
+  tooltipSection,
+  tooltipSectionLabel,
+  tooltipText,
+  tooltipTitle,
+  tooltipVariantDetailsLink
+} from '@/lib/tooltips'
+import {DisplayVariant} from '@/lib/variants'
+import {
+  consequenceBucket,
+  humanReadableConsequence,
+  EFFECT_BUCKETS,
+  EFFECT_TYPE_FILTER_OPTIONS,
+  DEFAULT_EFFECT_TYPE_FILTERS,
+  type EffectBucketName
+} from '@/lib/consequences'
+import {useVariantCoordinates} from '@/composables/use-variant-coordinates'
 import {components} from '@/schema/openapi'
 
-function naToUndefined(x: string | null | undefined) {
-  if (variantNotNullOrNA(x)) {
-    return x
-  }
-  return undefined
-}
-
 interface Margins {
   top: number
   right: number
@@ -269,7 +275,7 @@ export default defineComponent({
       default: 'distribution'
     },
     externalSelection: {
-      type: Object as PropType<Variant | null>,
+      type: Object as PropType<DisplayVariant | null>,
       default: null
     },
     // Margins must accommodate the X axis label and title.
@@ -291,7 +297,7 @@ export default defineComponent({
       required: true
     },
     variants: {
-      type: Array as PropType<Variant[]>,
+      type: Array as PropType<DisplayVariant[]>,
       required: true
     },
     hideStartAndStopLossByDefault: {
@@ -312,7 +318,8 @@ export default defineComponent({
 
   setup: () => {
     return {
-      ...useScopedId()
+      ...useScopedId(),
+      ...useVariantCoordinates()
     }
   },
 
@@ -345,13 +352,13 @@ export default defineComponent({
       clinicalSignificanceClassificationOptions: clinvarClinicalSignificanceClassifications(
         DEFAULT_CLINICAL_CONTROL_VERSION
       ),
-      variantTypeOptions: VARIANT_EFFECT_TYPE_OPTIONS,
+      variantTypeOptions: EFFECT_TYPE_FILTER_OPTIONS,
       customMinStarRating: DEFAULT_MIN_STAR_RATING,
       customSelectedClinicalSignificanceClassifications: DEFAULT_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS,
-      customSelectedVariantTypeFilters: [] as string[],
-      customSelectedControlVariantTypeFilters: DEFAULT_VARIANT_EFFECT_TYPES.concat(
+      customSelectedVariantTypeFilters: [] as EffectBucketName[],
+      customSelectedControlVariantTypeFilters: DEFAULT_EFFECT_TYPE_FILTERS.concat(
         this.hideStartAndStopLossByDefault ? [] : ['Start/Stop Loss']
-      ),
+      ) as EffectBucketName[],
       calibrationClassVariantsByUrn: {} as Record<string, Record<number, FunctionalClassificationVariant[]>>,
       calibrationClassVariantsLoadingByUrn: {} as Record<string, boolean>,
       histogram: null as Histogram | null
@@ -360,7 +367,8 @@ export default defineComponent({
 
   computed: {
     proteinEffectOptionsAvailable: function () {
-      return allCodingVariantsHaveProteinConsequence(this.variants)
+      // Worth offering as soon as some variant carries a VEP consequence (anything but 'No consequence').
+      return this.variants.some((v) => consequenceBucket(v.consequence) !== 'No consequence')
     },
     selectedCalibrationIsClassBased: function () {
       return (
@@ -430,8 +438,8 @@ export default defineComponent({
 
           return this.activeCalibration.value?.functionalClassifications?.map((fc, i) => ({
             classifier: (d: HistogramDatum) => {
-              if (!d.accession) return false
-              return selectedCalibrationClassMap[d.accession] === fc.class
+              if (!d.variantUrn) return false
+              return selectedCalibrationClassMap[d.variantUrn] === fc.class
             },
             options: {
               color: CATEGORICAL_SERIES_COLORS[i % CATEGORICAL_SERIES_COLORS.length],
@@ -465,48 +473,14 @@ export default defineComponent({
             }
           ]
 
-        case 'effect':
-          return [
-            {
-              classifier: (d: HistogramDatum) => variantIsMissense(d),
-              options: {
-                color: '#ffcd3a',
-                title: 'Missense'
-              }
-            },
-            {
-              classifier: (d: HistogramDatum) => variantIsSynonymous(d),
-              options: {
-                color: '#6aa84f',
-                title: 'Synonymous'
-              }
-            },
-            {
-              classifier: (d: HistogramDatum) => variantIsNonsense(d),
-              options: {
-                color: '#681a1a',
-                title: 'Nonsense'
-              }
-            },
-            ...(this.hideStartAndStopLossByDefault
-              ? []
-              : [
-                  {
-                    classifier: (d: HistogramDatum) => isStartOrStopLoss(d),
-                    options: {
-                      color: '#cd3aff',
-                      title: 'Start/Stop Loss'
-                    }
-                  }
-                ]),
-            {
-              classifier: (d: HistogramDatum) => variantIsOther(d),
-              options: {
-                color: '#3affcd',
-                title: 'Other'
-              }
-            }
-          ]
+        case 'effect': {
+          // The dedicated effect view shows every annotated bucket (Start/Stop Loss omitted for
+          // synthetic targets); 'No consequence' is not a protein effect and is left out here.
+          const buckets = EFFECT_BUCKETS.map((b) => b.name).filter(
+            (name) => name !== 'No consequence' && !(name === 'Start/Stop Loss' && this.hideStartAndStopLossByDefault)
+          )
+          return this.proteinEffectSeries(buckets)
+        }
 
         case 'custom': {
           const series = [
@@ -540,7 +514,7 @@ export default defineComponent({
 
           if (this.selectedClinicalSignificanceClassifications.includes('Uncertain significance')) {
             series.push({
-              classifier: (d: Variant) =>
+              classifier: (d: DisplayVariant) =>
                 d.control?.[DEFAULT_CLNSIG_FIELD] == 'Uncertain significance' &&
                 (CLINVAR_REVIEW_STATUS_STARS[d.control?.[DEFAULT_CLNREVSTAT_FIELD]] ?? -1) >= this.minStarRating &&
                 this.filterControlVariantByEffect(d),
@@ -573,54 +547,8 @@ export default defineComponent({
             })
           }
 
-          if (this.proteinEffectOptionsAvailable && this.selectedVariantTypeFilters.includes('Missense')) {
-            series.push({
-              classifier: (d: HistogramDatum) => variantIsMissense(d),
-              options: {
-                color: '#ffcd3a',
-                title: 'Missense'
-              }
-            })
-          }
-
-          if (this.proteinEffectOptionsAvailable && this.selectedVariantTypeFilters.includes('Synonymous')) {
-            series.push({
-              classifier: (d: HistogramDatum) => variantIsSynonymous(d),
-              options: {
-                color: '#6aa84f',
-                title: 'Synonymous'
-              }
-            })
-          }
-
-          if (this.proteinEffectOptionsAvailable && this.selectedVariantTypeFilters.includes('Nonsense')) {
-            series.push({
-              classifier: (d: HistogramDatum) => variantIsNonsense(d),
-              options: {
-                color: '#681a1a',
-                title: 'Nonsense'
-              }
-            })
-          }
-
-          if (this.proteinEffectOptionsAvailable && this.selectedVariantTypeFilters.includes('Start/Stop Loss')) {
-            series.push({
-              classifier: (d: HistogramDatum) => isStartOrStopLoss(d),
-              options: {
-                color: '#cd3aff',
-                title: 'Start/Stop Loss'
-              }
-            })
-          }
-
-          if (this.proteinEffectOptionsAvailable && this.selectedVariantTypeFilters.includes('Other')) {
-            series.push({
-              classifier: (d: HistogramDatum) => variantIsOther(d),
-              options: {
-                color: '#3affcd',
-                title: 'Other'
-              }
-            })
+          if (this.proteinEffectOptionsAvailable) {
+            series.push(...this.proteinEffectSeries(this.selectedVariantTypeFilters))
           }
 
           return series
@@ -771,191 +699,15 @@ export default defineComponent({
 
     tooltipHtmlGetter: function () {
       return (
-        variant: Variant | null, // HistogramDatum | null,
+        variant: DisplayVariant | null,
         bin: HistogramBin | null,
         seriesContainingVariant: HistogramSerieOptions[],
         allSeries: HistogramSerieOptions[]
       ) => {
-        const parts = []
-
-        if (variant) {
-          // Line 1: Variant identifier
-          const mappedDnaHgvs = naToUndefined(variant.mavedb?.post_mapped_hgvs_c)
-          const mappedProteinHgvs =
-            naToUndefined(variant.mavedb?.post_mapped_hgvs_p) ?? naToUndefined(variant.translated_hgvs_p)
-          const unmappedDnaHgvs = naToUndefined(variant.hgvs_nt)
-          const unmappedProteinHgvs = naToUndefined(variant.hgvs_pro)
-          const unmappedSpliceHgvs = naToUndefined(variant.hgvs_splice)
-          // const variantLabel = variant.mavedb_label || (
-          //   proteinHgvs ?
-          //     (dnaHgvs ? `${proteinHgvs} (${dnaHgvs})` : proteinHgvs)
-          //     : spliceHgvs ?
-          //       (dnaHgvs ? `${spliceHgvs} (${dnaHgvs})` : spliceHgvs)
-          //       : dnaHgvs
-          // )
-          const mappedVariantLabel = mappedProteinHgvs
-            ? mappedDnaHgvs
-              ? `${mappedProteinHgvs} (${mappedDnaHgvs})`
-              : mappedProteinHgvs
-            : mappedDnaHgvs
-          const unmappedVariantLabel = unmappedProteinHgvs
-            ? unmappedDnaHgvs
-              ? `${unmappedProteinHgvs} (${unmappedDnaHgvs})`
-              : unmappedProteinHgvs
-            : unmappedSpliceHgvs
-              ? unmappedDnaHgvs
-                ? `${unmappedSpliceHgvs} (${unmappedDnaHgvs})`
-                : unmappedSpliceHgvs
-              : unmappedDnaHgvs
-
-          const variantLabel =
-            this.coordinates == 'mapped'
-              ? (mappedVariantLabel ?? variant.mavedb_label ?? unmappedVariantLabel)
-              : (variant.mavedb_label ?? unmappedVariantLabel)
-          if (variantLabel) {
-            parts.push(variantLabel)
-          }
-
-          // Line 2: Variant description
-          const variantDescriptionParts = []
-          if (seriesContainingVariant.length == 0) {
-            variantDescriptionParts.push('(not shown in currently visible series)')
-          } else {
-            for (const series of seriesContainingVariant) {
-              if (series.title) {
-                variantDescriptionParts.push(
-                  '<span class="mavedb-histogram-tooltip-variant-color"' +
-                    ` style="background-color: ${series.color || DEFAULT_SERIES_COLOR}"></span>`
-                )
-              }
-            }
-          }
-
-          const variantHasClinicalSignificance =
-            variant.control && variant.control[DEFAULT_CLNSIG_FIELD] && variant.control[DEFAULT_CLNSIG_FIELD] != 'NA'
-          const variantHasReviewStatus =
-            variant.control &&
-            variant.control[DEFAULT_CLNREVSTAT_FIELD] &&
-            variant.control[DEFAULT_CLNREVSTAT_FIELD] != 'NA'
-          if (variantHasClinicalSignificance) {
-            const classification = clinvarClinicalSignificanceClassifications(
-              this.controlVersion ? this.controlVersion : DEFAULT_CLINICAL_CONTROL_VERSION
-            ).find((c) => c.name == variant.control?.[DEFAULT_CLNSIG_FIELD])
-            if (classification) {
-              variantDescriptionParts.push(classification.description)
-            }
-          }
-          if (variantHasReviewStatus) {
-            const numStars = CLINVAR_REVIEW_STATUS_STARS[variant.control?.[DEFAULT_CLNREVSTAT_FIELD]]
-            if (numStars != null) {
-              // Create an array of 4 stars to hold clinical review status a la ClinVar.
-              const stars = new Array(4)
-                .fill(
-                  '<span class="mavedb-histogram-tooltip-variant-star mavedb-histogram-tooltip-variant-star-filled">★</span>'
-                )
-                .fill('<span class="mavedb-histogram-tooltip-variant-star">☆</span>', numStars)
-              variantDescriptionParts.push(`(${stars.join('')})`)
-            }
-          }
-          if (variantDescriptionParts.length > 0) {
-            parts.push(variantDescriptionParts.join(' '))
-          }
-          if (variantHasClinicalSignificance && variantHasReviewStatus) {
-            const clinVarLinkOut = `<a href="http://www.ncbi.nlm.nih.gov/clinvar/?term=${variant.control.dbIdentifier}[alleleid]" target="_blank" class="text-link">View in ClinVar</a>`
-            parts.push(clinVarLinkOut)
-          }
-
-          const clingenAlleleId = variant.clingen?.clingen_allele_id
-          if (clingenAlleleId) {
-            parts.push(
-              `<a href="/variants/${clingenAlleleId}" target="_blank" class="text-link">View variant details</a>`
-            )
-          }
-
-          // Line 3: Score and classification
-          if (variant.scores.score && variant.scores.score != 'NA') {
-            let binClassificationLabel = null
-            if (this.activeCalibration.value?.urn && this.activeCalibration.value?.functionalClassifications) {
-              // TODO#491: Refactor this calculation into the creation of variant objects so we may just access the property of the variant which tells us its classification.
-              const classifications = this.activeCalibration.value.functionalClassifications
-
-              // Try range-based match first, then fall back to class-based membership lookup.
-              let matchedClassification =
-                classifications.find((fc) => functionalClassificationContainsVariant(fc, variant.scores.score)) ?? null
-
-              if (!matchedClassification && this.selectedCalibrationIsClassBased) {
-                const variantsByClassificationId = this.calibrationClassVariantsByUrn[this.activeCalibration.value.urn]
-                if (variantsByClassificationId) {
-                  matchedClassification =
-                    classifications.find((fc) =>
-                      variantsByClassificationId[fc.id]?.some((v) => v.urn === variant.accession)
-                    ) ?? null
-                }
-              }
-
-              if (matchedClassification) {
-                const color = getClassificationColor(matchedClassification)
-                binClassificationLabel = `<span class="mavedb-range-classification-badge" style="margin-left: 6px; background-color:${color}; color:white;">${matchedClassification.label}</span>`
-              }
-            }
-
-            if (binClassificationLabel) {
-              parts.push(`Score: ${variant.scores.score.toPrecision(4)} ${binClassificationLabel}`)
-            }
-          }
-
-          // Line 4: Blank line
-          parts.push('')
-        }
-
-        if (bin) {
-          // Line 5: Bin range
-          parts.push(`Bin range: ${bin.x0} to ${bin.x1}`)
-
-          //Line 6: Bin Classification
-          if (this.activeCalibration.value?.urn) {
-            // TODO#491: Refactor this calculation into the creation of histogram bins so we don't need to repeat it every time we construct a tooltip.
-            const binClassifications =
-              this.histogramShaders[this.activeCalibration.value.urn]
-                ?.filter((calibration: HistogramShader) => shaderOverlapsBin(calibration, bin))
-                .sort(
-                  (a: HistogramShader, b: HistogramShader) => (a.min ? a.min : -Infinity) - (b.min ? b.min : -Infinity)
-                ) || []
-
-            if (binClassifications.length > 0) {
-              const binClassificationLabels = binClassifications.map((binClassification: HistogramShader) => {
-                const calibrationMin = binClassification.min ?? -Infinity
-                const calibrationMax = binClassification.max ?? Infinity
-
-                const spanStart = Math.max(bin.x0, calibrationMin).toPrecision(3)
-                const spanEnd = Math.min(bin.x1, calibrationMax).toPrecision(3)
-
-                const binSpansMultipleShaders = bin.x0 < calibrationMin || bin.x1 > calibrationMax
-                const multipleShaderRangeText = spanStart != spanEnd ? `(${spanStart} to ${spanEnd})` : `(${spanStart})`
-
-                return `<span class="mavedb-range-classification-badge" style="background-color:${binClassification.color}; color:white;">${binClassification.title} ${binSpansMultipleShaders ? `${multipleShaderRangeText}` : ''}</span>`
-              })
-
-              // If the bin spans many classifications, show the first two and then the rest on a new line.
-              if (binClassificationLabels.length <= 2) {
-                parts.push(`Bin classification(s): ${binClassificationLabels.join(', ')}`)
-              } else {
-                parts.push(`Bin classification(s): ${binClassificationLabels.slice(0, 2).join(', ')},`)
-                parts.push(binClassificationLabels.slice(2).join(', '))
-              }
-            }
-          } else {
-            parts.push('Bin classification(s): N/A')
-          }
-
-          // Line 7: Bin series counts
-          bin.seriesBins.forEach((serieBin, i) => {
-            const label = allSeries[i].title ? allSeries[i].title : allSeries.length > 1 ? `Series ${i + 1}` : null
-            parts.push((label ? `${label}: ` : '') + `${serieBin.length} variants in bin`)
-          })
-        }
-
-        return parts.length > 0 ? parts.join('<br />') : null
+        return tooltipRoot([
+          variant ? this.tooltipVariantSections(variant) : null,
+          bin ? this.tooltipBinSection(bin, allSeries, seriesContainingVariant, Boolean(variant)) : null
+        ])
       }
     }
   },
@@ -1149,6 +901,170 @@ export default defineComponent({
   },
 
   methods: {
+    // ---- Histogram tooltip construction ----
+
+    /** Variant identity + ClinVar annotation, as one or two stacked tooltip sections. */
+    tooltipVariantSections(variant: DisplayVariant): string {
+      const identity = []
+
+      const label = this.labelForVariant(variant, this.coordinates)
+      if (label) {
+        identity.push(tooltipTitle(label))
+      }
+      // In the mapped frame an unmapped variant's label is its submitted (target-frame) HGVS; flag it so
+      // the string isn't mistaken for a mapped coordinate.
+      if (this.coordinates == 'mapped' && this.isUnmapped(variant)) {
+        identity.push(tooltipNote('Could not be mapped'))
+      }
+
+      const consequence = humanReadableConsequence(variant.consequence)
+      if (consequence) {
+        identity.push(tooltipConsequence(consequence))
+      }
+
+      if (variant.score != null) {
+        identity.push(tooltipText(`Score ${variant.score.toPrecision(4)}`))
+        const classification = this.matchVariantClassification(variant)
+        if (classification) {
+          identity.push(tooltipBadgeBlock(getClassificationColor(classification), classification.label))
+        }
+      }
+
+      if (variant.clingenAlleleId) {
+        identity.push(tooltipVariantDetailsLink(variant.clingenAlleleId))
+      }
+
+      return [tooltipSection(identity), this.tooltipClinvarSection(variant)].filter(Boolean).join('')
+    },
+
+    /** ClinVar significance, review stars, and link — or null when the variant has no ClinVar annotation. */
+    tooltipClinvarSection(variant: DisplayVariant): string | null {
+      const control = variant.control
+      if (!control) {
+        return null
+      }
+      const significance = control[DEFAULT_CLNSIG_FIELD]
+      const reviewStatus = control[DEFAULT_CLNREVSTAT_FIELD]
+      const hasSignificance = Boolean(significance) && significance != 'NA'
+      const hasReviewStatus = Boolean(reviewStatus) && reviewStatus != 'NA'
+      if (!hasSignificance) {
+        return null
+      }
+
+      const description =
+        clinvarClinicalSignificanceClassifications(this.controlVersion || DEFAULT_CLINICAL_CONTROL_VERSION).find(
+          (c) => c.name == significance
+        )?.description ?? significance
+      const numStars = hasReviewStatus ? CLINVAR_REVIEW_STATUS_STARS[reviewStatus] : null
+      const stars = numStars != null ? ` ${tooltipReviewStars(numStars)}` : ''
+
+      return tooltipSection([
+        tooltipSectionLabel('ClinVar'),
+        tooltipText(`${description}${stars}`),
+        hasReviewStatus
+          ? tooltipLink(
+              `http://www.ncbi.nlm.nih.gov/clinvar/?term=${control.dbIdentifier}[alleleid]`,
+              'View in ClinVar'
+            )
+          : null
+      ])
+    },
+
+    /** The functional classification a variant falls into, matched by score range then class membership. */
+    // TODO#491: Attach this to the variant object so the tooltip can read it directly.
+    matchVariantClassification(variant: DisplayVariant) {
+      const score = variant.score
+      const calibration = this.activeCalibration.value
+      if (score == null || !calibration?.urn || !calibration.functionalClassifications) {
+        return null
+      }
+      const classifications = calibration.functionalClassifications
+
+      const byScore = classifications.find((fc) => functionalClassificationContainsVariant(fc, score)) ?? null
+      if (byScore) {
+        return byScore
+      }
+      if (this.selectedCalibrationIsClassBased) {
+        const variantsByClassificationId = this.calibrationClassVariantsByUrn[calibration.urn]
+        if (variantsByClassificationId) {
+          return (
+            classifications.find((fc) =>
+              variantsByClassificationId[fc.id]?.some((v) => v.urn === variant.variantUrn)
+            ) ?? null
+          )
+        }
+      }
+      return null
+    },
+
+    /** Bin range, overlapping calibration classifications, and per-series counts (member series highlighted). */
+    tooltipBinSection(
+      bin: HistogramBin,
+      allSeries: HistogramSerieOptions[],
+      seriesContainingVariant: HistogramSerieOptions[],
+      variantHovered: boolean
+    ): string {
+      const rows = [tooltipSectionLabel(`Bin details (${bin.x0} to ${bin.x1})`)]
+
+      // Bin classifications are only useful on a bare bin hover; a hovered variant already shows its own
+      // classification badge above.
+      if (!variantHovered) {
+        rows.push(this.tooltipBinClassifications(bin))
+      }
+
+      // When a variant is hovered, its series are bolded below. State the negative explicitly so an
+      // absence of bold isn't left to interpretation.
+      if (variantHovered && seriesContainingVariant.length == 0) {
+        rows.push(tooltipNote('This variant is not within the displayed series'))
+      }
+
+      bin.seriesBins.forEach((serieBin, i) => {
+        const series = allSeries[i]
+        rows.push(
+          tooltipCountRow({
+            color: series?.color || DEFAULT_SERIES_COLOR,
+            label: series?.title || (allSeries.length > 1 ? `Series ${i + 1}` : ''),
+            count: serieBin.length,
+            active: seriesContainingVariant.includes(series)
+          })
+        )
+      })
+
+      return tooltipSection(rows)
+    },
+
+    /** Compact "Classes: ..." line of calibration classifications overlapping a bin, or empty when none. */
+    // TODO#491: Precompute per-bin classifications so the tooltip doesn't recompute them on every hover.
+    tooltipBinClassifications(bin: HistogramBin): string {
+      const urn = this.activeCalibration.value?.urn
+      if (!urn) {
+        return ''
+      }
+      const shaders = (this.histogramShaders[urn] || [])
+        .filter((shader: HistogramShader) => shaderOverlapsBin(shader, bin))
+        .sort((a: HistogramShader, b: HistogramShader) => (a.min ?? -Infinity) - (b.min ?? -Infinity))
+      if (shaders.length == 0) {
+        return ''
+      }
+
+      const names = shaders.map((shader: HistogramShader) => {
+        const min = shader.min ?? -Infinity
+        const max = shader.max ?? Infinity
+        const spanStart = Math.max(bin.x0, min).toPrecision(3)
+        const spanEnd = Math.min(bin.x1, max).toPrecision(3)
+        // Note the covered sub-range only when a shader boundary cuts through the bin.
+        const shaderSplitsBin = bin.x0 < min || bin.x1 > max
+        const range = shaderSplitsBin
+          ? spanStart != spanEnd
+            ? ` (${spanStart} to ${spanEnd})`
+            : ` (${spanStart})`
+          : ''
+        return `${shader.title ?? ''}${range}`
+      })
+
+      return tooltipKeyValue('Overlapped classes', names.join(', '))
+    },
+
     toggleThresholdsPopover(event: Event) {
       ;(this.$refs.thresholdsPopoverRef as InstanceType<typeof Popover>)?.toggle(event)
     },
@@ -1156,22 +1072,19 @@ export default defineComponent({
       this.activeCalibration = option
       ;(this.$refs.thresholdsPopoverRef as InstanceType<typeof Popover>)?.hide()
     },
-    filterControlVariantByEffect(variant: Variant) {
-      // Do not filter control variants unless we have protein consequences for all coding variants.
+    // A histogram series per named protein-effect bucket, classified by VEP consequence.
+    proteinEffectSeries(bucketNames: string[]) {
+      return EFFECT_BUCKETS.filter((bucket) => bucketNames.includes(bucket.name)).map((bucket) => ({
+        classifier: (d: HistogramDatum) => consequenceBucket(d.consequence) === bucket.name,
+        options: {color: bucket.color, title: bucket.name}
+      }))
+    },
+    filterControlVariantByEffect(variant: DisplayVariant) {
+      // Keep a control variant only when its effect bucket is among the selected filters.
       if (!this.proteinEffectOptionsAvailable) {
         return true
       }
-      return (
-        (this.selectedControlVariantTypeFilters.includes('Missense') && variantIsMissense(variant)) ||
-        (this.selectedControlVariantTypeFilters.includes('Synonymous') && variantIsSynonymous(variant)) ||
-        (this.selectedControlVariantTypeFilters.includes('Nonsense') && variantIsNonsense(variant)) ||
-        (this.selectedControlVariantTypeFilters.includes('Start/Stop Loss') && isStartOrStopLoss(variant)) ||
-        (this.selectedControlVariantTypeFilters.includes('Other') &&
-          !variantIsMissense(variant) &&
-          !variantIsSynonymous(variant) &&
-          !variantIsNonsense(variant) &&
-          !isStartOrStopLoss(variant))
-      )
+      return this.selectedControlVariantTypeFilters.includes(consequenceBucket(variant.consequence))
     },
     buildExportFns() {
       return {
@@ -1209,8 +1122,8 @@ export default defineComponent({
           .bottomAxisLabel('Functional Score')
           .leftAxisLabel('Number of Variants')
           .numBins(30)
-          .valueField((variant: Variant) => variant?.scores?.score)
-          .accessorField((variant: Variant) => variant?.accession)
+          .valueField((variant: DisplayVariant) => variant?.score)
+          .accessorField((variant: DisplayVariant) => variant?.variantUrn)
           .tooltipHtml(this.tooltipHtmlGetter)
           .selectionChanged(this.onHistogramSelectionChanged)
       }
@@ -1256,10 +1169,14 @@ export default defineComponent({
       }
     },
 
-    onHistogramSelectionChanged(payload: {bin: HistogramBin | null; datum: Variant | null; source: 'histogram'}) {
+    onHistogramSelectionChanged(payload: {
+      bin: HistogramBin | null
+      datum: DisplayVariant | null
+      source: 'histogram'
+    }) {
       if (this.lockSelection) {
-        const currentAccession = (this.externalSelection as any)?.accession
-        const nextAccession = (payload?.datum as any)?.accession
+        const currentAccession = (this.externalSelection as any)?.variantUrn
+        const nextAccession = (payload?.datum as any)?.variantUrn
         // Block clears and changes; immediately restore selection
         if (!nextAccession || (currentAccession && nextAccession !== currentAccession)) {
           if (this.histogram && this.externalSelection) {
@@ -1419,7 +1336,7 @@ export default defineComponent({
 
       for (const clinicalControl of this.clinicalControls) {
         clinicalControl.mappedVariants.forEach((mappedVariant) => {
-          const variant = this.variants.find((variant) => variant.accession === mappedVariant.variantUrn)
+          const variant = this.variants.find((variant) => variant.variantUrn === mappedVariant.variantUrn)
           if (variant) {
             associatedAnyControlsWithVariants = true
             variant.control = clinicalControl
@@ -1697,32 +1614,10 @@ export default defineComponent({
   position: absolute;
 }
 
-.mavedb-histogram-tooltip-variant-color {
-  display: inline-block;
-  height: 12px;
-  width: 12px;
-  margin-right: 4px;
-  border-radius: 100%;
-}
-
 .mavedb-histogram-container {
   height: 350px;
 }
 
-.mavedb-histogram-tooltip-variant-star {
-  margin: 0 1.5px;
-}
-.mavedb-histogram-tooltip-variant-star-filled {
-  color: #fdb81e;
-}
-
-.mavedb-range-classification-badge {
-  padding: 2px 4px;
-  border-radius: 4px;
-  font-size: 11px;
-  font-weight: bold;
-}
-
 .mavedb-class-based-calibration-note {
   margin-top: 0.25rem;
   font-size: 12px;
diff --git a/src/components/score-set/ScoreSetVisualizer.vue b/src/components/score-set/ScoreSetVisualizer.vue
index bc7ae4a7..b5f136a1 100644
--- a/src/components/score-set/ScoreSetVisualizer.vue
+++ b/src/components/score-set/ScoreSetVisualizer.vue
@@ -41,7 +41,7 @@ import Splitter from 'primevue/splitter'
 import SplitterPanel from 'primevue/splitterpanel'
 import _ from 'lodash'
 import {AMINO_ACIDS} from '@/lib/amino-acids'
-import type {Variant} from '@/lib/variants'
+import type {DisplayVariant} from '@/lib/variants'
 import type {components} from '@/schema/openapi'
 
 type ScoreSet = components['schemas']['ScoreSet']
@@ -54,8 +54,8 @@ export default defineComponent({
   components: {ProteinStructureView, ScoreSetHeatmap, Splitter, SplitterPanel},
 
   props: {
-    heatmapVariants: {type: Array as PropType<Variant[] | null>, default: null},
-    scores: {type: Array as PropType<Variant[] | null>, default: null},
+    heatmapVariants: {type: Array as PropType<DisplayVariant[] | null>, default: null},
+    scores: {type: Array as PropType<DisplayVariant[] | null>, default: null},
     scoreSet: {type: Object as PropType<ScoreSet | null>, default: null},
     uniprotId: {type: String as PropType<string | null>, default: null}
   },
diff --git a/src/components/screens/ScoreSetView.vue b/src/components/screens/ScoreSetView.vue
index 992d34f1..35f0de51 100644
--- a/src/components/screens/ScoreSetView.vue
+++ b/src/components/screens/ScoreSetView.vue
@@ -81,13 +81,21 @@
                   dropdown
                   fluid
                   :input-style="variantToVisualize ? {paddingRight: '2.25rem'} : undefined"
-                  option-label="mavedb_label"
+                  :option-label="variantOptionLabel"
                   scroll-height="175px"
                   select-on-focus
                   :suggestions="variantSearchSuggestions"
                   :virtual-scroller-options="{itemSize: 50}"
                   @complete="variantSearch"
                 >
+                  <template #option="{option}">
+                    <div class="flex flex-col justify-center leading-tight">
+                      <span>{{ variantOptionLabel(option) }}</span>
+                      <span v-if="frame === 'mapped' && isUnmapped(option)" class="text-xs italic text-text-muted">
+                        Variant could not be mapped
+                      </span>
+                    </div>
+                  </template>
                   <template #empty>
                     <div class="p-2.5 text-center text-sm text-text-muted">No matching variants found.</div>
                   </template>
@@ -111,12 +119,21 @@
               ]"
               >Raw variants</span
             >
-            <ToggleSwitch
-              :aria-label="`Click to change to ${clinicalMode ? 'raw data' : 'clinical view'}.`"
-              :disabled="coordinateSwitching"
-              :model-value="clinicalMode"
-              @update:model-value="toggleClinicalMode"
-            />
+            <!-- Wrapper so the tooltip fires even when the switch is disabled (a disabled control has
+                 pointer-events: none and won't trigger a tooltip on itself). Only shown when mapped
+                 mode is unavailable — clinicalModeHelpText returns the "no mapped variants" reason then. -->
+            <span
+              v-tooltip.top="mappedModeAvailable ? undefined : clinicalModeHelpText"
+              class="inline-flex"
+              :class="{'cursor-not-allowed': !mappedModeAvailable}"
+            >
+              <ToggleSwitch
+                :aria-label="`Click to change to ${clinicalMode ? 'raw data' : 'clinical view'}.`"
+                :disabled="coordinateSwitching || !mappedModeAvailable"
+                :model-value="clinicalMode"
+                @update:model-value="toggleClinicalMode"
+              />
+            </span>
             <span
               :class="[
                 clinicalMode ? 'font-semibold text-sage' : 'text-text-muted',
@@ -134,7 +151,7 @@
         </div>
 
         <!-- Variants loading spinner -->
-        <div v-if="variants == null && scoresDataStatus !== 'Loaded'" class="flex items-center justify-center py-6">
+        <div v-if="variants == null && variantsDataStatus !== 'Loaded'" class="flex items-center justify-center py-6">
           <MvLoader text="Loading variants..." />
         </div>
 
@@ -162,7 +179,7 @@
             <div class="p-3 tablet:p-5">
               <ScoreSetHistogram
                 ref="distHistogram"
-                :coordinates="clinicalMode ? 'mapped' : 'raw'"
+                :coordinates="frame"
                 :default-histogram="'distribution'"
                 :external-selection="variantToVisualize"
                 :hide-start-and-stop-loss-by-default="hideStartAndStopLoss"
@@ -222,7 +239,7 @@
             <div class="p-3 tablet:p-5">
               <ScoreSetHistogram
                 ref="clinicalHistogram"
-                :coordinates="clinicalMode ? 'mapped' : 'raw'"
+                :coordinates="frame"
                 :default-histogram="'clinical'"
                 :external-selection="variantToVisualize"
                 :hide-start-and-stop-loss-by-default="hideStartAndStopLoss"
@@ -305,7 +322,7 @@
             <div class="p-3 tablet:p-5">
               <ScoreSetHeatmap
                 ref="heatmap"
-                :coordinates="clinicalMode ? 'mapped' : 'raw'"
+                :coordinates="frame"
                 :external-selection="variantToVisualize"
                 :hide-start-and-stop-loss="hideStartAndStopLoss"
                 :layout="heatmapLayout"
@@ -498,19 +515,12 @@ import useRemoteData from '@/composition/remote-data'
 import {useDatasetPermissions} from '@/composables/use-dataset-permissions'
 import {useCalibrationDialog} from '@/composables/use-calibration-dialog'
 import {useChartExport, type ChartExportFns} from '@/composables/use-chart-export'
-import {useVariantCoordinates} from '@/composables/use-variant-coordinates'
+import {useVariantCoordinates, type CoordinateFrame} from '@/composables/use-variant-coordinates'
 import config from '@/config'
 import {hasPathogenicityCalibrations, hasFunctionalCalibrations} from '@/lib/calibrations'
-import {variantNotNullOrNA} from '@/lib/mave-hgvs'
 import {getScoreSetShortName} from '@/lib/score-sets'
-import {parseScoreSetVariantData, type Variant, type LeanVariant} from '@/lib/variants'
-import {
-  deleteScoreSet,
-  publishScoreSet,
-  getScoreSetClinicalControlOptions,
-  histogramScoreSetVariantDataUrl,
-  leanScoreSetVariantsUrl
-} from '@/api/mavedb'
+import {type DisplayVariant} from '@/lib/variants'
+import {deleteScoreSet, publishScoreSet, getScoreSetClinicalControlOptions, leanScoreSetVariantsUrl} from '@/api/mavedb'
 import {components} from '@/schema/openapi'
 import MvLoader from '@/components/common/MvLoader.vue'
 import MvEmptyState from '@/components/common/MvEmptyState.vue'
@@ -566,11 +576,8 @@ export default {
 
   setup(props) {
     const head = useHead()
-    const scoresRemoteData = useRemoteData()
-    // Transitional: the lean whole-set view fetched alongside the legacy CSV `scoresData` channel.
-    // Consumers migrate onto `leanVariants` slice by slice; the CSV channel is removed once they have.
-    const leanVariantsRemoteData = useRemoteData()
-    const variantSearchSuggestions = ref<Variant[]>([])
+    const variantsRemoteData = useRemoteData()
+    const variantSearchSuggestions = ref<DisplayVariant[]>([])
     const selectedCalibrations = ref<(string | null)[]>([null, null])
     const urnRef = ref(props.itemId)
 
@@ -593,14 +600,10 @@ export default {
       ...useItem<ScoreSet>({itemTypeName: 'scoreSet'}),
       ...useScopedId(),
       ...useVariantCoordinates(),
-      scoresData: scoresRemoteData.data,
-      scoresDataStatus: scoresRemoteData.remoteDataStatus,
-      setScoresDataUrl: scoresRemoteData.setDataUrl,
-      ensureScoresDataLoaded: scoresRemoteData.ensureDataLoaded,
-      leanVariants: leanVariantsRemoteData.data,
-      leanVariantsStatus: leanVariantsRemoteData.remoteDataStatus,
-      setLeanVariantsUrl: leanVariantsRemoteData.setDataUrl,
-      ensureLeanVariantsLoaded: leanVariantsRemoteData.ensureDataLoaded,
+      variantsData: variantsRemoteData.data,
+      variantsDataStatus: variantsRemoteData.remoteDataStatus,
+      setVariantsDataUrl: variantsRemoteData.setDataUrl,
+      ensureVariantsDataLoaded: variantsRemoteData.ensureDataLoaded,
       variantSearchSuggestions,
 
       distHistogramExportFn,
@@ -621,12 +624,12 @@ export default {
   data: () => ({
     clinicalMode: true,
     coordinateSwitching: false,
-    variants: null as Variant[] | null,
+    variants: null as DisplayVariant[] | null,
     showHeatmap: true,
     isScoreSetVisualizerVisible: false,
     hasClinicalVariants: false,
     heatmapExists: false,
-    selectedVariant: null as Variant | null,
+    selectedVariant: null as DisplayVariant | null,
     heatmapSequenceType: 'protein' as 'dna' | 'protein',
     heatmapLayout: 'normal' as 'normal' | 'compact',
     syncingBinSelection: false
@@ -634,6 +637,9 @@ export default {
 
   computed: {
     clinicalModeHelpText() {
+      if (!this.mappedModeAvailable) {
+        return 'This score set has no mapped variants, so only raw (submitted) coordinates are available.'
+      }
       if (this.item?.targetGenes?.[0]?.targetSequence) {
         return 'In clinical mode, mapped variant coordinates are used when available, and start- and stop-loss codons are omitted because this score set was produced using a synthetic target sequence.'
       }
@@ -645,9 +651,20 @@ export default {
         .filter((c) => c.orcidId !== creatorId)
         .sort((a, b) => (a.familyName ?? '').localeCompare(b.familyName ?? ''))
     },
+    // The coordinate frame the page is displaying in: clinical mode reads the mapped (reference)
+    // numbering, non-clinical the raw (submitted/target) numbering.
+    frame(): CoordinateFrame {
+      return this.clinicalMode ? 'mapped' : 'raw'
+    },
+    // Whether the mapped frame has anything to show — some variant carries a mapped coordinate at some
+    // level. When false the score set has no mapped data (unmapped or unmappable), so mapped mode is
+    // disabled and the page makes only the raw frame available.
+    mappedModeAvailable(): boolean {
+      return !!this.variants?.length && this.sequenceTypeOptions(this.variants, 'mapped').length > 0
+    },
     heatmapSequenceTypeOptions(): Array<{title: string; value: string}> {
       if (!this.variants?.length) return []
-      return this.sequenceTypeOptions(this.variants as Variant[], this.clinicalMode)
+      return this.sequenceTypeOptions(this.variants, this.frame)
     },
     hasCounts() {
       const allCountColumns = this.item?.datasetColumns?.countColumns ?? []
@@ -694,10 +711,6 @@ export default {
     isMetaDataEmpty() {
       return Object.keys(this.item?.extraMetadata || {}).length === 0
     },
-    // Typed handle on the lean whole-set view. Consumers migrate onto this from `variants` slice by slice.
-    leanVariantRecords(): LeanVariant[] | null {
-      return (this.leanVariants as LeanVariant[] | null) ?? null
-    },
     selectedCalibrationObjects() {
       if (this.item?.scoreCalibrations && this.selectedCalibrations) {
         return this.selectedCalibrations.map(
@@ -729,24 +742,24 @@ export default {
       handler(newValue, oldValue) {
         if (newValue !== oldValue) {
           this.setItemId(newValue)
-          let scoresUrl = null
-          let leanUrl = null
+          let variantsUrl = null
           if (this.itemType?.restCollectionName && this.itemId) {
-            scoresUrl = histogramScoreSetVariantDataUrl(this.itemId)
-            leanUrl = leanScoreSetVariantsUrl(this.itemId)
+            variantsUrl = leanScoreSetVariantsUrl(this.itemId)
           }
-          this.setScoresDataUrl(scoresUrl)
-          this.ensureScoresDataLoaded()
-          this.setLeanVariantsUrl(leanUrl)
-          this.ensureLeanVariantsLoaded()
+          this.setVariantsDataUrl(variantsUrl)
+          this.ensureVariantsDataLoaded()
         }
       },
       immediate: true
     },
-    scoresData(newValue: unknown) {
-      const parsed = newValue ? parseScoreSetVariantData(newValue as string) : null
-      this.variants = parsed ? (Object.freeze(parsed) as Variant[]) : null
+    variantsData(newValue: unknown) {
+      const records = (newValue as DisplayVariant[] | null) ?? null
+      this.variants = records ? (Object.freeze(records) as DisplayVariant[]) : null
+      // Start in mapped mode only when the score set actually has mapped data; otherwise fall back to
+      // the raw frame (where the toggle is also disabled). Re-decided per score set as its variants load.
+      this.clinicalMode = this.mappedModeAvailable
       this.applyUrlState()
+      this.reconcileHeatmapLevel()
     },
     selectedVariant: 'refreshUrlState',
     selectedCalibrations: {handler: 'refreshUrlState', deep: true}
@@ -760,7 +773,7 @@ export default {
     refreshUrlState() {
       const query = {...this.$route.query}
       if (this.selectedVariant) {
-        query.variant = this.selectedVariant.accession
+        query.variant = this.selectedVariant.variantUrn
       } else {
         delete query.variant
       }
@@ -779,11 +792,25 @@ export default {
     toggleClinicalMode(value: boolean) {
       this.coordinateSwitching = true
       this.clinicalMode = value
+      this.reconcileHeatmapLevel()
       requestAnimationFrame(() => {
         this.coordinateSwitching = false
       })
     },
 
+    reconcileHeatmapLevel() {
+      // The frame toggle can strand the current sequence level: a level that exists in one frame may
+      // not exist in the other (e.g. a nucleotide accession-based set has mapped protein but no raw
+      // protein). Fall back to an available level so we never leave the heatmap on an empty view.
+      if (!this.variants?.length) {
+        return
+      }
+      const resolved = this.resolveLevel(this.variants, this.heatmapSequenceType, this.frame)
+      if (resolved && resolved !== this.heatmapSequenceType) {
+        this.heatmapSequenceType = resolved
+      }
+    },
+
     async checkClinicalVariants() {
       if (!this.item) return
       try {
@@ -853,55 +880,58 @@ export default {
 
     variantSearch(event: {query: string}) {
       const query = event.query.toLowerCase()
-      const useMapped = this.clinicalMode
-      const matches: Variant[] = []
-      const MAX_RESULTS = 100
-
-      for (const variant of (this.variants || []) as Variant[]) {
-        if (matches.length >= MAX_RESULTS) break
-        if (!_.isNumber(variant.scores?.score)) continue
-
-        const nt = this.getHgvsNt(variant, useMapped)
-        const pro = this.getHgvsPro(variant, useMapped)
-
-        // Empty query: show all variants with their preferred label
-        if (!query) {
-          matches.push(Object.assign(variant, this.variantLabel(variant)))
-        } else if (variantNotNullOrNA(nt) && nt!.toLowerCase().includes(query)) {
-          matches.push(Object.assign(variant, {mavedb_label: nt}))
-        } else if (variantNotNullOrNA(variant.hgvs_splice) && variant.hgvs_splice!.toLowerCase().includes(query)) {
-          matches.push(Object.assign(variant, {mavedb_label: variant.hgvs_splice}))
-        } else if (variantNotNullOrNA(pro) && pro!.toLowerCase().includes(query)) {
-          matches.push(Object.assign(variant, {mavedb_label: pro}))
-        } else if (variantNotNullOrNA(variant.accession) && variant.accession.toLowerCase().includes(query)) {
-          matches.push(Object.assign(variant, {mavedb_label: variant.accession}))
+      const matches: DisplayVariant[] = []
+
+      for (const variant of this.variants || []) {
+        if (!_.isNumber(variant.score)) continue
+        // Empty query lists every scored variant; otherwise keep those whose coordinate strings match.
+        if (!query || this.variantMatchesQuery(variant, query)) {
+          matches.push(variant)
         }
       }
       this.variantSearchSuggestions = matches
     },
 
-    variantLabel(variant: Variant): {mavedb_label: string} {
-      return this.labelForVariant(variant, this.clinicalMode)
+    // Whether any of a variant's coordinate strings contains the query. Matches the current frame's
+    // coordinates plus the submitted (target-frame) strings, so a search finds the submitted HGVS the
+    // label falls back to for an unmapped variant — not just the mapped representation.
+    variantMatchesQuery(variant: DisplayVariant, query: string): boolean {
+      const candidates = [
+        this.getHgvsNt(variant, this.frame),
+        this.getHgvsPro(variant, this.frame),
+        variant.hgvsNt?.hgvs,
+        variant.hgvsPro?.hgvs,
+        variant.hgvsSplice?.hgvs,
+        variant.variantUrn
+      ]
+      return candidates.some((candidate) => candidate != null && candidate.toLowerCase().includes(query))
+    },
+
+    // Label for the AutoComplete chip and suggestions. A function (not a materialized field) so it
+    // re-resolves from the current frame — flipping the clinical toggle re-labels reactively. PrimeVue
+    // may hand back the raw typed string before a selection is made, so tolerate that.
+    variantOptionLabel(variant: DisplayVariant | string): string {
+      return typeof variant === 'string' ? variant : this.labelForVariant(variant, this.frame)
     },
 
-    childComponentSelectedVariant(variant: Variant | null) {
+    childComponentSelectedVariant(variant: DisplayVariant | null) {
       if (variant == null) {
         this.selectedVariant = null
         return
       }
-      if (!variant.accession) return
-      const selected = this.variants?.find((v) => v.accession === variant.accession)
-      this.selectedVariant = selected ? Object.assign(selected, this.variantLabel(selected)) : null
+      if (!variant.variantUrn) return
+      const selected = this.variants?.find((v) => v.variantUrn === variant.variantUrn)
+      this.selectedVariant = selected ?? null
     },
 
     onHistogramSelectionChanged(
-      payload: {datum?: {accession?: string; urn?: string}; bin?: unknown},
+      payload: {datum?: {variantUrn?: string}; bin?: unknown},
       options: {syncTarget?: string}
     ) {
-      const accession = payload?.datum?.accession || payload?.datum?.urn
-      if (accession) {
-        const selected = this.variants?.find((v) => v.accession === accession)
-        this.selectedVariant = selected ? Object.assign(selected, this.variantLabel(selected)) : null
+      const urn = payload?.datum?.variantUrn
+      if (urn) {
+        const selected = this.variants?.find((v) => v.variantUrn === urn)
+        this.selectedVariant = selected ?? null
       } else {
         if (this.syncingBinSelection || !payload?.bin) return
         this.syncingBinSelection = true
@@ -922,8 +952,8 @@ export default {
 
     applyUrlState() {
       if (this.$route.query.variant) {
-        const selected = this.variants?.find((v) => v.accession === this.$route.query.variant)
-        if (selected) this.selectedVariant = Object.assign(selected, this.variantLabel(selected))
+        const selected = this.variants?.find((v) => v.variantUrn === this.$route.query.variant)
+        if (selected) this.selectedVariant = selected
       }
       if (this.$route.query.calibration) {
         const cal = String(this.$route.query.calibration)
diff --git a/src/components/screens/VariantScreen.vue b/src/components/screens/VariantScreen.vue
index 14239880..9a24ad32 100644
--- a/src/components/screens/VariantScreen.vue
+++ b/src/components/screens/VariantScreen.vue
@@ -177,11 +177,7 @@
               <div class="mb-1.5 text-xs-minus font-bold uppercase tracking-[0.5px] text-black">Classification</div>
               <MvDetailRow
                 label="Functional score"
-                :value="
-                  lookup.selectedVariantScore.value !== 'NA'
-                    ? Number(lookup.selectedVariantScore.value).toPrecision(4)
-                    : undefined
-                "
+                :value="lookup.selectedVariantScore.value?.toPrecision(4)"
               />
               <MvDetailRow label="ACMG code">
                 <MvEvidenceTag
@@ -352,8 +348,7 @@ export default defineComponent({
       const currentMapped = activeVariant.mappedVariants.find((m) => m.current)
       const hasMappingData = !!currentMapped?.postMapped
 
-      const score = this.lookup.selectedVariantScore.value
-      const hasScore = score !== null && score !== 'NA'
+      const hasScore = this.lookup.selectedVariantScore.value !== null
 
       if (hasMappingData && hasScore && hasPathogenicityCalibrations(activeVariant.scoreSet)) {
         options.push({
diff --git a/src/composables/use-variant-coordinates.test.ts b/src/composables/use-variant-coordinates.test.ts
new file mode 100644
index 00000000..cdf6fa6a
--- /dev/null
+++ b/src/composables/use-variant-coordinates.test.ts
@@ -0,0 +1,143 @@
+import {describe, expect, it} from 'vitest'
+
+import {useVariantCoordinates} from '@/composables/use-variant-coordinates'
+import type {HgvsField, LeanVariant} from '@/lib/variants'
+
+const {coordinateFor, getHgvsNt, getHgvsPro, labelForVariant, levelAvailable, sequenceTypeOptions, resolveLevel} =
+  useVariantCoordinates()
+
+function field(hgvs: string, position?: number, ref?: string, alt?: string): HgvsField {
+  return {hgvs, position, ref, alt}
+}
+
+function variant(overrides: Partial<LeanVariant>): LeanVariant {
+  return {variantUrn: 'urn:mavedb:00000001-a-1#1', ...overrides} as LeanVariant
+}
+
+// A coding/genomic assay: measured at the nucleotide level, mapped up to protein.
+const dnaAssay = variant({
+  variantUrn: 'urn:dna#1',
+  hgvsNt: field('c.6C>T', 6, 'C', 'T'),
+  hgvsPro: field('p.Leu2Phe', 2, 'Leu', 'Phe'),
+  assayLevelHgvs: field('NM_x:c.6C>T', 6, 'C', 'T'),
+  proteinLevelHgvs: field('NP_x:p.Leu2Phe', 2, 'Leu', 'Phe')
+})
+
+// A protein assay: measured at the protein level; there is no mapped coding (mavedb-api#784).
+const proteinAssay = variant({
+  variantUrn: 'urn:pro#1',
+  hgvsPro: field('p.Leu6Gly', 6, 'Leu', 'Gly'),
+  assayLevelHgvs: field('NP_x:p.Leu6Gly', 6, 'Leu', 'Gly'),
+  proteinLevelHgvs: field('NP_x:p.Leu6Gly', 6, 'Leu', 'Gly')
+})
+
+describe('coordinateFor — the 2×2 (level, frame) resolution', () => {
+  it('raw frame reads the submitted slots', () => {
+    expect(coordinateFor(dnaAssay, 'dna', 'raw')).toBe(dnaAssay.hgvsNt)
+    expect(coordinateFor(dnaAssay, 'protein', 'raw')).toBe(dnaAssay.hgvsPro)
+  })
+
+  it('mapped protein reads proteinLevelHgvs for either assay type', () => {
+    expect(coordinateFor(dnaAssay, 'protein', 'mapped')).toBe(dnaAssay.proteinLevelHgvs)
+    expect(coordinateFor(proteinAssay, 'protein', 'mapped')).toBe(proteinAssay.proteinLevelHgvs)
+  })
+
+  it('mapped dna reads assayLevelHgvs only when it is nucleotide (coding/genomic assay)', () => {
+    expect(coordinateFor(dnaAssay, 'dna', 'mapped')).toBe(dnaAssay.assayLevelHgvs)
+  })
+
+  it('mapped dna is null for a protein assay — never fabricates a coding coordinate (#784)', () => {
+    expect(coordinateFor(proteinAssay, 'dna', 'mapped')).toBeNull()
+  })
+
+  it('returns null for an absent slot', () => {
+    expect(coordinateFor(proteinAssay, 'dna', 'raw')).toBeNull() // protein assay has no submitted nt
+    expect(coordinateFor(variant({}), 'protein', 'raw')).toBeNull()
+  })
+})
+
+describe('getHgvsNt / getHgvsPro — string convenience over coordinateFor', () => {
+  it('return the resolved hgvs string or undefined', () => {
+    expect(getHgvsNt(dnaAssay, 'raw')).toBe('c.6C>T')
+    expect(getHgvsNt(dnaAssay, 'mapped')).toBe('NM_x:c.6C>T')
+    expect(getHgvsNt(proteinAssay, 'mapped')).toBeUndefined()
+    expect(getHgvsPro(proteinAssay, 'raw')).toBe('p.Leu6Gly')
+  })
+})
+
+describe('labelForVariant — frame coords → submitted HGVS → URN', () => {
+  it('prefers protein, in the requested frame', () => {
+    expect(labelForVariant(dnaAssay, 'raw')).toBe('p.Leu2Phe')
+    expect(labelForVariant(dnaAssay, 'mapped')).toBe('NP_x:p.Leu2Phe')
+  })
+
+  it('falls back to nucleotide when protein is absent', () => {
+    const ntOnly = variant({variantUrn: 'urn:nt', hgvsNt: field('c.9A>G', 9, 'A', 'G')})
+    expect(labelForVariant(ntOnly, 'raw')).toBe('c.9A>G')
+  })
+
+  it('in the mapped frame, an unmapped variant falls back to its submitted HGVS, not the URN', () => {
+    // No mapped coordinates (unmapped), but a submitted intronic nucleotide string is present.
+    const unmappedIntronic = variant({variantUrn: 'urn:intron', hgvsNt: field('c.122-6T>A')})
+    expect(labelForVariant(unmappedIntronic, 'mapped')).toBe('c.122-6T>A')
+  })
+
+  it('prefers submitted protein over submitted nucleotide in the fallback', () => {
+    const unmapped = variant({
+      variantUrn: 'urn:u',
+      hgvsNt: field('c.6C>T', 6, 'C', 'T'),
+      hgvsPro: field('p.Leu2Phe', 2, 'Leu', 'Phe')
+    })
+    expect(labelForVariant(unmapped, 'mapped')).toBe('p.Leu2Phe')
+  })
+
+  it('falls back to splice, then to the URN when no other HGVS exists', () => {
+    const spliceOnly = variant({variantUrn: 'urn:sp', hgvsSplice: field('c.1-2A>G')})
+    expect(labelForVariant(spliceOnly, 'raw')).toBe('c.1-2A>G')
+    expect(labelForVariant(spliceOnly, 'mapped')).toBe('c.1-2A>G')
+    expect(labelForVariant(variant({variantUrn: 'urn:bare'}), 'raw')).toBe('urn:bare')
+    expect(labelForVariant(variant({variantUrn: 'urn:bare'}), 'mapped')).toBe('urn:bare')
+  })
+})
+
+describe('levelAvailable / sequenceTypeOptions — availability per frame', () => {
+  it('a coding assay offers both levels in both frames', () => {
+    expect(sequenceTypeOptions([dnaAssay], 'raw')).toEqual([
+      {title: 'DNA', value: 'dna'},
+      {title: 'Protein', value: 'protein'}
+    ])
+    expect(sequenceTypeOptions([dnaAssay], 'mapped')).toEqual([
+      {title: 'DNA', value: 'dna'},
+      {title: 'Protein', value: 'protein'}
+    ])
+  })
+
+  it('a protein assay never offers DNA — in either frame (#784)', () => {
+    expect(sequenceTypeOptions([proteinAssay], 'raw')).toEqual([{title: 'Protein', value: 'protein'}])
+    expect(sequenceTypeOptions([proteinAssay], 'mapped')).toEqual([{title: 'Protein', value: 'protein'}])
+    expect(levelAvailable([proteinAssay], 'dna', 'mapped')).toBe(false)
+  })
+
+  it('availability is a set-wide OR across variants', () => {
+    expect(sequenceTypeOptions([dnaAssay, proteinAssay], 'mapped')).toEqual([
+      {title: 'DNA', value: 'dna'},
+      {title: 'Protein', value: 'protein'}
+    ])
+  })
+})
+
+describe('resolveLevel — explicit frame→level coupling', () => {
+  it('keeps the desired level when available', () => {
+    expect(resolveLevel([dnaAssay], 'protein', 'mapped')).toBe('protein')
+    expect(resolveLevel([dnaAssay], 'dna', 'mapped')).toBe('dna')
+  })
+
+  it('falls back deterministically when the desired level is stranded', () => {
+    // Protein assay: desiring DNA in mapped frame falls back to the only available level.
+    expect(resolveLevel([proteinAssay], 'dna', 'mapped')).toBe('protein')
+  })
+
+  it('returns null when no level is available', () => {
+    expect(resolveLevel([variant({variantUrn: 'urn:bare'})], 'protein', 'raw')).toBeNull()
+  })
+})
diff --git a/src/composables/use-variant-coordinates.ts b/src/composables/use-variant-coordinates.ts
index e6e18cd7..aae4a52f 100644
--- a/src/composables/use-variant-coordinates.ts
+++ b/src/composables/use-variant-coordinates.ts
@@ -1,84 +1,133 @@
-import {variantNotNullOrNA, preferredVariantLabel, type SimpleMaveVariant} from '@/lib/mave-hgvs'
-import type {Variant} from '@/lib/variants'
+import {isNucleotideHgvs} from '@/lib/mave-hgvs'
+import type {HgvsField, LeanVariant} from '@/lib/variants'
+
+/** The sequence level a coordinate is expressed in. */
+export type SequenceLevel = 'dna' | 'protein'
+
+/** The coordinate frame: `raw` = submitted/target numbering, `mapped` = reference numbering. */
+export type CoordinateFrame = 'raw' | 'mapped'
 
 /**
- * Stateless composable for resolving variant HGVS coordinates based on
- * the current display mode (raw vs mapped). Shared between ScoreSetView
- * (variant search, labels, sequence type detection) and ScoreSetHeatmap.
+ * Stateless resolution of a variant's HGVS coordinate across two orthogonal axes — sequence
+ * **level** (dna ↔ protein) and **frame** (raw/submitted ↔ mapped/reference).
+ *
+ * `coordinateFor` is the single source of truth: every downstream derivation (heatmap x/y,
+ * axis availability, labels, tooltips) resolves through it, so the (level, frame) → coordinate
+ * mapping lives in exactly one place. The frame axis is load-bearing — raw and mapped are
+ * genuinely different coordinate systems, not the same grid with different captions.
+ *
+ * Shared between ScoreSetView (search, labels, level options) and ScoreSetHeatmap (plotting).
  */
 export function useVariantCoordinates() {
   /**
-   * Get the best nucleotide HGVS string for a variant.
-   * In mapped mode, prefers post_mapped_hgvs_c when available.
+   * Resolve the HGVS coordinate for a variant at a given level and frame, or `null` when that
+   * cell does not exist for the variant.
+   *
+   * The 2×2 mapping onto the lean record's slots:
+   *
+   * |         | raw       | mapped                                |
+   * | ------- | --------- | ------------------------------------- |
+   * | dna     | `hgvsNt`  | `assayLevelHgvs` iff it is nucleotide |
+   * | protein | `hgvsPro` | `proteinLevelHgvs`                    |
+   *
+   * The (mapped, dna) cell is `null` for a protein assay: a protein measurement has no mapped
+   * coding representation (mavedb-api#784), so we never fabricate one from a degenerate sibling.
    */
-  function getHgvsNt(variant: Variant, useMapped: boolean): string | undefined {
-    if (useMapped && variantNotNullOrNA(variant.mavedb?.post_mapped_hgvs_c)) {
-      return variant.mavedb!.post_mapped_hgvs_c!
+  function coordinateFor(variant: LeanVariant, level: SequenceLevel, frame: CoordinateFrame): HgvsField | null {
+    if (frame === 'raw') {
+      return (level === 'dna' ? variant.hgvsNt : variant.hgvsPro) ?? null
     }
-    return variant.hgvs_nt
+    if (level === 'protein') {
+      return variant.proteinLevelHgvs ?? null
+    }
+    // mapped + dna: only when the assay-level mapped representation is itself nucleotide.
+    const assayLevel = variant.assayLevelHgvs
+    return assayLevel && isNucleotideHgvs(assayLevel.hgvs) ? assayLevel : null
   }
 
-  /**
-   * Get the best protein HGVS string for a variant.
-   * In mapped mode, prefers translated_hgvs_p or post_mapped_hgvs_p.
-   * In raw mode, falls back through hgvs_pro → translated_hgvs_p.
-   */
-  function getHgvsPro(variant: Variant, useMapped: boolean): string | undefined {
-    if (useMapped) {
-      if (variantNotNullOrNA(variant.translated_hgvs_p)) return variant.translated_hgvs_p
-      if (variantNotNullOrNA(variant.mavedb?.post_mapped_hgvs_p)) return variant.mavedb!.post_mapped_hgvs_p!
-    }
-    if (variantNotNullOrNA(variant.hgvs_pro)) return variant.hgvs_pro
-    if (variantNotNullOrNA(variant.translated_hgvs_p)) return variant.translated_hgvs_p
-    return undefined
+  /** The nucleotide HGVS string for a variant in the given frame, if any. */
+  function getHgvsNt(variant: LeanVariant, frame: CoordinateFrame): string | undefined {
+    return coordinateFor(variant, 'dna', frame)?.hgvs
+  }
+
+  /** The protein HGVS string for a variant in the given frame, if any. */
+  function getHgvsPro(variant: LeanVariant, frame: CoordinateFrame): string | undefined {
+    return coordinateFor(variant, 'protein', frame)?.hgvs
   }
 
   /**
-   * Get the preferred display label for a variant, respecting coordinate mode.
-   * Prefers protein > nucleotide > splice > accession.
+   * Preferred display label in the given frame, most to least specific:
+   *   frame protein → frame nucleotide → submitted protein → submitted nucleotide → submitted splice → URN.
+   *
+   * The mapped frame has no coordinate for an unmapped variant, so before giving up to the bare URN we
+   * fall back to the variant's submitted (target-frame) HGVS: an unmapped intronic variant still carries
+   * its `c.122-6T>A`, which is far more informative than the URN. In the raw frame the first two slots
+   * already are the submitted strings, so the fallback is inert there. The URN surfaces only when the
+   * variant carries no HGVS at all.
    */
-  function labelForVariant(variant: Variant, useMapped: boolean): {mavedb_label: string} {
-    const pro = getHgvsPro(variant, useMapped)
-    if (variantNotNullOrNA(pro)) return {mavedb_label: pro!}
-
-    const nt = getHgvsNt(variant, useMapped)
-    if (variantNotNullOrNA(nt)) return {mavedb_label: nt!}
-
-    if (variantNotNullOrNA(variant.hgvs_splice)) return {mavedb_label: variant.hgvs_splice!}
+  function labelForVariant(variant: LeanVariant, frame: CoordinateFrame): string {
+    return (
+      coordinateFor(variant, 'protein', frame)?.hgvs ??
+      coordinateFor(variant, 'dna', frame)?.hgvs ??
+      variant.hgvsPro?.hgvs ??
+      variant.hgvsNt?.hgvs ??
+      variant.hgvsSplice?.hgvs ??
+      variant.variantUrn
+    )
+  }
 
-    return preferredVariantLabel(variant as SimpleMaveVariant)
+  /** Whether any variant resolves a coordinate at the given level and frame. */
+  function levelAvailable(variants: LeanVariant[], level: SequenceLevel, frame: CoordinateFrame): boolean {
+    return variants.some((v) => coordinateFor(v, level, frame) != null)
   }
 
-  /**
-   * Check whether any variants have DNA (nucleotide) HGVS data available.
-   */
-  function hasDnaVariants(variants: Variant[], useMapped: boolean): boolean {
-    return variants.some((v) => variantNotNullOrNA(getHgvsNt(v, useMapped)))
+  /** The level options to offer for the given frame, in display order (DNA before Protein). */
+  function sequenceTypeOptions(
+    variants: LeanVariant[],
+    frame: CoordinateFrame
+  ): Array<{title: string; value: SequenceLevel}> {
+    const options: Array<{title: string; value: SequenceLevel}> = []
+    if (levelAvailable(variants, 'dna', frame)) options.push({title: 'DNA', value: 'dna'})
+    if (levelAvailable(variants, 'protein', frame)) options.push({title: 'Protein', value: 'protein'})
+    return options
   }
 
   /**
-   * Check whether any variants have protein HGVS data available.
+   * Resolve which level to actually display: keep `desiredLevel` if it is available in this
+   * frame, otherwise fall back to the first available level, or `null` if none are. Makes the
+   * frame→level coupling explicit — when a frame flip strands the current level, the fallback is
+   * deterministic rather than dependent on a watcher firing.
    */
-  function hasProteinVariants(variants: Variant[], useMapped: boolean): boolean {
-    return variants.some((v) => variantNotNullOrNA(getHgvsPro(v, useMapped)))
+  function resolveLevel(
+    variants: LeanVariant[],
+    desiredLevel: SequenceLevel,
+    frame: CoordinateFrame
+  ): SequenceLevel | null {
+    const available = sequenceTypeOptions(variants, frame).map((option) => option.value)
+    if (available.includes(desiredLevel)) return desiredLevel
+    return available[0] ?? null
   }
 
   /**
-   * Build the sequence type options array for heatmap/display controls.
+   * Whether the mapping/annotation step produced no mapped allele for this variant — keyed on the
+   * authoritative allele digest, which is null exactly when nothing was mapped. In the mapped frame
+   * such a variant has no mapped coordinate, so its label falls back to the submitted (target-frame)
+   * HGVS. That fallback string can look mapped (accession-based target) or plainly unmapped
+   * (sequence-based target, bare `c.` coordinate), so callers gate a "could not be mapped" note on this
+   * being true and the frame being mapped. The submitted string is shown by intent in the raw frame.
    */
-  function sequenceTypeOptions(variants: Variant[], useMapped: boolean): Array<{title: string; value: string}> {
-    const options: Array<{title: string; value: string}> = []
-    if (hasDnaVariants(variants, useMapped)) options.push({title: 'DNA', value: 'dna'})
-    if (hasProteinVariants(variants, useMapped)) options.push({title: 'Protein', value: 'protein'})
-    return options
+  function isUnmapped(variant: LeanVariant): boolean {
+    return variant.assayLevelDigest == null
   }
 
   return {
+    coordinateFor,
     getHgvsNt,
     getHgvsPro,
     labelForVariant,
-    hasDnaVariants,
-    hasProteinVariants,
-    sequenceTypeOptions
+    isUnmapped,
+    levelAvailable,
+    sequenceTypeOptions,
+    resolveLevel
   }
 }
diff --git a/src/composables/use-variant-lookup.ts b/src/composables/use-variant-lookup.ts
index f7b6bd57..94a92a1c 100644
--- a/src/composables/use-variant-lookup.ts
+++ b/src/composables/use-variant-lookup.ts
@@ -1,12 +1,8 @@
 import axios from 'axios'
 import {computed, ref, shallowRef, watch, type ComputedRef, type Ref} from 'vue'
 
-import {
-  getVariantAnnotation,
-  getVariantDetail,
-  getHistogramVariantData,
-  lookupVariantsByClingenId
-} from '@/api/mavedb/variants'
+import {getVariantAnnotation, getVariantDetail, lookupVariantsByClingenId} from '@/api/mavedb/variants'
+import {getLeanScoreSetVariants} from '@/api/mavedb/score-sets'
 import {useCalibrationResolution, type UseCalibrationResolutionReturn} from '@/composables/use-calibration-resolution'
 import {useClingenAllele, type UseClingenAlleleReturn} from '@/composables/use-clingen-allele'
 
@@ -18,7 +14,7 @@ import {
 } from '@/lib/calibrations'
 import {triggerDownload} from '@/lib/downloads'
 import {getExperimentKeyword} from '@/lib/experiments'
-import {parseScoreSetVariantData, type Variant} from '@/lib/variants'
+import type {DisplayVariant} from '@/lib/variants'
 import type {MeasurementType} from '@/lib/measurement-types'
 import type {components} from '@/schema/openapi'
 
@@ -62,9 +58,9 @@ export interface UseVariantLookupReturn {
   // Scores
   selectedScoreSet: ComputedRef<ScoreSet | null>
   selectedScoreSetUrn: ComputedRef<string | null>
-  scores: ComputedRef<Variant[] | null>
-  variantScoreRow: ComputedRef<Variant | undefined>
-  selectedVariantScore: ComputedRef<number | string | null>
+  scores: ComputedRef<DisplayVariant[] | null>
+  variantScoreRow: ComputedRef<DisplayVariant | undefined>
+  selectedVariantScore: ComputedRef<number | null>
 
   // Calibration
   selectedCalibration: Ref<string | null>
@@ -119,7 +115,7 @@ export function useVariantLookup(
   const showProtein = ref(true)
   const showAssociatedNucleotide = ref(true)
   const variantDetailCache = ref<Record<string, VariantEffectMeasurementWithScoreSet>>({})
-  const scoresCache = shallowRef<Record<string, Variant[]>>({})
+  const scoresCache = shallowRef<Record<string, DisplayVariant[]>>({})
   const selectedCalibration = ref<string | null>(null)
 
   // ── Filters ───────────────────────────────────────────────
@@ -163,8 +159,8 @@ export function useVariantLookup(
     if (!selectedScoreSetUrn.value) return null
     return scoresCache.value[selectedScoreSetUrn.value] || null
   })
-  const variantScoreRow = computed(() => (scores.value || []).find((s) => s.accession === selectedVariantUrn.value))
-  const selectedVariantScore = computed(() => variantScoreRow.value?.scores?.score ?? null)
+  const variantScoreRow = computed(() => (scores.value || []).find((s) => s.variantUrn === selectedVariantUrn.value))
+  const selectedVariantScore = computed(() => variantScoreRow.value?.score ?? null)
 
   // ── Calibration ───────────────────────────────────────────
   const selectedCalibrationObject = computed<ScoreCalibration | null>(() => {
@@ -175,12 +171,7 @@ export function useVariantLookup(
     )
   })
 
-  const selectedVariantScoreAsNumber = computed<number | null>(() => {
-    const s = selectedVariantScore.value
-    if (s == null || s === 'NA') return null
-    const n = typeof s === 'number' ? s : Number(s)
-    return Number.isNaN(n) ? null : n
-  })
+  const selectedVariantScoreAsNumber = computed<number | null>(() => selectedVariantScore.value)
 
   const calibrationResolution = useCalibrationResolution(
     selectedCalibrationObject,
@@ -217,10 +208,10 @@ export function useVariantLookup(
   async function fetchScores(scoreSetUrn: string) {
     if (scoresCache.value[scoreSetUrn]) return
     try {
-      const data = await getHistogramVariantData(scoreSetUrn)
+      const data = await getLeanScoreSetVariants(scoreSetUrn)
       scoresCache.value = {
         ...scoresCache.value,
-        [scoreSetUrn]: parseScoreSetVariantData(data)
+        [scoreSetUrn]: data
       }
     } catch (error) {
       console.error(`Error fetching scores for score set "${scoreSetUrn}"`, error)
@@ -336,11 +327,9 @@ export function useVariantLookup(
     const cachedScores = scoresCache.value[scoreSetUrn]
     if (!cachedScores) return null
 
-    const scoreRow = cachedScores.find((s) => s.accession === variantUrn)
-    const rawScore = scoreRow?.scores?.score
-    if (rawScore == null || rawScore === 'NA') return null
-    const score = typeof rawScore === 'number' ? rawScore : Number(rawScore)
-    if (Number.isNaN(score)) return null
+    const scoreRow = cachedScores.find((s) => s.variantUrn === variantUrn)
+    const score = scoreRow?.score
+    if (score == null) return null
 
     const cal = getPrimaryCalibration(detail?.scoreSet)
     if (!cal?.functionalClassifications) return null
diff --git a/src/lib/consequences.test.ts b/src/lib/consequences.test.ts
new file mode 100644
index 00000000..6a5fd44f
--- /dev/null
+++ b/src/lib/consequences.test.ts
@@ -0,0 +1,124 @@
+import {describe, expect, it} from 'vitest'
+
+import {
+  consequenceBucket,
+  humanReadableConsequence,
+  EFFECT_BUCKETS,
+  type EffectBucketName
+} from '@/lib/consequences'
+
+// The full VEP consequence set the API can emit.
+const ALL_CONSEQUENCES = [
+  'transcript_ablation',
+  'splice_acceptor_variant',
+  'splice_donor_variant',
+  'stop_gained',
+  'frameshift_variant',
+  'stop_lost',
+  'start_lost',
+  'transcript_amplification',
+  'inframe_insertion',
+  'inframe_deletion',
+  'missense_variant',
+  'disruptive_inframe_insertion',
+  'disruptive_inframe_deletion',
+  'protein_altering_variant',
+  'splice_region_variant',
+  'incomplete_terminal_codon_variant',
+  'start_retained',
+  'stop_retained',
+  'synonymous_variant',
+  'coding_sequence_variant',
+  'mature_miRNA_variant',
+  '5_prime_UTR_premature_start_codon_gain_variant',
+  '5_prime_UTR_variant',
+  '3_prime_UTR_variant',
+  'non_coding_transcript_exon_variant',
+  'non_coding_exon_variant',
+  'non_coding_transcript_variant',
+  'nc_transcript_variant',
+  'upstream_gene_variant',
+  'downstream_gene_variant',
+  'TFBS_ablation',
+  'TFBS_amplification',
+  'TF_binding_site_variant',
+  'regulatory_region_ablation',
+  'enhancer_ablation',
+  'regulatory_region_amplification',
+  'enhancer_amplification',
+  'regulatory_region_variant',
+  'feature_elongation',
+  'regulatory_region',
+  'TFBS',
+  'feature_truncation',
+  'exon_variant',
+  'gene_variant',
+  'variant_affecting_coding_sequence_conservation',
+  'variant_affecting_genome_assembly_quality',
+  'variant_of_unknown_significance',
+  'sequence_variant',
+  'rare_amino_acid_variant',
+  'intron_variant',
+  'intergenic_variant'
+]
+
+describe('consequenceBucket', () => {
+  it('maps headline terms to their bucket', () => {
+    expect(consequenceBucket('missense_variant')).toBe('Missense')
+    expect(consequenceBucket('synonymous_variant')).toBe('Synonymous')
+    expect(consequenceBucket('stop_gained')).toBe('Nonsense')
+    expect(consequenceBucket('start_lost')).toBe('Start/Stop Loss')
+    expect(consequenceBucket('stop_lost')).toBe('Start/Stop Loss')
+    expect(consequenceBucket('frameshift_variant')).toBe('Indel/Frameshift')
+    expect(consequenceBucket('inframe_deletion')).toBe('Indel/Frameshift')
+    expect(consequenceBucket('splice_acceptor_variant')).toBe('Splice')
+  })
+
+  it('maps an unrecognized but present term to Other', () => {
+    expect(consequenceBucket('intron_variant')).toBe('Other')
+    expect(consequenceBucket('some_future_so_term')).toBe('Other')
+  })
+
+  it('maps an absent consequence to No consequence', () => {
+    expect(consequenceBucket(null)).toBe('No consequence')
+    expect(consequenceBucket(undefined)).toBe('No consequence')
+    expect(consequenceBucket('')).toBe('No consequence')
+    expect(consequenceBucket('NA')).toBe('No consequence')
+  })
+
+  it('never maps a real consequence term to No consequence, and always to a defined bucket', () => {
+    const bucketNames = new Set<EffectBucketName>(EFFECT_BUCKETS.map((b) => b.name))
+    for (const term of ALL_CONSEQUENCES) {
+      const bucket = consequenceBucket(term)
+      expect(bucket).not.toBe('No consequence')
+      expect(bucketNames.has(bucket)).toBe(true)
+    }
+  })
+
+  it('lists each SO term in at most one bucket', () => {
+    const seen = new Set<string>()
+    for (const bucket of EFFECT_BUCKETS) {
+      for (const term of bucket.soTerms) {
+        expect(seen.has(term)).toBe(false)
+        seen.add(term)
+      }
+    }
+  })
+})
+
+describe('humanReadableConsequence', () => {
+  it('uses curated labels where the raw term reads poorly', () => {
+    expect(humanReadableConsequence('stop_gained')).toBe('Nonsense (stop gained)')
+    expect(humanReadableConsequence('start_lost')).toBe('Start loss')
+  })
+
+  it('de-underscores and capitalizes the long tail, preserving embedded casing', () => {
+    expect(humanReadableConsequence('splice_acceptor_variant')).toBe('Splice acceptor variant')
+    expect(humanReadableConsequence('5_prime_UTR_variant')).toBe('5 prime UTR variant')
+  })
+
+  it('returns null for an absent consequence', () => {
+    expect(humanReadableConsequence(null)).toBeNull()
+    expect(humanReadableConsequence('NA')).toBeNull()
+  })
+})
diff --git a/src/lib/consequences.ts b/src/lib/consequences.ts
new file mode 100644
index 00000000..98bbbeab
--- /dev/null
+++ b/src/lib/consequences.ts
@@ -0,0 +1,160 @@
+/**
+ * VEP consequence taxonomy for the score-set views.
+ *
+ * The API annotates each variant with a VEP functional consequence — a free-form Sequence Ontology
+ * (SO) term (`missense_variant`, `splice_acceptor_variant`, …). This module is the single source of
+ * truth for grouping that open-ended set into a small, fixed set of display buckets (the histogram
+ * effect series) and for rendering a term human-readably (tooltips). It operates on the consequence
+ * *string*, so it has no dependency on any variant shape and stays trivially testable.
+ */
+
+export type EffectBucketName =
+  | 'Missense'
+  | 'Synonymous'
+  | 'Nonsense'
+  | 'Start/Stop Loss'
+  | 'Indel/Frameshift'
+  | 'Splice'
+  | 'Other'
+  | 'No consequence'
+
+export interface EffectBucket {
+  name: EffectBucketName
+  color: string
+  description: string
+  /** VEP SO terms mapped into this bucket. Empty for the two catch-alls (`Other`, `No consequence`). */
+  soTerms: string[]
+}
+
+/**
+ * The display buckets, in series order. Every VEP consequence resolves to exactly one:
+ * - a term listed below → that bucket,
+ * - a term present but not listed → `Other` (so new API terms never break the UI — they still render
+ *   their specific term in the tooltip),
+ * - no consequence at all (unmapped / unannotated) → `No consequence`.
+ */
+export const EFFECT_BUCKETS: EffectBucket[] = [
+  {
+    name: 'Missense',
+    color: '#ffcd3a',
+    description: 'Missense variants',
+    soTerms: ['missense_variant', 'rare_amino_acid_variant']
+  },
+  {
+    name: 'Synonymous',
+    color: '#6aa84f',
+    description: 'Synonymous variants',
+    soTerms: ['synonymous_variant', 'stop_retained', 'start_retained', 'incomplete_terminal_codon_variant']
+  },
+  {
+    name: 'Nonsense',
+    color: '#681a1a',
+    description: 'Nonsense (stop-gained) variants',
+    soTerms: ['stop_gained']
+  },
+  {
+    name: 'Start/Stop Loss',
+    color: '#cd3aff',
+    description: 'Start- and stop-loss variants',
+    soTerms: ['start_lost', 'stop_lost']
+  },
+  {
+    name: 'Indel/Frameshift',
+    color: '#ff8c00',
+    description: 'In-frame indels and frameshifts',
+    soTerms: [
+      'frameshift_variant',
+      'inframe_insertion',
+      'inframe_deletion',
+      'disruptive_inframe_insertion',
+      'disruptive_inframe_deletion',
+      'protein_altering_variant'
+    ]
+  },
+  {
+    name: 'Splice',
+    color: '#1f77b4',
+    description: 'Splice-site variants',
+    soTerms: ['splice_acceptor_variant', 'splice_donor_variant', 'splice_region_variant']
+  },
+  {
+    name: 'Other',
+    color: '#3affcd',
+    description: 'Other annotated consequences (non-coding, regulatory, …)',
+    soTerms: []
+  },
+  {
+    name: 'No consequence',
+    color: '#9e9e9e',
+    description: 'No VEP consequence (unmapped or unannotated)',
+    soTerms: []
+  }
+]
+
+const CONSEQUENCE_TO_BUCKET: Record<string, EffectBucketName> = Object.fromEntries(
+  EFFECT_BUCKETS.flatMap((bucket) => bucket.soTerms.map((term) => [term, bucket.name]))
+)
+
+/**
+ * The display bucket for a VEP consequence term. `No consequence` when the term is absent/`NA`
+ * (unmapped or unannotated); `Other` when it is present but not one of the headline categories.
+ */
+export function consequenceBucket(consequence: string | null | undefined): EffectBucketName {
+  if (!consequence || consequence === 'NA') {
+    return 'No consequence'
+  }
+  return CONSEQUENCE_TO_BUCKET[consequence] ?? 'Other'
+}
+
+// A curated label where the raw SO term reads poorly as an effect (`stop_gained` is really "nonsense").
+// The long tail falls back to the de-underscored term with a capitalised first letter.
+const CONSEQUENCE_LABELS: Record<string, string> = {
+  stop_gained: 'Nonsense (stop gained)',
+  stop_lost: 'Stop loss',
+  start_lost: 'Start loss'
+}
+
+/**
+ * A human-readable rendering of a VEP consequence term for tooltips. Known terms get a curated label;
+ * the long tail is the de-underscored term with its first letter capitalised, preserving embedded
+ * casing (`splice_acceptor_variant` → 'Splice acceptor variant', `5_prime_UTR_variant` → '5 prime UTR
+ * variant'). Returns `null` when there is no consequence.
+ */
+export function humanReadableConsequence(consequence: string | null | undefined): string | null {
+  if (!consequence || consequence === 'NA') {
+    return null
+  }
+  if (CONSEQUENCE_LABELS[consequence]) {
+    return CONSEQUENCE_LABELS[consequence]
+  }
+  const spaced = consequence.replace(/_/g, ' ').trim()
+  return spaced ? spaced.charAt(0).toUpperCase() + spaced.slice(1) : consequence
+}
+
+export interface EffectTypeFilterOption {
+  name: EffectBucketName
+  shortDescription: string
+  description: string
+}
+
+/** Filter checkbox options for the protein-effect and control panels — one per bucket, in series order. */
+export const EFFECT_TYPE_FILTER_OPTIONS: EffectTypeFilterOption[] = EFFECT_BUCKETS.map((bucket) => ({
+  name: bucket.name,
+  shortDescription: bucket.name,
+  description: bucket.description
+}))
+
+/**
+ * Buckets selected by default. Covers every annotated coding/other category so control variants of any
+ * kind still show without opt-in (as they did when `Other` was a catch-all). Excludes `Start/Stop Loss`
+ * (added conditionally by callers that hide it for synthetic targets) and `No consequence` (the
+ * unannotated pile is opt-in).
+ */
+export const DEFAULT_EFFECT_TYPE_FILTERS: EffectBucketName[] = [
+  'Missense',
+  'Synonymous',
+  'Nonsense',
+  'Indel/Frameshift',
+  'Splice',
+  'Other'
+]
diff --git a/src/lib/heatmap.ts b/src/lib/heatmap.ts
index 5d6addc0..33c26262 100644
--- a/src/lib/heatmap.ts
+++ b/src/lib/heatmap.ts
@@ -717,12 +717,34 @@ export default function makeHeatmap(): Heatmap {
     }
   }
 
+  // Position the hover tooltip near the pointer, flipping left/up when it would spill past the viewport
+  // edge. Without this a tall tooltip on a thin (DNA) heatmap runs off the bottom of the screen.
+  const positionHoverTooltip = (event: MouseEvent) => {
+    if (!hoverTooltip) {
+      return
+    }
+    const node = hoverTooltip.node() as HTMLElement | null
+    const [pageX, pageY] = d3.pointer(event, document.body)
+    const width = node?.offsetWidth ?? 0
+    const height = node?.offsetHeight ?? 0
+    const margin = 8
+    const viewportRight = window.scrollX + document.documentElement.clientWidth
+    const viewportBottom = window.scrollY + document.documentElement.clientHeight
+
+    let left = pageX + 30
+    if (left + width > viewportRight - margin) {
+      left = pageX - 30 - width
+    }
+    let top = pageY
+    if (top + height > viewportBottom - margin) {
+      top = Math.max(window.scrollY + margin, pageY - height)
+    }
+    hoverTooltip.style('left', left + 'px').style('top', top + 'px')
+  }
+
   const mousemove = (event: MouseEvent, d: HeatmapDatum) => {
     if (!selectionStartDatum && hoverTooltip) {
-      // Move tooltip to be 30px to the right of the pointer.
-      hoverTooltip
-        .style('left', d3.pointer(event, document.body)[0] + 30 + 'px')
-        .style('top', d3.pointer(event, document.body)[1] + 'px')
+      positionHoverTooltip(event)
     }
   }
 
@@ -751,9 +773,7 @@ export default function makeHeatmap(): Heatmap {
 
     if (hoverTooltip && target instanceof Element) {
       showTickLabelTooltip(hoverTooltip, rowNumber)
-      hoverTooltip
-        .style('left', d3.pointer(event, document.body)[0] + 30 + 'px')
-        .style('top', d3.pointer(event, document.body)[1] + 'px')
+      positionHoverTooltip(event)
     }
   }
 
diff --git a/src/lib/mave-hgvs.test.ts b/src/lib/mave-hgvs.test.ts
new file mode 100644
index 00000000..f5e58d9f
--- /dev/null
+++ b/src/lib/mave-hgvs.test.ts
@@ -0,0 +1,25 @@
+import {describe, expect, it} from 'vitest'
+
+import {isNucleotideHgvs} from '@/lib/mave-hgvs'
+
+describe('isNucleotideHgvs', () => {
+  it('recognizes nucleotide-level prefixes, with or without an accession', () => {
+    expect(isNucleotideHgvs('NM_003345.4:c.324T>G')).toBe(true)
+    expect(isNucleotideHgvs('c.6C>T')).toBe(true)
+    expect(isNucleotideHgvs('g.123A>G')).toBe(true)
+    expect(isNucleotideHgvs('n.76A>C')).toBe(true)
+    expect(isNucleotideHgvs('m.8993T>G')).toBe(true)
+  })
+
+  it('rejects protein-level expressions', () => {
+    expect(isNucleotideHgvs('NP_000528.2:p.Leu6Gly')).toBe(false)
+    expect(isNucleotideHgvs('p.(Leu6Gly)')).toBe(false)
+  })
+
+  it('rejects empty / untyped input', () => {
+    expect(isNucleotideHgvs(null)).toBe(false)
+    expect(isNucleotideHgvs(undefined)).toBe(false)
+    expect(isNucleotideHgvs('')).toBe(false)
+    expect(isNucleotideHgvs('NA')).toBe(false)
+  })
+})
diff --git a/src/lib/mave-hgvs.ts b/src/lib/mave-hgvs.ts
index 8fb4c766..21122547 100644
--- a/src/lib/mave-hgvs.ts
+++ b/src/lib/mave-hgvs.ts
@@ -116,6 +116,24 @@ export function variantNotNullOrNA(variant: string | null | undefined): boolean
   return variant ? variant.toLowerCase() !== 'na' : false
 }
 
+/**
+ * Extract the HGVS "type" prefix — the single letter before the dot in an HGVS expression
+ * (e.g. `c` in `NM_003345.4:c.324T>G`, `p` in `NP_000528.2:p.Leu6Gly`). The prefix may sit
+ * at the start of the string or after an accession/colon. Returns the lowercased letter, or
+ * null if the string is empty or not recognizably typed.
+ */
+function hgvsTypePrefix(hgvs: string | null | undefined): string | null {
+  if (!hgvs) return null
+  const match = hgvs.match(/(?:^|:)\s*([cgmnrp])\./i)
+  return match ? match[1].toLowerCase() : null
+}
+
+/** Whether an HGVS expression is nucleotide-level (c./g./n./m./r.) rather than protein (p.). */
+export function isNucleotideHgvs(hgvs: string | null | undefined): boolean {
+  const prefix = hgvsTypePrefix(hgvs)
+  return prefix != null && prefix !== 'p'
+}
+
 /**
  * Return the preferred variant label for a given variant. Protein variation is preferred
  * to nucleotide variation, which is preferred to splice variation.
diff --git a/src/lib/tooltips.ts b/src/lib/tooltips.ts
new file mode 100644
index 00000000..255a3c3a
--- /dev/null
+++ b/src/lib/tooltips.ts
@@ -0,0 +1,97 @@
+// Shared builders for the d3-injected chart tooltips (histogram + heatmap).
+//
+// These tooltips are appended to document.body and rendered via d3 `.html()`, so they live
+// outside the Vue component tree: styling uses global Tailwind utilities (no scoped CSS would
+// reach them), and only data-driven colors are inline. Keep class strings literal so Tailwind's
+// scanner picks them up.
+
+/** Wrap composed sections in the tooltip root, or return null when there is nothing to show. */
+export function tooltipRoot(sections: (string | null | undefined)[]): string | null {
+  const html = sections.filter(Boolean).join('')
+  return html ? `<div class="text-xs leading-snug max-w-[320px]">${html}</div>` : null
+}
+
+// A tooltip section. Sections after the first are separated by a divider. Returns empty when it has no
+// content, so callers can compose optional sections without leaving stray dividers behind.
+export function tooltipSection(rows: (string | null | undefined)[]): string {
+  const body = rows.filter(Boolean).join('')
+  if (!body) {
+    return ''
+  }
+  return `<div class="mt-1.5 pt-1.5 border-t border-black/10 first:mt-0 first:pt-0 first:border-t-0">${body}</div>`
+}
+
+/** A small, muted, uppercase section heading (e.g. "ClinVar", "Bin 1 to 1.05"). */
+export function tooltipSectionLabel(text: string): string {
+  return `<div class="uppercase text-[10px] tracking-[0.04em] opacity-[.55] mb-0.5">${text}</div>`
+}
+
+export function tooltipTitle(text: string): string {
+  return `<div class="font-semibold">${text}</div>`
+}
+
+export function tooltipConsequence(text: string): string {
+  return `<div class="italic opacity-[.85]">${text}</div>`
+}
+
+/** A muted, italicized aside (e.g. "Could not be mapped"). */
+export function tooltipNote(text: string): string {
+  return `<div class="italic opacity-[.75]">${text}</div>`
+}
+
+export function tooltipText(text: string): string {
+  return `<div>${text}</div>`
+}
+
+export function tooltipKeyValue(label: string, value: string | number | null | undefined): string {
+  return `<div><span class="opacity-60">${label}:</span> ${value ?? ''}</div>`
+}
+
+export function tooltipLink(href: string, text: string): string {
+  return `<a href="${href}" target="_blank" class="text-link block mt-0.5">${text}</a>`
+}
+
+/** ClinGen variant-details link — shared by both charts. */
+export function tooltipVariantDetailsLink(clingenAlleleId: string): string {
+  return tooltipLink(`/variants/${clingenAlleleId}`, 'View variant details')
+}
+
+/** A round color swatch, used to tie series/legend colors to their labels. */
+export function tooltipSwatch(color: string): string {
+  return `<span class="inline-block h-3 w-3 mr-1.5 rounded-full shrink-0" style="background-color: ${color}"></span>`
+}
+
+/** A colored, titled classification/shader badge. */
+export function tooltipBadge(color: string, text: string): string {
+  return `<span class="inline-block px-1 py-0.5 rounded text-[11px] font-bold text-white" style="background-color: ${color}">${text}</span>`
+}
+
+/** A badge on its own line, spaced from the line above (e.g. a classification under a score). */
+export function tooltipBadgeBlock(color: string, text: string): string {
+  return `<div class="mt-1">${tooltipBadge(color, text)}</div>`
+}
+
+/** A wrapping row of badges. */
+export function tooltipBadgeRow(badges: string[]): string {
+  return `<div class="flex flex-wrap gap-1 mb-1">${badges.join('')}</div>`
+}
+
+/** A `swatch · label · count` row. `active` bolds it (e.g. the hovered variant's series). */
+export function tooltipCountRow(options: {color: string; label: string; count: number; active?: boolean}): string {
+  const {color, label, count, active = false} = options
+  return (
+    `<div class="flex items-center${active ? ' font-semibold' : ''}">` +
+    tooltipSwatch(color) +
+    `<span class="flex-auto">${label ? label : '<i>No series label</i>'}</span>` +
+    `<span class="ml-4 tabular-nums">${count}</span>` +
+    '</div>'
+  )
+}
+
+/** Four-star review rating, ClinVar-style (filled stars first). */
+export function tooltipReviewStars(numStars: number): string {
+  const filled = '<span class="mx-px text-[#fdb81e]">★</span>'
+  const empty = '<span class="mx-px">☆</span>'
+  const stars = new Array(4).fill(filled).fill(empty, numStars)
+  return `(${stars.join('')})`
+}
diff --git a/src/lib/variants.ts b/src/lib/variants.ts
index 7432d5e8..8e1c1ac3 100644
--- a/src/lib/variants.ts
+++ b/src/lib/variants.ts
@@ -1,6 +1,6 @@
 import _ from 'lodash'
 
-import {AMINO_ACIDS, AMINO_ACIDS_WITH_TER, singleLetterAminoAcidOrHgvsCode} from '@/lib/amino-acids'
+import {AMINO_ACIDS_WITH_TER, singleLetterAminoAcidOrHgvsCode} from '@/lib/amino-acids'
 import {DEFAULT_CLNREVSTAT_FIELD, DEFAULT_CLNSIG_FIELD} from '@/lib/clinical-controls'
 import geneticCodes from '@/lib/genetic-codes'
 import {parseSimpleNtVariant, parseSimpleProVariant} from '@/lib/mave-hgvs'
@@ -16,6 +16,15 @@ import type {SimpleDnaVariation, SimpleProteinVariation} from '@/lib/mave-hgvs'
 export type HgvsField = components['schemas']['HgvsField']
 export type LeanVariant = components['schemas']['LeanVariant']
 
+/**
+ * A lean variant as displayed on the score-set page, with the one client-side augmentation the views
+ * add on top of the API record: `control` (clinical-control data merged in by variant URN). Score-set
+ * visualizations and search consume this shape.
+ */
+export type DisplayVariant = LeanVariant & {
+  control?: ClinicalControlVariant | null
+}
+
 export type HgvsReferenceSequenceType = 'c' | 'p' // | 'n'
 
 export interface SequenceRange {
@@ -26,6 +35,7 @@ export interface SequenceRange {
 export interface ClinicalControlVariant {
   [DEFAULT_CLNSIG_FIELD]: string
   [DEFAULT_CLNREVSTAT_FIELD]: string
+  dbIdentifier?: string
 }
 
 type ParsedSimpleDnaVariation = SimpleDnaVariation & {
@@ -94,36 +104,6 @@ export interface ParsedPostMappedVariantProperties {
   [type: string]: keyof VariantPropertiesAddedByPreparingCodingVariants
 }
 
-export const VARIANT_EFFECT_TYPE_OPTIONS = [
-  {
-    name: 'Synonymous',
-    description: 'Show all synonymous variants',
-    shortDescription: 'Synonymous variants'
-  },
-  {
-    name: 'Missense',
-    description: 'Show all missense variants',
-    shortDescription: 'Missense variants'
-  },
-  {
-    name: 'Nonsense',
-    description: 'Show all nonsense variants',
-    shortDescription: 'Nonsense variants'
-  },
-  {
-    name: 'Start/Stop Loss',
-    description: 'Show all start/stop loss variants',
-    shortDescription: 'Start/Stop Loss variants'
-  },
-  {
-    name: 'Other',
-    description: 'Show all other variant types',
-    shortDescription: 'Others'
-  }
-]
-
-export const DEFAULT_VARIANT_EFFECT_TYPES = ['Missense', 'Nonsense', 'Synonymous', 'Other']
-
 export function parseScoreSetVariantData(csvData: string): Variant[] {
   const variants = parseScoresOrCounts(csvData, true) as Variant[]
   prepareScoreSetVariantData(variants)
@@ -308,6 +288,41 @@ export function inferReferenceSequenceFromVariants(variants: Variant[], referenc
   }
 }
 
+/**
+ * Infer a wild-type reference sequence from lean variant records, in whatever coordinate frame the
+ * caller's block accessor resolves. `getBlock` returns the HGVS block (with `position`/`ref`) for a
+ * variant in the desired (level, frame); the reference residue at each position is taken from the
+ * first block that covers it. Positions with no covering variant are filled with the unknown residue
+ * (`X` for protein, `N` for nucleotide). This is the Option A analogue of
+ * `inferReferenceSequenceFromVariants` — it works off the resolved blocks, so it reprojects with the
+ * frame instead of assuming the post-mapped parse.
+ */
+export function inferReferenceSequenceFromBlocks(
+  variants: DisplayVariant[],
+  getBlock: (variant: DisplayVariant) => HgvsField | null,
+  residueType: 'nt' | 'aa'
+): {referenceSequence: string; referenceSequenceRange: SequenceRange} {
+  const blocks = variants.map(getBlock).filter((block): block is HgvsField => block != null && block.position != null)
+  if (blocks.length == 0) {
+    return {referenceSequence: '', referenceSequenceRange: {start: 0, length: 0}}
+  }
+  const start = _.min(blocks.map((block) => block.position!))!
+  const end = _.max(blocks.map((block) => block.position!))!
+  const length = end - start + 1
+  const unknownResidue = residueType == 'aa' ? 'X' : 'N'
+  const referenceSequenceArr = Array(length).fill(unknownResidue)
+  for (const block of blocks) {
+    const index = block.position! - start
+    if (referenceSequenceArr[index] == unknownResidue && block.ref != null) {
+      const oneChar = residueType == 'aa' ? singleLetterAminoAcidOrHgvsCode(block.ref) : block.ref
+      if (oneChar != null) {
+        referenceSequenceArr[index] = oneChar
+      }
+    }
+  }
+  return {referenceSequence: referenceSequenceArr.join(''), referenceSequenceRange: {start, length}}
+}
+
 /**
  * Translate simple coding variants, adding an translated_hgvs_p column and setting parsedPostMappedHgvsP.
  *
@@ -403,25 +418,34 @@ function translateSimpleCodingHgvsCVariant(
   return `p.${originalAaTriple}${aaPosition}${variantAaTriple}`
 }
 
+/**
+ * The protein-level HGVS block used to classify a variant's consequence when a VEP consequence is
+ * absent: the mapped protein representation preferred, falling back to the submitted protein HGVS.
+ */
+function proteinConsequenceBlock(variant: DisplayVariant): HgvsField | null {
+  return variant.proteinLevelHgvs ?? variant.hgvsPro ?? null
+}
+
 /**
  * Determines whether a given variant represents either a start-loss (loss of the initiator methionine)
  * or a stop-loss (loss of a terminal stop/termination signal) event based on its protein-level HGVS notation.
  *
  * Detection logic:
- * 1. Selects the first available, non-null / non-"NA" protein HGVS string from:
+ * 1. If the variant has a VEP consequence, it is used directly to determine start-loss or stop-loss.
+ * 2. If no VEP consequence is available, the function attempts to extract a protein-level HGVS block from the variant.
+ * 3. Selects the first available, non-null / non-"NA" protein HGVS string from:
  *    - variant.post_mapped_hgvs_p
  *    - variant.hgvs_pro_inferred
  *    - variant.hgvs_pro
- * 2. Parses the HGVS protein string via parseSimpleProVariant (external utility).
- * 3. Returns:
+ * 4. Parses the HGVS protein string via parseSimpleProVariant (external utility).
+ * 5. Returns:
  *    - true if the variant alters the initiator methionine at position 1 (original == 'Met') to a different residue.
  *    - true if the variant alters a termination symbol at position 1 (original == 'Ter' or '*') to a non-stop residue.
- * 4. Returns false if no suitable HGVS string is found, parsing fails, or the criteria above are not met.
+ * 6. Returns false if no suitable HGVS string is found, parsing fails, or the criteria above are not met.
  *
  * Notes:
  * - The function currently infers start-loss strictly when position == 1 and original is 'Met'.
  *
- *
  * Parameter requirements:
  * - variant should be an object containing at least one of the HGVS protein fields listed above.
  * - External helpers required: variantNotNullOrNA, parseSimpleProVariant.
@@ -429,30 +453,19 @@ function translateSimpleCodingHgvsCVariant(
  * @param variant Arbitrary variant-like object holding HGVS protein annotations.
  * @returns true if the variant is classified as start-loss or stop-loss; false (or undefined) otherwise.
  */
-export function isStartOrStopLoss(variant: any) {
-  if (variant.vep && variant.vep.vep_functional_consequence && variant.vep.vep_functional_consequence != 'NA') {
-    if (
-      variant.vep.vep_functional_consequence == 'start_lost' ||
-      variant.vep.vep_functional_consequence == 'stop_lost'
-    ) {
-      return true
-    } else {
-      return false
-    }
+export function isStartOrStopLoss(variant: DisplayVariant): boolean {
+  if (variant.consequence && variant.consequence != 'NA') {
+    return variant.consequence == 'start_lost' || variant.consequence == 'stop_lost'
   }
-  const parsedVariant = variant.parsedPostMappedHgvsP
-  if (!parsedVariant) {
+  const block = proteinConsequenceBlock(variant)
+  if (!block || block.ref == null || block.alt == null) {
     return false
   }
-  if (parsedVariant.position == 1 && parsedVariant.original == 'Met' && parsedVariant.substitution != 'Met') {
+  if (block.position == 1 && block.ref == 'Met' && block.alt != 'Met') {
     // Start loss
     return true
   }
-  if (
-    (parsedVariant.original == 'Ter' || parsedVariant.original == '*') &&
-    parsedVariant.substitution != 'Ter' &&
-    parsedVariant.substitution != '*'
-  ) {
+  if ((block.ref == 'Ter' || block.ref == '*') && block.alt != 'Ter' && block.alt != '*') {
     // Stop loss
     return true
   }
@@ -460,85 +473,7 @@ export function isStartOrStopLoss(variant: any) {
   return false
 }
 
-export function variantIsMissense(variant: Variant) {
-  if (variant.vep && variant.vep.vep_functional_consequence && variant.vep.vep_functional_consequence != 'NA') {
-    if (variant.vep.vep_functional_consequence == 'missense_variant') {
-      return true
-    } else {
-      return false
-    }
-  }
-  const parsedVariant = variant.parsedPostMappedHgvsP
-  if (!parsedVariant) {
-    return false
-  }
-  const refAllele = parsedVariant.original.toUpperCase()
-  const altAllele = parsedVariant.substitution.toUpperCase()
-  const refAlleleIsAA = AMINO_ACIDS.find((aa) => aa.codes.triple == refAllele)
-  const altAlleleIsAA = AMINO_ACIDS.find((aa) => aa.codes.triple == altAllele)
-  const startLoss = parsedVariant.position == 1 && refAllele == 'MET'
-  return !!(refAlleleIsAA && altAlleleIsAA && !startLoss && refAllele != altAllele)
-}
-
-export function variantIsSynonymous(variant: Variant) {
-  if (variant.vep && variant.vep.vep_functional_consequence && variant.vep.vep_functional_consequence != 'NA') {
-    if (variant.vep.vep_functional_consequence == 'synonymous_variant') {
-      return true
-    } else {
-      return false
-    }
-  }
-  const parsedVariant = variant.parsedPostMappedHgvsP
-  if (!parsedVariant) {
-    return false
-  }
-  const refAllele = parsedVariant.original.toUpperCase()
-  const altAllele = parsedVariant.substitution.toUpperCase()
-  const refAlleleIsAA = AMINO_ACIDS.find((aa) => aa.codes.triple == refAllele)
-  return !!(refAlleleIsAA && (refAllele == altAllele || altAllele == '='))
-}
-
-export function variantIsNonsense(variant: Variant) {
-  if (variant.vep && variant.vep.vep_functional_consequence && variant.vep.vep_functional_consequence != 'NA') {
-    if (variant.vep.vep_functional_consequence == 'stop_gained') {
-      return true
-    } else {
-      return false
-    }
-  }
-  const parsedVariant = variant.parsedPostMappedHgvsP
-  if (!parsedVariant) {
-    return false
-  }
-  const altAllele = parsedVariant.substitution.toUpperCase()
-  return altAllele == 'TER' || altAllele == '*'
-}
-
-export function variantIsOther(variant: Variant) {
-  return (
-    !variantIsMissense(variant) &&
-    !variantIsSynonymous(variant) &&
-    !variantIsNonsense(variant) &&
-    !isStartOrStopLoss(variant)
-  )
-}
-
-/**
- * Check that this application is able to determine the protein consequence of every variant.
- *
- * This means that every variant either has a parseable protein HGVS string or is known to be non-coding.
- *
- * Here we distinguish known a non-coding variant by the facts that (a) it has a parsed HGVS c. string and (b) the
- * position in this string is not an integer.
- *
- * @param variants A list of variants.
- * @returns True if every variant has a protein consequence determinable by this application.
- */
-export function allCodingVariantsHaveProteinConsequence(variants: Variant[]) {
-  return variants.every(
-    (v) =>
-      (v.vep && v.vep.vep_functional_consequence && v.vep.vep_functional_consequence != 'NA') ||
-      v.parsedPostMappedHgvsP != null ||
-      (v.parsedPostMappedHgvsC?.referenceType == 'c' && v.parsedPostMappedHgvsC?.position == null)
-  )
-}
+// Protein-effect classification by VEP consequence now lives in `lib/consequences.ts`
+// (`consequenceBucket`). `isStartOrStopLoss` above is intentionally block-aware and stays here: it is
+// the heatmap's plotted-representation filter (hiding start/stop-loss cells on synthetic targets),
+// where VEP may be absent and the amino-acid change being drawn is the right signal.

From f7447f5f5364acafe775a9d917fa5d66825f43fc Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Tue, 7 Jul 2026 11:56:36 -0700
Subject: [PATCH 03/84] feat(variant): detail panel and ClinVar-version display
 on the new API

Consume the reworked GET /variants/{urn} envelope: a self-contained
VariantDetailPanel (assay-level facts, primary classification, gnomAD/ClinVar,
supersession badge, link to the variant page) wired into ScoreSetView on the
?variant= selection, plus use-variant-lookup / VariantScreen / the legacy
measurement-URN redirect repointed off the deleted VariantEffectMeasurementWithScoreSet
onto the flat envelope fields (clingenAlleleId bridge, separately fetched score set).

Clinical controls: drop the hard-coded DEFAULT_CLINICAL_CONTROL_VERSION, accept a
nullable version end to end, and render human-readable ClinVar versions
(formatClinvarVersion) in the heatmap/histogram clinical mode. openapi.d.ts
regenerated for the new API shapes.
---
 src/api/mavedb/variants.ts                    |   4 +-
 src/components/score-set/ScoreSetHeatmap.vue  |  23 +-
 .../score-set/ScoreSetHistogram.vue           |  49 ++-
 src/components/screens/ScoreSetView.vue       | 186 ++++++-----
 src/components/screens/VariantScreen.vue      |  27 +-
 src/components/variant/VariantDetailPanel.vue | 288 ++++++++++++++++++
 src/composables/use-variant-lookup.ts         |  70 +++--
 src/lib/clinical-controls.ts                  |  15 +-
 src/lib/formats.ts                            |   7 +
 src/router/index.ts                           |   7 +-
 src/schema/openapi.d.ts                       | 205 ++++++++++---
 11 files changed, 674 insertions(+), 207 deletions(-)
 create mode 100644 src/components/variant/VariantDetailPanel.vue

diff --git a/src/api/mavedb/variants.ts b/src/api/mavedb/variants.ts
index f0db95a4..1ecc9910 100644
--- a/src/api/mavedb/variants.ts
+++ b/src/api/mavedb/variants.ts
@@ -5,7 +5,7 @@ import {histogramScoreSetVariantDataUrl} from '@/api/mavedb/score-sets'
 import {components} from '@/schema/openapi'
 
 type ScoreSet = components['schemas']['ScoreSet']
-type VariantEffectMeasurementWithScoreSet = components['schemas']['VariantEffectMeasurementWithScoreSet']
+type VariantDetail = components['schemas']['VariantDetail']
 type ClingenAlleleIdVariantLookupResponse = components['schemas']['ClingenAlleleIdVariantLookupResponse']
 type MappedVariant = components['schemas']['MappedVariant']
 
@@ -25,7 +25,7 @@ export async function lookupVariantsByVrsDigest(identifier: string): Promise<Map
   return response.data
 }
 
-export async function getVariantDetail(urn: string): Promise<VariantEffectMeasurementWithScoreSet> {
+export async function getVariantDetail(urn: string): Promise<VariantDetail> {
   const response = await axios.get(`${config.apiBaseUrl}/variants/${encodeURIComponent(urn)}`)
   return response.data
 }
diff --git a/src/components/score-set/ScoreSetHeatmap.vue b/src/components/score-set/ScoreSetHeatmap.vue
index 34f4aadc..a083f9ff 100644
--- a/src/components/score-set/ScoreSetHeatmap.vue
+++ b/src/components/score-set/ScoreSetHeatmap.vue
@@ -72,6 +72,7 @@ import type {Heatmap, HeatmapDatum, HeatmapRowSpecification} from '@/lib/heatmap
 import {NUCLEOTIDE_BASES} from '@/lib/nucleotides'
 import {
   tooltipKeyValue,
+  tooltipNote,
   tooltipRoot,
   tooltipSection,
   tooltipTitle,
@@ -1044,23 +1045,25 @@ export default defineComponent({
 
     tooltipHtmlGetter: function (v: VariantClassHeatmapDatum) {
       // Identity: WT flag plus the variant's identifiers, resolved in the current coordinate frame.
+      // Prefers the HGVS in the coordinate frame of the current heatmap display, with HGVS in the
+      // non-displayed frame displayed as the secondary HGVS label when they differ.
       const identity = []
       if (v.wt) {
         identity.push(tooltipTitle('Wild-type'))
       }
       const instance = v.instance
       if (instance) {
-        const protein = this.getHgvsPro(instance, this.coordinates)
-        const nucleotide = this.getHgvsNt(instance, this.coordinates)
-        const splice = instance.hgvsSplice?.hgvs
-        if (protein) {
-          identity.push(tooltipKeyValue('Protein variant', protein))
+        const ntHgvs = this.getHgvsNt(instance, this.coordinates)
+        const primaryLabel =
+          this.sequenceType === 'dna'
+            ? (ntHgvs ?? this.labelForVariant(instance, this.coordinates))
+            : this.labelForVariant(instance, this.coordinates)
+        if (primaryLabel) {
+          identity.push(tooltipTitle(primaryLabel))
         }
-        if (nucleotide) {
-          identity.push(tooltipKeyValue('NT variant', nucleotide))
-        }
-        if (!protein && !nucleotide && splice) {
-          identity.push(tooltipKeyValue('Splice variant', splice))
+        const underlyingLabel = this.sequenceType === 'dna' ? this.getHgvsPro(instance, this.coordinates) : ntHgvs
+        if (underlyingLabel && underlyingLabel !== primaryLabel) {
+          identity.push(tooltipNote(underlyingLabel))
         }
       }
       if (instance?.clingenAlleleId) {
diff --git a/src/components/score-set/ScoreSetHistogram.vue b/src/components/score-set/ScoreSetHistogram.vue
index 4558d1ab..d4dcae31 100644
--- a/src/components/score-set/ScoreSetHistogram.vue
+++ b/src/components/score-set/ScoreSetHistogram.vue
@@ -194,7 +194,6 @@ import {
   DEFAULT_CLNREVSTAT_FIELD,
   DEFAULT_CLNSIG_FIELD,
   DEFAULT_CLINICAL_CONTROL_DB,
-  DEFAULT_CLINICAL_CONTROL_VERSION,
   DEFAULT_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS,
   DEFAULT_MIN_STAR_RATING,
   PATHOGENIC_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS,
@@ -222,7 +221,6 @@ import {
 import type {FunctionalClassificationVariant} from '@/lib/calibrations'
 import {
   tooltipBadgeBlock,
-  tooltipConsequence,
   tooltipCountRow,
   tooltipKeyValue,
   tooltipLink,
@@ -238,7 +236,6 @@ import {
 import {DisplayVariant} from '@/lib/variants'
 import {
   consequenceBucket,
-  humanReadableConsequence,
   EFFECT_BUCKETS,
   EFFECT_TYPE_FILTER_OPTIONS,
   DEFAULT_EFFECT_TYPE_FILTERS,
@@ -349,9 +346,7 @@ export default defineComponent({
       controlDb: null as ClinicalControlOption | null,
       controlVersion: null as string | null,
 
-      clinicalSignificanceClassificationOptions: clinvarClinicalSignificanceClassifications(
-        DEFAULT_CLINICAL_CONTROL_VERSION
-      ),
+      clinicalSignificanceClassificationOptions: clinvarClinicalSignificanceClassifications(null),
       variantTypeOptions: EFFECT_TYPE_FILTER_OPTIONS,
       customMinStarRating: DEFAULT_MIN_STAR_RATING,
       customSelectedClinicalSignificanceClassifications: DEFAULT_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS,
@@ -540,9 +535,7 @@ export default defineComponent({
                 this.filterControlVariantByEffect(d),
               options: {
                 color: '#984ea3',
-                title: conflictingClinicalSignificanceSeriesLabelForVersion(
-                  this.controlVersion ? this.controlVersion : DEFAULT_CLINICAL_CONTROL_VERSION
-                )
+                title: conflictingClinicalSignificanceSeriesLabelForVersion(this.controlVersion)
               }
             })
           }
@@ -794,9 +787,7 @@ export default defineComponent({
         this.customSelectedClinicalSignificanceClassifications =
           this.customSelectedClinicalSignificanceClassifications.map((classification) => {
             if (CONFLICTING_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS.includes(classification)) {
-              return clinvarConflictingSignificanceClassificationForVersion(
-                this.controlVersion ? this.controlVersion : DEFAULT_CLINICAL_CONTROL_VERSION
-              ).name
+              return clinvarConflictingSignificanceClassificationForVersion(this.controlVersion).name
             }
             return classification
           })
@@ -826,10 +817,7 @@ export default defineComponent({
           this.controlDb = defaultControlDb ? defaultControlDb : this.clinicalControlOptions[0]
         }
         if (!this.controlVersion) {
-          const defaultControlVersion = this.controlDb?.availableVersions.find(
-            (version) => version == DEFAULT_CLINICAL_CONTROL_VERSION
-          )
-          this.controlVersion = defaultControlVersion ? defaultControlVersion : this.controlDb?.availableVersions[0]
+          this.controlVersion = this.controlDb?.availableVersions[0]
         }
         const cache: Record<string, Record<string, ClinicalControl[]>> = {}
         for (const dbOption of this.clinicalControlOptions) {
@@ -843,9 +831,7 @@ export default defineComponent({
     },
     controlDbAndVersion: {
       handler: function () {
-        this.clinicalSignificanceClassificationOptions = clinvarClinicalSignificanceClassifications(
-          this.controlVersion ? this.controlVersion : DEFAULT_CLINICAL_CONTROL_VERSION
-        )
+        this.clinicalSignificanceClassificationOptions = clinvarClinicalSignificanceClassifications(this.controlVersion)
         this.loadClinicalControls()
       }
     },
@@ -911,17 +897,16 @@ export default defineComponent({
       if (label) {
         identity.push(tooltipTitle(label))
       }
+      const underlyingNt = this.getHgvsNt(variant, this.coordinates)
+      if (underlyingNt && underlyingNt !== label) {
+        identity.push(tooltipNote(underlyingNt))
+      }
       // In the mapped frame an unmapped variant's label is its submitted (target-frame) HGVS; flag it so
       // the string isn't mistaken for a mapped coordinate.
       if (this.coordinates == 'mapped' && this.isUnmapped(variant)) {
         identity.push(tooltipNote('Could not be mapped'))
       }
 
-      const consequence = humanReadableConsequence(variant.consequence)
-      if (consequence) {
-        identity.push(tooltipConsequence(consequence))
-      }
-
       if (variant.score != null) {
         identity.push(tooltipText(`Score ${variant.score.toPrecision(4)}`))
         const classification = this.matchVariantClassification(variant)
@@ -934,7 +919,16 @@ export default defineComponent({
         identity.push(tooltipVariantDetailsLink(variant.clingenAlleleId))
       }
 
-      return [tooltipSection(identity), this.tooltipClinvarSection(variant)].filter(Boolean).join('')
+      const sections = [tooltipSection(identity)]
+
+      if (this.vizOptions[this.activeViz].view == 'clinical') {
+        const clinvarSection = this.tooltipClinvarSection(variant)
+        if (clinvarSection) {
+          sections.push(clinvarSection)
+        }
+      }
+
+      return sections.filter(Boolean).join('')
     },
 
     /** ClinVar significance, review stars, and link — or null when the variant has no ClinVar annotation. */
@@ -952,9 +946,8 @@ export default defineComponent({
       }
 
       const description =
-        clinvarClinicalSignificanceClassifications(this.controlVersion || DEFAULT_CLINICAL_CONTROL_VERSION).find(
-          (c) => c.name == significance
-        )?.description ?? significance
+        clinvarClinicalSignificanceClassifications(this.controlVersion).find((c) => c.name == significance)
+          ?.description ?? significance
       const numStars = hasReviewStatus ? CLINVAR_REVIEW_STATUS_STARS[reviewStatus] : null
       const stars = numStars != null ? ` ${tooltipReviewStars(numStars)}` : ''
 
diff --git a/src/components/screens/ScoreSetView.vue b/src/components/screens/ScoreSetView.vue
index 35f0de51..2b47f6eb 100644
--- a/src/components/screens/ScoreSetView.vue
+++ b/src/components/screens/ScoreSetView.vue
@@ -65,89 +65,106 @@
       />
 
       <div class="mx-auto w-full px-4 py-6 tablet:px-6 tablet:py-8" style="max-width: 1000px">
-        <!-- Variant search + clinical toggle -->
+        <!-- Variant search + selected-variant detail — one unit -->
         <div
           v-if="variants?.length"
-          class="mb-4 flex flex-col gap-3 rounded-lg border border-border bg-white px-4 py-3 tablet:flex-row tablet:items-center"
+          class="mave-gradient-bar relative mb-4 overflow-hidden rounded-lg border border-border bg-surface"
         >
-          <div class="relative min-w-0 flex-1">
-            <MvFloatField label="Search variants">
-              <template #default="{id}">
-                <AutoComplete
-                  :id="id"
-                  v-model="selectedVariant"
-                  class="w-full"
-                  :delay="300"
-                  dropdown
-                  fluid
-                  :input-style="variantToVisualize ? {paddingRight: '2.25rem'} : undefined"
-                  :option-label="variantOptionLabel"
-                  scroll-height="175px"
-                  select-on-focus
-                  :suggestions="variantSearchSuggestions"
-                  :virtual-scroller-options="{itemSize: 50}"
-                  @complete="variantSearch"
-                >
-                  <template #option="{option}">
-                    <div class="flex flex-col justify-center leading-tight">
-                      <span>{{ variantOptionLabel(option) }}</span>
-                      <span v-if="frame === 'mapped' && isUnmapped(option)" class="text-xs italic text-text-muted">
-                        Variant could not be mapped
-                      </span>
-                    </div>
-                  </template>
-                  <template #empty>
-                    <div class="p-2.5 text-center text-sm text-text-muted">No matching variants found.</div>
-                  </template>
-                </AutoComplete>
-              </template>
-            </MvFloatField>
-            <button
-              v-if="variantToVisualize"
-              aria-label="Clear"
-              class="absolute right-12 top-1/2 flex size-5 -translate-y-1/2 cursor-pointer items-center justify-center rounded-full text-text-muted hover:bg-red-50 hover:text-red-600"
-              @click="selectedVariant = null"
-            >
-              <i class="pi pi-times text-[10px]" />
-            </button>
-          </div>
-          <div class="flex items-center gap-2 text-sm text-text-secondary tablet:ml-auto">
-            <span
-              :class="[
-                clinicalMode ? 'text-text-muted' : 'font-semibold text-sage',
-                {'opacity-50': coordinateSwitching}
-              ]"
-              >Raw variants</span
-            >
-            <!-- Wrapper so the tooltip fires even when the switch is disabled (a disabled control has
+          <div class="flex flex-col gap-3 px-4 py-3 tablet:flex-row tablet:items-center">
+            <div class="relative min-w-0 flex-1 mt-2">
+              <MvFloatField label="Search variants">
+                <template #default="{id}">
+                  <AutoComplete
+                    :id="id"
+                    v-model="selectedVariant"
+                    class="w-full"
+                    :delay="300"
+                    dropdown
+                    fluid
+                    :input-style="variantToVisualize ? {paddingRight: '2.25rem'} : undefined"
+                    :option-label="variantOptionLabel"
+                    scroll-height="175px"
+                    select-on-focus
+                    :suggestions="variantSearchSuggestions"
+                    :virtual-scroller-options="{itemSize: 50}"
+                    @complete="variantSearch"
+                  >
+                    <template #option="{option}">
+                      <div class="flex flex-col justify-center leading-tight">
+                        <span>{{ variantOptionLabel(option) }}</span>
+                        <span v-if="variantUnderlyingLabel(option)" class="font-mono text-xs text-text-muted">
+                          {{ variantUnderlyingLabel(option) }}
+                        </span>
+                        <span v-if="frame === 'mapped' && isUnmapped(option)" class="text-xs italic text-text-muted">
+                          Variant could not be mapped
+                        </span>
+                      </div>
+                    </template>
+                    <template #empty>
+                      <div class="p-2.5 text-center text-sm text-text-muted">No matching variants found.</div>
+                    </template>
+                  </AutoComplete>
+                </template>
+              </MvFloatField>
+              <button
+                v-if="variantToVisualize"
+                aria-label="Clear"
+                class="absolute right-12 top-1/2 flex size-5 -translate-y-1/2 cursor-pointer items-center justify-center rounded-full text-text-muted hover:bg-red-50 hover:text-red-600"
+                @click="selectedVariant = null"
+              >
+                <i class="pi pi-times text-[10px]" />
+              </button>
+            </div>
+            <div class="flex items-center gap-2 text-sm text-text-secondary tablet:ml-auto">
+              <span
+                :class="[
+                  clinicalMode ? 'text-text-muted' : 'font-semibold text-sage',
+                  {'opacity-50': coordinateSwitching}
+                ]"
+                >Raw variants</span
+              >
+              <!-- Wrapper so the tooltip fires even when the switch is disabled (a disabled control has
                  pointer-events: none and won't trigger a tooltip on itself). Only shown when mapped
                  mode is unavailable — clinicalModeHelpText returns the "no mapped variants" reason then. -->
-            <span
-              v-tooltip.top="mappedModeAvailable ? undefined : clinicalModeHelpText"
-              class="inline-flex"
-              :class="{'cursor-not-allowed': !mappedModeAvailable}"
-            >
-              <ToggleSwitch
-                :aria-label="`Click to change to ${clinicalMode ? 'raw data' : 'clinical view'}.`"
-                :disabled="coordinateSwitching || !mappedModeAvailable"
-                :model-value="clinicalMode"
-                @update:model-value="toggleClinicalMode"
-              />
-            </span>
-            <span
-              :class="[
-                clinicalMode ? 'font-semibold text-sage' : 'text-text-muted',
-                {'opacity-50': coordinateSwitching}
-              ]"
-              >Mapped variants</span
-            >
-            <i v-if="coordinateSwitching" class="pi pi-spinner pi-spin text-xs text-sage" />
-            <span
-              v-tooltip.top="clinicalModeHelpText"
-              class="inline-flex size-4 shrink-0 cursor-help items-center justify-center rounded-full bg-sage text-[10px] font-bold text-white"
-              >?</span
-            >
+              <span
+                v-tooltip.top="mappedModeAvailable ? undefined : clinicalModeHelpText"
+                class="inline-flex"
+                :class="{'cursor-not-allowed': !mappedModeAvailable}"
+              >
+                <ToggleSwitch
+                  :aria-label="`Click to change to ${clinicalMode ? 'raw data' : 'clinical view'}.`"
+                  :disabled="coordinateSwitching || !mappedModeAvailable"
+                  :model-value="clinicalMode"
+                  @update:model-value="toggleClinicalMode"
+                />
+              </span>
+              <span
+                :class="[
+                  clinicalMode ? 'font-semibold text-sage' : 'text-text-muted',
+                  {'opacity-50': coordinateSwitching}
+                ]"
+                >Mapped variants</span
+              >
+              <i v-if="coordinateSwitching" class="pi pi-spinner pi-spin text-xs text-sage" />
+              <span
+                v-tooltip.top="clinicalModeHelpText"
+                class="inline-flex size-4 shrink-0 cursor-help items-center justify-center rounded-full bg-sage text-[10px] font-bold text-white"
+                >?</span
+              >
+            </div>
           </div>
+
+          <!-- Selected-variant detail (assayed variant envelope: GET /variants/{urn}), flush within the card -->
+          <VariantDetailPanel
+            v-if="variantToVisualize?.variantUrn"
+            :key="variantToVisualize.variantUrn"
+            :coordinate="variantOptionLabel(variantToVisualize)"
+            :flush="true"
+            :identify="false"
+            :selected-calibration-id="selectedCalibrationObjects[0]?.id ?? null"
+            :underlying-coordinate="variantUnderlyingLabel(variantToVisualize) ?? ''"
+            :urn="variantToVisualize.variantUrn"
+          />
         </div>
 
         <!-- Variants loading spinner -->
@@ -351,8 +368,8 @@
         <div class="mb-6">
           <ScoreSetDownloads
             :has-counts="hasCounts"
-            :has-pathogenicity-calibrations="hasPathogenicityCalibrations"
             :has-functional-impact-calibrations="hasFunctionalImpactCalibrations"
+            :has-pathogenicity-calibrations="hasPathogenicityCalibrations"
             :is-meta-data-empty="isMetaDataEmpty"
             :score-set="item"
           />
@@ -506,6 +523,7 @@ import ScoreSetMetadataCard from '@/components/score-set/ScoreSetMetadataCard.vu
 import ScoreSetHeatmap from '@/components/score-set/ScoreSetHeatmap.vue'
 import ScoreSetHistogram from '@/components/score-set/ScoreSetHistogram.vue'
 import MvVariantPreview from '@/components/common/MvVariantPreview.vue'
+import VariantDetailPanel from '@/components/variant/VariantDetailPanel.vue'
 import ScoreSetProcessingStatus from '@/components/score-set/ScoreSetProcessingStatus.vue'
 import ScoreSetVisualizer from '@/components/score-set/ScoreSetVisualizer.vue'
 
@@ -564,7 +582,8 @@ export default {
     ScoreSetProcessingStatus,
     ScoreSetVisualizer,
     SelectButton,
-    ToggleSwitch
+    ToggleSwitch,
+    VariantDetailPanel
   },
 
   props: {
@@ -914,6 +933,15 @@ export default {
       return typeof variant === 'string' ? variant : this.labelForVariant(variant, this.frame)
     },
 
+    // The underlying nucleotide coordinate in the current frame, when it differs from the (protein-
+    // preferred) display label — surfaced to disambiguate distinct coding variants that share a
+    // protein label, and as provenance. Null when the label already is the nucleotide coordinate.
+    variantUnderlyingLabel(variant: DisplayVariant | string): string | null {
+      if (typeof variant === 'string') return null
+      const nt = this.getHgvsNt(variant, this.frame)
+      return nt && nt !== this.variantOptionLabel(variant) ? nt : null
+    },
+
     childComponentSelectedVariant(variant: DisplayVariant | null) {
       if (variant == null) {
         this.selectedVariant = null
diff --git a/src/components/screens/VariantScreen.vue b/src/components/screens/VariantScreen.vue
index 9a24ad32..d114af1e 100644
--- a/src/components/screens/VariantScreen.vue
+++ b/src/components/screens/VariantScreen.vue
@@ -197,7 +197,15 @@
               <div class="mb-1.5 text-xs-minus font-bold uppercase tracking-[0.5px] text-black">
                 Population Frequency
               </div>
-              <p class="text-xs-plus italic text-text-muted">Data coming soon</p>
+              <template v-if="lookup.selectedGnomad.value">
+                <MvDetailRow label="gnomAD AF" :value="formatFrequency(lookup.selectedGnomad.value.alleleFrequency)" />
+                <MvDetailRow
+                  v-if="lookup.selectedGnomad.value.faf95Max != null"
+                  label="FAF95 max"
+                  :value="formatFrequency(lookup.selectedGnomad.value.faf95Max)"
+                />
+              </template>
+              <p v-else class="text-xs-plus italic text-text-muted">No gnomAD data</p>
             </div>
             <div
               class="border-t border-border-light pt-4 tablet:border-t-0 tablet:pt-0 tablet:border-l tablet:border-border-light tablet:pl-[18px]"
@@ -345,18 +353,18 @@ export default defineComponent({
       const activeVariant = this.lookup.selectedVariantDetail.value
       if (!activeVariant) return options
 
-      const currentMapped = activeVariant.mappedVariants.find((m) => m.current)
-      const hasMappingData = !!currentMapped?.postMapped
-
+      // Mapping is present iff the envelope built a molecular representation (Cat-VRS) for the variant.
+      const hasMappingData = !!activeVariant.molecularRepresentation
+      const scoreSet = this.lookup.selectedScoreSet.value
       const hasScore = this.lookup.selectedVariantScore.value !== null
 
-      if (hasMappingData && hasScore && hasPathogenicityCalibrations(activeVariant.scoreSet)) {
+      if (hasMappingData && hasScore && hasPathogenicityCalibrations(scoreSet)) {
         options.push({
           label: 'Pathogenicity Statement',
           command: () => this.lookup.fetchVariantAnnotations('pathogenicity-statement')
         })
       }
-      if (hasMappingData && hasScore && hasFunctionalCalibrations(activeVariant.scoreSet)) {
+      if (hasMappingData && hasScore && hasFunctionalCalibrations(scoreSet)) {
         options.push({
           label: 'Functional Impact Statement',
           command: () => this.lookup.fetchVariantAnnotations('functional-statement')
@@ -379,7 +387,12 @@ export default defineComponent({
     }
   },
 
-  methods: {}
+  methods: {
+    formatFrequency(value: number | null | undefined): string {
+      if (value == null) return '—'
+      return value < 0.0001 ? value.toExponential(2) : value.toPrecision(3)
+    }
+  }
 })
 </script>
 
diff --git a/src/components/variant/VariantDetailPanel.vue b/src/components/variant/VariantDetailPanel.vue
new file mode 100644
index 00000000..18b67627
--- /dev/null
+++ b/src/components/variant/VariantDetailPanel.vue
@@ -0,0 +1,288 @@
+<template>
+  <div
+    :class="
+      flush
+        ? 'border-t border-border-light bg-surface'
+        : 'mave-gradient-bar relative overflow-hidden rounded-lg border border-border bg-surface'
+    "
+  >
+    <!-- Loading / error -->
+    <div v-if="status === 'loading'" class="flex items-center justify-center px-5 py-4">
+      <MvLoader text="Loading variant..." />
+    </div>
+    <div v-else-if="status === 'error'" class="px-5 py-4 text-sm text-red-600">Could not load variant detail.</div>
+
+    <template v-else-if="detail">
+      <!-- Identity -->
+      <div class="flex flex-wrap items-baseline gap-x-2.5 gap-y-1 px-4 pb-3 pt-3.5 tablet:px-5">
+        <span class="font-mono text-base font-bold leading-none text-text-primary">{{ coordinate || detail.urn }}</span>
+        <span
+          v-if="underlyingCoordinate && underlyingCoordinate !== coordinate"
+          v-tooltip.top="'Underlying nucleotide coordinate'"
+          class="font-mono text-xs text-text-muted"
+        >
+          {{ underlyingCoordinate }}
+        </span>
+      </div>
+
+      <!-- Facts -->
+      <div class="grid grid-cols-2 gap-px border-t border-border-light bg-border-light tablet:grid-cols-4">
+        <div class="stat">
+          <span class="stat-label">Consequence</span>
+          <span class="stat-value font-semibold">{{ consequence ? formatToken(consequence) : '—' }}</span>
+        </div>
+
+        <div class="stat">
+          <span class="stat-label">Classification</span>
+          <span v-if="selectedClassification" class="flex flex-wrap items-center gap-1.5">
+            <span class="rounded px-1.5 py-0.5 text-xs-plus" :class="classificationClass">
+              {{ formatToken(selectedClassification.classification.functionalClassification) }}
+            </span>
+            <MvEvidenceTag v-if="acmgCode" :code="acmgCode" />
+          </span>
+          <span v-else class="stat-value font-semibold">—</span>
+          <span v-if="oddspathsRatio != null" class="mt-0.5 text-xs"> OddsPath {{ oddspathsRatio }} </span>
+        </div>
+
+        <div class="stat">
+          <span class="stat-label">gnomAD</span>
+          <a
+            v-if="gnomad"
+            class="stat-value font-semibold hover:underline"
+            :href="`https://gnomad.broadinstitute.org/variant/${gnomad.dbIdentifier}`"
+            target="_blank"
+            rel="noopener noreferrer"
+          >
+            AF {{ formatFrequency(gnomad.alleleFrequency) }}
+          </a>
+          <span v-else class="stat-value">—</span>
+          <span v-if="gnomad?.faf95Max != null" class="text-xs text-text-muted">
+            FAF95 {{ formatFrequency(gnomad.faf95Max) }}
+          </span>
+        </div>
+
+        <div class="stat">
+          <span class="stat-label">ClinVar</span>
+          <a
+            v-if="latestClinvar?.clinvarVariationId"
+            class="stat-value font-semibold hover:underline"
+            :style="{color: clinvarColor}"
+            :href="`https://www.ncbi.nlm.nih.gov/clinvar/?term=${latestClinvar.clinvarAlleleId}[alleleId]`"
+            target="_blank"
+            rel="noopener noreferrer"
+          >
+            {{ latestClinvar.clinicalSignificance }}
+          </a>
+          <span v-else-if="latestClinvar" class="stat-value font-semibold" :style="{color: clinvarColor}">
+            {{ latestClinvar.clinicalSignificance }}
+          </span>
+          <span v-else class="stat-value">—</span>
+          <span
+            v-if="clinvarStars != null"
+            v-tooltip.top="latestClinvar?.clinicalReviewStatus"
+            class="flex items-center gap-0.5 text-amber-400"
+            aria-label="ClinVar review stars"
+          >
+            <i
+              v-for="n in 4"
+              :key="n"
+              :class="n <= clinvarStars ? 'pi pi-star-fill' : 'pi pi-star'"
+              class="text-[9px]"
+            />
+          </span>
+          <span v-if="latestClinvar" class="text-xs text-text-muted"
+            >As of {{ formatClinvarVersion(latestClinvar.dbVersion) }}</span
+          >
+        </div>
+      </div>
+
+      <!-- Status and Links -->
+      <div
+        class="border-t border-border-light bg-surface flex flex-wrap items-baseline gap-x-2.5 gap-y-1 px-4 pb-3 pt-3.5 tablet:px-5"
+      >
+        <span
+          v-if="!detail.isCurrent"
+          v-tooltip.top="supersededTooltip"
+          class="inline-flex items-center gap-1 rounded-full bg-amber-100 px-2 py-0.5 text-xs font-semibold text-amber-800"
+        >
+          <i class="pi pi-exclamation-triangle text-[10px]" />
+          Superseded
+        </span>
+        <router-link
+          v-if="detail.clingenAlleleId"
+          class="ml-auto shrink-0 text-xs font-semibold text-link hover:underline"
+          :to="{name: 'variant', params: {clingenAlleleId: detail.clingenAlleleId}}"
+        >
+          View full details <i class="pi pi-arrow-right text-[10px]" />
+        </router-link>
+      </div>
+    </template>
+  </div>
+</template>
+
+<script lang="ts">
+import {defineComponent, type PropType} from 'vue'
+
+import MvEvidenceTag from '@/components/common/MvEvidenceTag.vue'
+import MvLoader from '@/components/common/MvLoader.vue'
+import {getVariantDetail} from '@/api/mavedb/variants'
+import {formatClinvarVersion} from '@/lib/formats'
+import {CLINVAR_REVIEW_STATUS_STARS} from '@/lib/clinical-controls'
+import type {components} from '@/schema/openapi'
+
+type VariantDetail = components['schemas']['VariantDetail']
+type VariantClassification = components['schemas']['VariantClassification']
+type AlleleAnnotations = components['schemas']['AlleleAnnotations']
+
+/**
+ * Compact selected-variant summary for the score-set page, consuming `GET /variants/{urn}`.
+ *
+ * Deliberately lean: the assay-level facts only (identity, consequence, the selected calibration's
+ * classification, the assay allele's key annotations) as distinct, color-coded stats, plus a link out
+ * to the full variant page. Coordinates follow the page's current frame; the classification follows the
+ * page's selected calibration. The deep per-allele annotation breakdown and the Cat-VRS structure
+ * belong on the dedicated variant page — VRS digests are join keys, never surfaced here.
+ */
+export default defineComponent({
+  name: 'VariantDetailPanel',
+
+  components: {MvEvidenceTag, MvLoader},
+
+  props: {
+    urn: {type: String, required: true},
+    // The display label for the variant in the page's current frame — the SAME string the search box
+    // and heatmap use (`labelForVariant`, protein-preferred). Passed in so the panel's identity never
+    // disagrees with the rest of the page (e.g. panel showing coding while the heatmap shows protein).
+    coordinate: {type: String, default: ''},
+    // The underlying nucleotide HGVS in the current frame. Shown muted beside the (protein-preferred)
+    // primary label to disambiguate distinct coding variants that collapse to the same protein change,
+    // and as provenance for the actually-measured coordinate. Empty when it equals the primary label.
+    underlyingCoordinate: {type: String, default: ''},
+    // The calibration selected on the page (its numeric id); its classification is the one shown.
+    selectedCalibrationId: {type: Number as PropType<number | null>, default: null},
+    // When embedded inside another card (e.g. under the search box), drop the panel's own card chrome
+    // and separate from the row above with just a top divider, so the two read as one unit.
+    flush: {type: Boolean, default: false}
+  },
+
+  data() {
+    return {
+      detail: null as VariantDetail | null,
+      status: 'idle' as 'idle' | 'loading' | 'loaded' | 'error'
+    }
+  },
+
+  computed: {
+    // The assay-level allele's annotation block — the one relevant to this measurement.
+    assayAnnotations(): AlleleAnnotations | null {
+      const digest = this.detail?.assayLevelDigest
+      if (!this.detail?.annotations || !digest) return null
+      return this.detail.annotations[digest] ?? null
+    },
+    consequence(): string | null {
+      return this.assayAnnotations?.vep?.consequence ?? null
+    },
+    gnomad(): AlleleAnnotations['gnomad'] | null {
+      return this.assayAnnotations?.gnomad ?? null
+    },
+    latestClinvar(): NonNullable<AlleleAnnotations['clinvar']>[number] | null {
+      const clinvar = this.assayAnnotations?.clinvar
+      if (!clinvar?.length) return null
+      return clinvar.reduce((best, c) => (c.dbVersion > best.dbVersion ? c : best))
+    },
+    clinvarStars(): number | null {
+      const status = this.latestClinvar?.clinicalReviewStatus?.toLowerCase()
+      if (!status) return null
+      const stars = CLINVAR_REVIEW_STATUS_STARS[status] ?? null
+      return stars != null ? stars : null
+    },
+    clinvarColor(): string | undefined {
+      const s = this.latestClinvar?.clinicalSignificance?.toLowerCase() ?? ''
+      if (s.includes('conflicting')) return undefined
+      if (s.includes('pathogenic')) return 'var(--color-badge-pathogenic)'
+      if (s.includes('benign')) return 'var(--color-badge-benign)'
+      return undefined
+    },
+    // The classification for the page's selected calibration; falls back to primary, then first.
+    selectedClassification(): VariantClassification | null {
+      const classifications = this.detail?.classifications ?? []
+      if (this.selectedCalibrationId != null) {
+        const match = classifications.find((c) => c.calibrationId === this.selectedCalibrationId)
+        if (match) return match
+      }
+      return classifications.find((c) => c.primary) ?? classifications[0] ?? null
+    },
+    oddspathsRatio(): number | null {
+      return this.selectedClassification?.classification.oddspathsRatio ?? null
+    },
+    classificationClass(): string {
+      return `mave-classification-${this.selectedClassification?.classification.functionalClassification ?? 'not_specified'}`
+    },
+    acmgCode(): string | null {
+      const acmg = this.selectedClassification?.classification.acmgClassification
+      if (!acmg?.evidenceStrength) return null
+      return `${acmg.criterion}_${acmg.evidenceStrength.toUpperCase()}`
+    },
+    supersededTooltip(): string {
+      return this.detail?.supersededBy
+        ? `Superseded by ${this.detail.supersededBy}`
+        : 'This measurement has been superseded by a newer version.'
+    }
+  },
+
+  watch: {
+    urn: {immediate: true, handler: 'fetchDetail'}
+  },
+
+  methods: {
+    async fetchDetail(urn: string) {
+      if (!urn) return
+      this.status = 'loading'
+      this.detail = null
+      try {
+        const detail = await getVariantDetail(urn)
+        if (this.urn !== urn) return // selection changed mid-flight
+        this.detail = detail
+        this.status = 'loaded'
+      } catch (error) {
+        if (this.urn !== urn) return
+        console.error(`Error fetching variant detail for "${urn}"`, error)
+        this.status = 'error'
+      }
+    },
+    formatToken(value: string | null | undefined): string {
+      if (!value) return '—'
+      return value.replace(/_/g, ' ').replace(/\b\w/g, (ch) => ch.toUpperCase())
+    },
+    formatFrequency(value: number | null | undefined): string {
+      if (value == null) return '—'
+      return value < 0.0001 ? value.toExponential(2) : value.toPrecision(3)
+    },
+    formatClinvarVersion
+  }
+})
+</script>
+
+<style scoped>
+/* Each fact is its own cell on a shared light background; the 1px grid gap draws the dividers. */
+.stat {
+  display: flex;
+  flex-direction: column;
+  gap: 3px;
+  background: var(--color-surface);
+  padding: 10px 14px;
+}
+
+.stat-label {
+  font-size: 10px;
+  font-weight: 700;
+  text-transform: uppercase;
+  letter-spacing: 0.5px;
+  color: var(--color-text-muted);
+}
+
+.stat-value {
+  font-size: 0.875rem;
+  color: var(--color-text-primary);
+}
+</style>
diff --git a/src/composables/use-variant-lookup.ts b/src/composables/use-variant-lookup.ts
index 94a92a1c..9cd152de 100644
--- a/src/composables/use-variant-lookup.ts
+++ b/src/composables/use-variant-lookup.ts
@@ -1,7 +1,7 @@
 import axios from 'axios'
 import {computed, ref, shallowRef, watch, type ComputedRef, type Ref} from 'vue'
 
-import {getVariantAnnotation, getVariantDetail, lookupVariantsByClingenId} from '@/api/mavedb/variants'
+import {getScoreSet, getVariantAnnotation, getVariantDetail, lookupVariantsByClingenId} from '@/api/mavedb/variants'
 import {getLeanScoreSetVariants} from '@/api/mavedb/score-sets'
 import {useCalibrationResolution, type UseCalibrationResolutionReturn} from '@/composables/use-calibration-resolution'
 import {useClingenAllele, type UseClingenAlleleReturn} from '@/composables/use-clingen-allele'
@@ -23,7 +23,8 @@ export type {MeasurementType}
 type ScoreCalibration = components['schemas']['ScoreCalibration']
 type ScoreSet = components['schemas']['ScoreSet']
 type VariantEffectMeasurementWithShortScoreSet = components['schemas']['VariantEffectMeasurementWithShortScoreSet']
-type VariantEffectMeasurementWithScoreSet = components['schemas']['VariantEffectMeasurementWithScoreSet']
+type VariantDetail = components['schemas']['VariantDetail']
+type AlleleAnnotations = components['schemas']['AlleleAnnotations']
 type FunctionalClassification =
   components['schemas']['mavedb__view_models__score_calibration__FunctionalClassification']
 
@@ -51,9 +52,10 @@ export interface UseVariantLookupReturn {
   selectedVariantUrn: Ref<string | null>
   selectVariant: (urn: string | null | undefined) => void
   selectedVariant: ComputedRef<VariantEntry | undefined>
-  selectedVariantDetail: ComputedRef<VariantEffectMeasurementWithScoreSet | null>
+  selectedVariantDetail: ComputedRef<VariantDetail | null>
   selectedVariantName: ComputedRef<string | null>
   selectedClingenAlleleId: ComputedRef<string | null>
+  selectedGnomad: ComputedRef<AlleleAnnotations['gnomad'] | null>
 
   // Scores
   selectedScoreSet: ComputedRef<ScoreSet | null>
@@ -114,10 +116,16 @@ export function useVariantLookup(
   const showNucleotide = ref(true)
   const showProtein = ref(true)
   const showAssociatedNucleotide = ref(true)
-  const variantDetailCache = ref<Record<string, VariantEffectMeasurementWithScoreSet>>({})
+  const variantDetailCache = ref<Record<string, VariantDetail>>({})
+  const scoreSetCache = shallowRef<Record<string, ScoreSet>>({})
   const scoresCache = shallowRef<Record<string, DisplayVariant[]>>({})
   const selectedCalibration = ref<string | null>(null)
 
+  // A variant URN is `<score-set-urn>#<n>`, so its score set is the URN's prefix — no extra lookup
+  // needed. The detail envelope deliberately doesn't embed the score set (it's its own resource), so
+  // score-set metadata (calibrations, target, experiment) is fetched separately and cached per URN.
+  const scoreSetUrnOf = (variantUrn: string): string => variantUrn.split('#')[0]
+
   // ── Filters ───────────────────────────────────────────────
   const nucleotideCount = computed(() => variants.value.filter((v) => v.type === 'nucleotide').length)
   const proteinCount = computed(() => variants.value.filter((v) => v.type === 'protein').length)
@@ -135,11 +143,14 @@ export function useVariantLookup(
 
   // ── Selection ─────────────────────────────────────────────
   const selectedVariant = computed(() => variants.value.find((v) => v.content.urn === selectedVariantUrn.value))
-  const selectedVariantDetail = computed<VariantEffectMeasurementWithScoreSet | null>(() => {
+  const selectedVariantDetail = computed<VariantDetail | null>(() => {
     if (!selectedVariantUrn.value) return null
     return variantDetailCache.value[selectedVariantUrn.value] || null
   })
-  const selectedScoreSet = computed<ScoreSet | null>(() => selectedVariantDetail.value?.scoreSet || null)
+  const selectedScoreSet = computed<ScoreSet | null>(() => {
+    if (!selectedVariantUrn.value) return null
+    return scoreSetCache.value[scoreSetUrnOf(selectedVariantUrn.value)] || null
+  })
   const selectedVariantName = computed(() => {
     if (!selectedVariant.value) return null
     const v = selectedVariant.value.content
@@ -148,9 +159,14 @@ export function useVariantLookup(
     const postMapped = mapped?.postMapped as {expressions?: {value?: string}[]} | undefined
     return postMapped?.expressions?.[0]?.value || v.hgvsNt || v.hgvsPro || v.hgvsSplice || null
   })
-  const selectedClingenAlleleId = computed(() => {
-    const mapped = selectedVariantDetail.value?.mappedVariants.find((m) => m.current)
-    return mapped?.clingenAlleleId || null
+  // The detail envelope carries the assay-level ClinGen id as a flat field (the URN→allele bridge).
+  const selectedClingenAlleleId = computed(() => selectedVariantDetail.value?.clingenAlleleId || null)
+  // Population frequency for the assay-level allele, from the envelope's digest-keyed annotation map.
+  const selectedGnomad = computed<AlleleAnnotations['gnomad'] | null>(() => {
+    const detail = selectedVariantDetail.value
+    const digest = detail?.assayLevelDigest
+    if (!detail?.annotations || !digest) return null
+    return detail.annotations[digest]?.gnomad ?? null
   })
 
   // ── Scores ────────────────────────────────────────────────
@@ -192,19 +208,29 @@ export function useVariantLookup(
 
   // ── Data fetching ─────────────────────────────────────────
   async function fetchVariantDetail(variantUrn: string) {
+    const scoreSetUrn = scoreSetUrnOf(variantUrn)
+    // The score set (calibrations, target, experiment) and lean scores are needed regardless of
+    // whether the envelope is already cached, so kick those off first.
+    fetchScoreSet(scoreSetUrn)
+    fetchScores(scoreSetUrn)
     if (variantDetailCache.value[variantUrn]) return
     try {
-      const detail = await getVariantDetail(variantUrn)
-      variantDetailCache.value[variantUrn] = detail
-      const scoreSetUrn = detail.scoreSet?.urn
-      if (scoreSetUrn) {
-        fetchScores(scoreSetUrn)
-      }
+      variantDetailCache.value[variantUrn] = await getVariantDetail(variantUrn)
     } catch (error) {
       console.error(`Error fetching variant detail for "${variantUrn}"`, error)
     }
   }
 
+  async function fetchScoreSet(scoreSetUrn: string) {
+    if (scoreSetCache.value[scoreSetUrn]) return
+    try {
+      const scoreSet = await getScoreSet(scoreSetUrn)
+      scoreSetCache.value = {...scoreSetCache.value, [scoreSetUrn]: scoreSet}
+    } catch (error) {
+      console.error(`Error fetching score set "${scoreSetUrn}"`, error)
+    }
+  }
+
   async function fetchScores(scoreSetUrn: string) {
     if (scoresCache.value[scoreSetUrn]) return
     try {
@@ -221,6 +247,7 @@ export function useVariantLookup(
   async function fetchVariants() {
     variants.value = []
     variantDetailCache.value = {}
+    scoreSetCache.value = {}
     scoresCache.value = {}
     variantsStatus.value = 'Loading'
     try {
@@ -310,19 +337,19 @@ export function useVariantLookup(
 
   function getAbnormalOddsPath(urn: string | null | undefined): string | null {
     if (!urn) return null
-    return getClassificationOddsPath(getPrimaryCalibration(variantDetailCache.value[urn]?.scoreSet), 'abnormal')
+    return getClassificationOddsPath(getPrimaryCalibration(scoreSetCache.value[scoreSetUrnOf(urn)]), 'abnormal')
   }
 
   function getNormalOddsPath(urn: string | null | undefined): string | null {
     if (!urn) return null
-    return getClassificationOddsPath(getPrimaryCalibration(variantDetailCache.value[urn]?.scoreSet), 'normal')
+    return getClassificationOddsPath(getPrimaryCalibration(scoreSetCache.value[scoreSetUrnOf(urn)]), 'normal')
   }
 
   function getVariantScoreRange(variantUrn: string | null | undefined): FunctionalClassification | null {
     if (!variantUrn) return null
-    const detail = variantDetailCache.value[variantUrn]
-    const scoreSetUrn = detail?.scoreSet?.urn
-    if (!scoreSetUrn) return null
+    const scoreSetUrn = scoreSetUrnOf(variantUrn)
+    const scoreSet = scoreSetCache.value[scoreSetUrn]
+    if (!scoreSet) return null
 
     const cachedScores = scoresCache.value[scoreSetUrn]
     if (!cachedScores) return null
@@ -331,7 +358,7 @@ export function useVariantLookup(
     const score = scoreRow?.score
     if (score == null) return null
 
-    const cal = getPrimaryCalibration(detail?.scoreSet)
+    const cal = getPrimaryCalibration(scoreSet)
     if (!cal?.functionalClassifications) return null
 
     return cal.functionalClassifications.find((r) => functionalClassificationContainsVariant(r, score)) || null
@@ -388,6 +415,7 @@ export function useVariantLookup(
     selectedVariantDetail,
     selectedVariantName,
     selectedClingenAlleleId,
+    selectedGnomad,
     selectedScoreSet,
     selectedScoreSetUrn,
     scores,
diff --git a/src/lib/clinical-controls.ts b/src/lib/clinical-controls.ts
index 3bde7d55..7d565456 100644
--- a/src/lib/clinical-controls.ts
+++ b/src/lib/clinical-controls.ts
@@ -65,7 +65,7 @@ export const CONFLICTING_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS = [
   'Conflicting classifications of pathogenicity'
 ]
 
-export const CLINVAR_REVIEW_STATUS_STARS: { [status: string]: number } = {
+export const CLINVAR_REVIEW_STATUS_STARS: {[status: string]: number} = {
   'no assertion criteria provided': 0,
   'criteria provided, conflicting interpretations': 1,
   'criteria provided, conflicting classifications': 1,
@@ -88,7 +88,6 @@ export const DEFAULT_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS = [
 export const DEFAULT_MIN_STAR_RATING = 1
 
 export const DEFAULT_CLINICAL_CONTROL_DB = 'ClinVar'
-export const DEFAULT_CLINICAL_CONTROL_VERSION = '01_2025'
 
 export interface ClinicalControlOption {
   dbName: string
@@ -122,11 +121,11 @@ export interface ClinicalControl {
  * @returns An array of clinical significance classification objects, including the appropriate "Conflicting" classification.
  */
 export function clinvarClinicalSignificanceClassifications(
-  version: string
+  version: string | null
 ): typeof CLINVAR_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS {
   return [
     ...CLINVAR_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS,
-    clinvarConflictingSignificanceClassificationForVersion(version),
+    clinvarConflictingSignificanceClassificationForVersion(version)
   ]
 }
 
@@ -140,12 +139,12 @@ export function clinvarClinicalSignificanceClassifications(
  * @param version - The version string, expected to contain a year after an underscore (e.g., "clinvar_2025").
  * @returns An object with `name`, `description`, and `shortDescription` fields describing the conflicting classification.
  */
-export function clinvarConflictingSignificanceClassificationForVersion(version: string): {
+export function clinvarConflictingSignificanceClassificationForVersion(version: string | null): {
   name: string
   description: string
   shortDescription: string
 } {
-  if (Number(version.split('_')[1]) > 2024) {
+  if (version === null || Number(version.split('_')[1]) > 2024) {
     return {
       name: 'Conflicting classifications of pathogenicity',
       description: 'Variant with conflicting classifications of pathogenicity',
@@ -170,8 +169,8 @@ export function clinvarConflictingSignificanceClassificationForVersion(version:
  * @param version - The version string in the format "prefix_number" (e.g., "v_2025").
  * @returns The label for conflicting clinical significance series.
  */
-export function conflictingClinicalSignificanceSeriesLabelForVersion(version: string): string {
-  if (Number(version.split('_')[1]) > 2024) {
+export function conflictingClinicalSignificanceSeriesLabelForVersion(version: string | null): string {
+  if (version === null || Number(version.split('_')[1]) > 2024) {
     return 'Conflicting classifications'
   } else {
     return 'Conflicting interpretations'
diff --git a/src/lib/formats.ts b/src/lib/formats.ts
index f8446199..09e1b41d 100644
--- a/src/lib/formats.ts
+++ b/src/lib/formats.ts
@@ -2,6 +2,13 @@ import moment from 'moment'
 import {Opts} from 'linkifyjs'
 import linkifyHtml from 'linkify-html'
 
+export function formatClinvarVersion(dbVersion: string): string {
+  const match = dbVersion.match(/^(\d{2})_(\d{4})$/)
+  if (!match) return dbVersion
+  const [, month, year] = match
+  return new Date(Number(year), Number(month) - 1).toLocaleString('en-US', {month: 'long', year: 'numeric'})
+}
+
 export function formatDate(x: string) {
   return moment(x).format('MMM DD, YYYY')
 }
diff --git a/src/router/index.ts b/src/router/index.ts
index 9fbdda9f..97437a42 100644
--- a/src/router/index.ts
+++ b/src/router/index.ts
@@ -190,10 +190,11 @@ const routes: RouteRecordRaw[] = [
     async beforeEnter(to) {
       const urn = Array.isArray(to.params.urn) ? to.params.urn[0] : to.params.urn
       try {
+        // The detail envelope carries the assay-level ClinGen id as a flat field (the URN→allele
+        // bridge), so resolving a legacy measurement URN to its allele page is a direct read.
         const detail = await getVariantDetail(urn)
-        const mapped = detail.mappedVariants.find((m) => m.current)
-        if (mapped?.clingenAlleleId) {
-          return {name: 'variant', params: {clingenAlleleId: mapped.clingenAlleleId}}
+        if (detail.clingenAlleleId) {
+          return {name: 'variant', params: {clingenAlleleId: detail.clingenAlleleId}}
         }
       } catch {
         // Fall through to 404 if the variant can't be resolved
diff --git a/src/schema/openapi.d.ts b/src/schema/openapi.d.ts
index 43af2041..5a843c2e 100644
--- a/src/schema/openapi.d.ts
+++ b/src/schema/openapi.d.ts
@@ -1337,8 +1337,12 @@ export interface paths {
   };
   "/api/v1/variants/{urn}": {
     /**
-     * Fetch variant by URN
-     * @description Fetch a single variant by URN.
+     * Fetch assayed variant detail by URN
+     * @description Fetch the two-tier detail envelope for a single assayed variant by URN.
+     *
+     * Flat assay-level fields for the common UI case plus the spec-pure GA4GH CategoricalVariant and a
+     * digest-keyed annotation map for machine/standard consumers. A superseded variant is served (it is
+     * the citable unit) but self-describes via isCurrent/supersededBy rather than reading as current.
      */
     get: operations["get_variant_api_v1_variants__urn__get"];
   };
@@ -1624,6 +1628,19 @@ export interface components {
        */
       state: components["schemas"]["LiteralSequenceExpression"] | components["schemas"]["ReferenceLengthExpression"] | components["schemas"]["LengthExpression"];
     };
+    /**
+     * AlleleAnnotations
+     * @description The external annotations for one allele, sparse — each source absent unless it has data.
+     */
+    AlleleAnnotations: {
+      vep?: components["schemas"]["VepAnnotation"] | null;
+      gnomad?: components["schemas"]["GnomadAnnotation"] | null;
+      /**
+       * Clinvar
+       * @default []
+       */
+      clinvar?: components["schemas"]["ClinvarAnnotation"][];
+    };
     /**
      * AnnotationLayer
      * @description Annotation layer for a variant mapping result.
@@ -1794,17 +1811,17 @@ export interface components {
     ClingenAlleleIdVariantLookupResponse: {
       /** Clingenalleleid */
       clingenAlleleId: string;
-      exactMatch?: components["schemas"]["Variant"] | null;
+      exactMatch?: components["schemas"]["ClingenAlleleVariants"] | null;
       /**
        * Equivalentnt
        * @default []
        */
-      equivalentNt?: components["schemas"]["Variant"][];
+      equivalentNt?: components["schemas"]["ClingenAlleleVariants"][];
       /**
        * Equivalentaa
        * @default []
        */
-      equivalentAa?: components["schemas"]["Variant"][];
+      equivalentAa?: components["schemas"]["ClingenAlleleVariants"][];
     };
     /**
      * ClingenAlleleIdVariantLookupsRequest
@@ -1814,6 +1831,19 @@ export interface components {
       /** Clingenalleleids */
       clingenAlleleIds: string[];
     };
+    /**
+     * ClingenAlleleVariants
+     * @description The assayed variants sharing one ClinGen allele id, with their variant effect measurements.
+     *
+     * An allele-side grouping (keyed by ClinGen allele id), it is the mapped-allele view of "which
+     * measurements share this molecular identity," not the assayed variant itself.
+     */
+    ClingenAlleleVariants: {
+      /** Clingenalleleid */
+      clingenAlleleId: string;
+      /** Varianteffectmeasurements */
+      variantEffectMeasurements: components["schemas"]["VariantEffectMeasurementWithShortScoreSet"][];
+    };
     /** ClinicalControlOptions */
     ClinicalControlOptions: {
       /** Dbname */
@@ -1852,6 +1882,22 @@ export interface components {
       /** Mappedvariants */
       mappedVariants: components["schemas"]["MappedVariantForClinicalControl"][];
     };
+    /**
+     * ClinvarAnnotation
+     * @description One ClinVar assertion for an allele (an allele may carry one per release).
+     */
+    ClinvarAnnotation: {
+      /** Clinicalsignificance */
+      clinicalSignificance: string;
+      /** Clinicalreviewstatus */
+      clinicalReviewStatus: string;
+      /** Clinvarvariationid */
+      clinvarVariationId?: string | null;
+      /** Clinvaralleleid */
+      clinvarAlleleId: string;
+      /** Dbversion */
+      dbVersion: string;
+    };
     /**
      * Coding
      * @description A structured representation of a code for a defined concept in a terminology or
@@ -3366,6 +3412,24 @@ export interface components {
       /** Mappedvariants */
       mappedVariants: components["schemas"]["MappedVariant"][];
     };
+    /**
+     * GnomadAnnotation
+     * @description gnomAD population frequency for an allele.
+     */
+    GnomadAnnotation: {
+      /** Allelefrequency */
+      alleleFrequency: number;
+      /** Allelecount */
+      alleleCount: number;
+      /** Allelenumber */
+      alleleNumber: number;
+      /** Faf95Max */
+      faf95Max?: number | null;
+      /** Dbversion */
+      dbVersion: string;
+      /** Dbidentifier */
+      dbIdentifier: string;
+    };
     /**
      * GroupBy
      * @enum {string}
@@ -5725,14 +5789,74 @@ export interface components {
       type: string;
     };
     /**
-     * Variant
-     * @description View model for a variant, defined by its ClinGen allele id, with associated variant effect measurements
+     * VariantClassification
+     * @description A functional classification the variant falls into, tagged with its calibration context.
+     *
+     * A score set may carry several calibrations, so a variant has one classification per calibration;
+     * ``primary`` flags the UI default. The classifications are calibration-derived but as-of-invariant
+     * (calibrations carry no valid-time), so they are always the current calibration state.
      */
-    Variant: {
+    VariantClassification: {
+      /** Calibrationid */
+      calibrationId: number;
+      /** Primary */
+      primary: boolean;
+      classification: components["schemas"]["SavedFunctionalClassification"];
+    };
+    /**
+     * VariantDetail
+     * @description The assayed variant-detail envelope (``GET /variants/{urn}``, design §7.1).
+     *
+     * Two tiers: flat, UI-ergonomic assay fields (the ``targetHgvs``/``referenceHgvs`` coordinate pair
+     * is a client-side toggle, no refetch) plus the spec-pure GA4GH ``molecularRepresentation``
+     * (``CategoricalVariant``, no MaveDB fields inside). The MaveDB layer rides alongside keyed by VRS
+     * digest: ``memberRelations`` (member→defining relation) and the ``annotations`` map. ``isCurrent``
+     * /``supersededBy`` let a superseded variant self-describe. Absent fields are omitted.
+     */
+    VariantDetail: {
+      /** Urn */
+      urn: string;
+      /** Scores */
+      scores?: Record<string, never> | null;
+      /** Counts */
+      counts?: Record<string, never> | null;
+      /**
+       * Classifications
+       * @default []
+       */
+      classifications?: components["schemas"]["VariantClassification"][];
+      /** Assaylevel */
+      assayLevel?: string | null;
+      /** Targethgvs */
+      targetHgvs?: string | null;
+      /** Referencehgvs */
+      referenceHgvs?: string | null;
+      /** Assayleveldigest */
+      assayLevelDigest?: string | null;
       /** Clingenalleleid */
-      clingenAlleleId: string;
-      /** Varianteffectmeasurements */
-      variantEffectMeasurements: components["schemas"]["VariantEffectMeasurementWithShortScoreSet"][];
+      clingenAlleleId?: string | null;
+      /** Molecularrepresentation */
+      molecularRepresentation?: Record<string, never> | null;
+      /** Mode */
+      mode?: string | null;
+      /**
+       * Memberrelations
+       * @default {}
+       */
+      memberRelations?: {
+        [key: string]: string;
+      };
+      /**
+       * Annotations
+       * @default {}
+       */
+      annotations?: {
+        [key: string]: components["schemas"]["AlleleAnnotations"];
+      };
+      /** Iscurrent */
+      isCurrent: boolean;
+      /** Supersededby */
+      supersededBy?: string | null;
     };
     /**
      * VariantDiagnosticProposition
@@ -5829,41 +5953,6 @@ export interface components {
       /** Recordtype */
       recordType?: string;
     };
-    /**
-     * VariantEffectMeasurementWithScoreSet
-     * @description Variant effect measurement view model with mapped variants and score set
-     */
-    VariantEffectMeasurementWithScoreSet: {
-      /** Urn */
-      urn?: string | null;
-      /** Data */
-      data: unknown;
-      /** Scoresetid */
-      scoreSetId: number;
-      /** Hgvsnt */
-      hgvsNt?: string | null;
-      /** Hgvspro */
-      hgvsPro?: string | null;
-      /** Hgvssplice */
-      hgvsSplice?: string | null;
-      /**
-       * Creationdate
-       * Format: date
-       */
-      creationDate: string;
-      /**
-       * Modificationdate
-       * Format: date
-       */
-      modificationDate: string;
-      /** Id */
-      id: number;
-      /** Recordtype */
-      recordType?: string;
-      scoreSet: components["schemas"]["ScoreSet"];
-      /** Mappedvariants */
-      mappedVariants: components["schemas"]["MappedVariant"][];
-    };
     /**
      * VariantEffectMeasurementWithShortScoreSet
      * @description Variant effect measurement view model with mapped variants and a limited set of score set details
@@ -6243,6 +6332,16 @@ export interface components {
      * @description A representation of the state of one or more biomolecules.
      */
     Variation: components["schemas"]["Allele"] | components["schemas"]["CisPhasedBlock"] | components["schemas"]["Adjacency"] | components["schemas"]["Terminus"] | components["schemas"]["DerivativeMolecule"] | components["schemas"]["CopyNumberChange"] | components["schemas"]["CopyNumberCount"];
+    /**
+     * VepAnnotation
+     * @description VEP most-severe functional consequence and the Ensembl release it resolved under.
+     */
+    VepAnnotation: {
+      /** Consequence */
+      consequence?: string | null;
+      /** Sourceversion */
+      sourceVersion: string;
+    };
     /**
      * code
      * @description Indicates that the value is taken from a set of controlled strings defined elsewhere. Technically, a code is restricted to a string which has at least one character and no leading or  trailing whitespace, and where there is no whitespace other than single spaces in the contents.
@@ -12538,11 +12637,19 @@ export interface operations {
     };
   };
   /**
-   * Fetch variant by URN
-   * @description Fetch a single variant by URN.
+   * Fetch assayed variant detail by URN
+   * @description Fetch the two-tier detail envelope for a single assayed variant by URN.
+   *
+   * Flat assay-level fields for the common UI case plus the spec-pure GA4GH CategoricalVariant and a
+   * digest-keyed annotation map for machine/standard consumers. A superseded variant is served (it is
+   * the citable unit) but self-describes via isCurrent/supersededBy rather than reading as current.
    */
   get_variant_api_v1_variants__urn__get: {
     parameters: {
+      query?: {
+        /** @description Reconstruct the molecular layer (Cat-VRS membership, VEP/gnomAD/ClinVar annotations) as it stood at this instant, over the variant's fixed score. ISO 8601, ideally timezone-aware. Content valid-time only — it never re-selects a score-set version, and scores/classifications are as-of-invariant. Defaults to current. */
+        as_of?: string | null;
+      };
       header?: {
         "x-active-roles"?: string | null;
       };
@@ -12554,7 +12661,7 @@ export interface operations {
       /** @description Successful Response */
       200: {
         content: {
-          "application/json": components["schemas"]["VariantEffectMeasurementWithScoreSet"];
+          "application/json": components["schemas"]["VariantDetail"];
         };
       };
       /** @description Authentication required. */

From d1a6cd5500d82934c7e4ed8e2d01a83085b2c099 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Tue, 7 Jul 2026 14:12:56 -0700
Subject: [PATCH 04/84] refactor(variant): rename supersededBy to
 supersededByScoreSet

Match the API field rename: the detail panel reads the superseding *score set*'s URN
(supersession is score-set-versioned), not a variant URN, and the tooltip now reads
"Superseded by score set X". Update the generated VariantDetail type to match. The /alleles/*
schema regen in openapi.d.ts is deliberately left for the alleles-slice work.
---
 src/components/variant/VariantDetailPanel.vue |  4 ++--
 src/schema/openapi.d.ts                       | 14 +++++++++-----
 2 files changed, 11 insertions(+), 7 deletions(-)

diff --git a/src/components/variant/VariantDetailPanel.vue b/src/components/variant/VariantDetailPanel.vue
index 18b67627..fd96bcdb 100644
--- a/src/components/variant/VariantDetailPanel.vue
+++ b/src/components/variant/VariantDetailPanel.vue
@@ -224,8 +224,8 @@ export default defineComponent({
       return `${acmg.criterion}_${acmg.evidenceStrength.toUpperCase()}`
     },
     supersededTooltip(): string {
-      return this.detail?.supersededBy
-        ? `Superseded by ${this.detail.supersededBy}`
+      return this.detail?.supersededByScoreSet
+        ? `Superseded by score set ${this.detail.supersededByScoreSet}`
         : 'This measurement has been superseded by a newer version.'
     }
   },
diff --git a/src/schema/openapi.d.ts b/src/schema/openapi.d.ts
index 5a843c2e..89c11931 100644
--- a/src/schema/openapi.d.ts
+++ b/src/schema/openapi.d.ts
@@ -1342,7 +1342,7 @@ export interface paths {
      *
      * Flat assay-level fields for the common UI case plus the spec-pure GA4GH CategoricalVariant and a
      * digest-keyed annotation map for machine/standard consumers. A superseded variant is served (it is
-     * the citable unit) but self-describes via isCurrent/supersededBy rather than reading as current.
+     * the citable unit) but self-describes via isCurrent/supersededByScoreSet rather than reading as current.
      */
     get: operations["get_variant_api_v1_variants__urn__get"];
   };
@@ -5811,7 +5811,11 @@ export interface components {
      * is a client-side toggle, no refetch) plus the spec-pure GA4GH ``molecularRepresentation``
      * (``CategoricalVariant``, no MaveDB fields inside). The MaveDB layer rides alongside keyed by VRS
      * digest: ``memberRelations`` (member→defining relation) and the ``annotations`` map. ``isCurrent``
-     * /``supersededBy`` let a superseded variant self-describe. Absent fields are omitted.
+     * /``supersededByScoreSet`` let a superseded variant self-describe: ``supersededByScoreSet`` is the
+     * superseding *score set*'s URN, not a variant URN. Supersession is versioned at the score-set level,
+     * and a newer version may add, drop, or renumber variants — so there is no stable
+     * superseding-*variant* pointer to hand back; a consumer resolves the current measurement by looking
+     * this variant up within that score set. Absent fields are omitted.
      */
     VariantDetail: {
       /** Urn */
@@ -5855,8 +5859,8 @@ export interface components {
       };
       /** Iscurrent */
       isCurrent: boolean;
-      /** Supersededby */
-      supersededBy?: string | null;
+      /** Supersededbyscoreset */
+      supersededByScoreSet?: string | null;
     };
     /**
      * VariantDiagnosticProposition
@@ -12642,7 +12646,7 @@ export interface operations {
    *
    * Flat assay-level fields for the common UI case plus the spec-pure GA4GH CategoricalVariant and a
    * digest-keyed annotation map for machine/standard consumers. A superseded variant is served (it is
-   * the citable unit) but self-describes via isCurrent/supersededBy rather than reading as current.
+   * the citable unit) but self-describes via isCurrent/supersededByScoreSet rather than reading as current.
    */
   get_variant_api_v1_variants__urn__get: {
     parameters: {

From 8bfdb2125644f29ec0c92f7d52e65aa8d61882fa Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 9 Jul 2026 10:52:10 -0700
Subject: [PATCH 05/84] feat(calibrations): implement request deduplication for
 score calibration variants

---
 src/api/mavedb/calibrations.ts | 26 +++++++++++++++++++++-----
 1 file changed, 21 insertions(+), 5 deletions(-)

diff --git a/src/api/mavedb/calibrations.ts b/src/api/mavedb/calibrations.ts
index 9355daa0..8ebbf4f8 100644
--- a/src/api/mavedb/calibrations.ts
+++ b/src/api/mavedb/calibrations.ts
@@ -98,16 +98,32 @@ export async function getScoreCalibrationClassificationVariants(
   return response.data
 }
 
+// In-flight requests for calibration variants, keyed by calibration URN. The variant page fetches these
+// from two independent consumers (the classification resolver and the histogram) at the same time; sharing
+// the pending request collapses the duplicate. Not a resolved-result cache — calibration edits flow through
+// this client, so a settled request is dropped and later reads go to the network fresh.
+const inFlightCalibrationVariants = new Map<
+  string,
+  Promise<components['schemas']['FunctionalClassificationVariants'][]>
+>()
+
 /**
- * Fetch variants for all functional classifications in a score calibration.
+ * Fetch variants for all functional classifications in a score calibration. Concurrent callers for the same
+ * calibration share one request.
  */
 export async function getScoreCalibrationVariants(
   calibrationUrn: string
 ): Promise<components['schemas']['FunctionalClassificationVariants'][]> {
-  const response = await axios.get(
-    `${config.apiBaseUrl}/score-calibrations/${encodeURIComponent(calibrationUrn)}/variants`
-  )
-  return response.data
+  const existing = inFlightCalibrationVariants.get(calibrationUrn)
+  if (existing) return existing
+  const promise = axios
+    .get(`${config.apiBaseUrl}/score-calibrations/${encodeURIComponent(calibrationUrn)}/variants`)
+    .then((response) => response.data)
+    .finally(() => {
+      if (inFlightCalibrationVariants.get(calibrationUrn) === promise) inFlightCalibrationVariants.delete(calibrationUrn)
+    })
+  inFlightCalibrationVariants.set(calibrationUrn, promise)
+  return promise
 }
 
 /**

From d0cdac4a0c57216c39a848fc8274445cf081dcff Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 9 Jul 2026 10:53:12 -0700
Subject: [PATCH 06/84] refactor(score-sets): add limit param to preview
 fetches, drop histogram url helper

- Support an optional `limit` on getScoreSetScoresPreview and
  getScoreSetCountsPreview so the preview table fetches only the rows it
  renders instead of the full dataset; document that `drop_na_columns`
  is evaluated over the sampled rows
- Remove the now-unused histogramScoreSetVariantDataUrl helper and its
  scoreSetVariantDataParams/namespace constant
---
 src/api/mavedb/score-sets.ts | 34 ++++++++++++----------------------
 1 file changed, 12 insertions(+), 22 deletions(-)

diff --git a/src/api/mavedb/score-sets.ts b/src/api/mavedb/score-sets.ts
index 6d97bb28..8ecc0216 100644
--- a/src/api/mavedb/score-sets.ts
+++ b/src/api/mavedb/score-sets.ts
@@ -8,30 +8,12 @@ type ScoreSetSearch = components['schemas']['ScoreSetsSearch']
 type ScoreSetsSearchResponse = components['schemas']['ScoreSetsSearchResponse']
 export type ScoreSetsSearchFilterOptionsResponse = components['schemas']['ScoreSetsSearchFilterOptionsResponse']
 
-const HISTOGRAM_VARIANT_DATA_NAMESPACES = ['vep', 'scores', 'clingen']
-
-function scoreSetVariantDataParams(
-  options: {includePostMappedHgvs?: boolean; namespaces?: string[]} = {}
-): URLSearchParams {
-  const params = new URLSearchParams()
-  if (options.includePostMappedHgvs) params.append('include_post_mapped_hgvs', 'true')
-  for (const namespace of options.namespaces ?? []) params.append('namespaces', namespace)
-  return params
-}
-
 function scoreSetVariantDataUrl(urn: string, params: URLSearchParams = new URLSearchParams()): string {
   const query = params.toString()
   const baseUrl = `${config.apiBaseUrl}/score-sets/${encodeURIComponent(urn)}/variants/data`
   return query ? `${baseUrl}?${query}` : baseUrl
 }
 
-export function histogramScoreSetVariantDataUrl(urn: string): string {
-  return scoreSetVariantDataUrl(
-    urn,
-    scoreSetVariantDataParams({includePostMappedHgvs: true, namespaces: HISTOGRAM_VARIANT_DATA_NAMESPACES})
-  )
-}
-
 // ---------------------------------------------------------------------------
 // Lean whole-set variant view (GET /score-sets/{urn}/variants)
 // ---------------------------------------------------------------------------
@@ -139,16 +121,24 @@ export async function downloadScoreSetVariantData(urn: string, params: URLSearch
   return response.data
 }
 
-export async function getScoreSetScoresPreview(urn: string): Promise<string> {
+// The preview table renders only a handful of rows, so it passes `limit` to fetch just those rather
+// than the whole dataset. Note: `drop_na_columns` is evaluated over the returned rows, so with a limit
+// the shown column set reflects the sampled rows (fine for a preview; the download buttons fetch the
+// full, unlimited file).
+export async function getScoreSetScoresPreview(urn: string, limit?: number): Promise<string> {
+  const params = new URLSearchParams({drop_na_columns: 'true'})
+  if (limit != null) params.append('limit', String(limit))
   const response = await axios.get(
-    `${config.apiBaseUrl}/score-sets/${encodeURIComponent(urn)}/scores?drop_na_columns=true`
+    `${config.apiBaseUrl}/score-sets/${encodeURIComponent(urn)}/scores?${params.toString()}`
   )
   return response.data
 }
 
-export async function getScoreSetCountsPreview(urn: string): Promise<string> {
+export async function getScoreSetCountsPreview(urn: string, limit?: number): Promise<string> {
+  const params = new URLSearchParams({drop_na_columns: 'true'})
+  if (limit != null) params.append('limit', String(limit))
   const response = await axios.get(
-    `${config.apiBaseUrl}/score-sets/${encodeURIComponent(urn)}/counts?drop_na_columns=true`
+    `${config.apiBaseUrl}/score-sets/${encodeURIComponent(urn)}/counts?${params.toString()}`
   )
   return response.data
 }

From 081e836d0d477c811001d52d3219ba9f539c10e6 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 9 Jul 2026 11:25:59 -0700
Subject: [PATCH 07/84] feat(tooltips): add optional variant urn to variant
 details link

Pass the variant's URN as a query param on the ClinGen variant-details
link so the destination page can disambiguate which variant to show
when a single ClinGen allele maps to multiple variants.
---
 src/lib/tooltips.ts | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/lib/tooltips.ts b/src/lib/tooltips.ts
index 255a3c3a..d9748e92 100644
--- a/src/lib/tooltips.ts
+++ b/src/lib/tooltips.ts
@@ -52,8 +52,9 @@ export function tooltipLink(href: string, text: string): string {
 }
 
 /** ClinGen variant-details link — shared by both charts. */
-export function tooltipVariantDetailsLink(clingenAlleleId: string): string {
-  return tooltipLink(`/variants/${clingenAlleleId}`, 'View variant details')
+export function tooltipVariantDetailsLink(clingenAlleleId: string, variantUrn?: string | null): string {
+  const query = variantUrn ? `?variant=${encodeURIComponent(variantUrn)}` : ''
+  return tooltipLink(`/variants/${clingenAlleleId}${query}`, 'View variant details')
 }
 
 /** A round color swatch, used to tie series/legend colors to their labels. */

From eb628406dfb1c7d3fc3761e727bf9f3e35217890 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 9 Jul 2026 11:31:22 -0700
Subject: [PATCH 08/84] feat(assay-facts-card): add urn display and assay level
 row

- Show the score set URN under its title when showUrn is set, so
  correlated score sets with identical facts can be told apart
- Add an "Assay level" detail row driven by a new assayLevel prop,
  surfacing the score-set-wide protein/cdna/genomic measurement level
- Scope the 2-col top-border reset to the new assay-facts-grid--2col
  class so the 1-col layout keeps a divider between every stacked row
---
 src/components/common/MvAssayFactsCard.vue | 17 ++++++++++++++---
 1 file changed, 14 insertions(+), 3 deletions(-)

diff --git a/src/components/common/MvAssayFactsCard.vue b/src/components/common/MvAssayFactsCard.vue
index 2e6719ff..88071373 100644
--- a/src/components/common/MvAssayFactsCard.vue
+++ b/src/components/common/MvAssayFactsCard.vue
@@ -12,6 +12,8 @@
         </router-link>
         <span v-else>{{ getScoreSetShortName(scoreSet) }}</span>
       </div>
+      <!-- URN disambiguates correlated score sets whose title/facts read identically across measurements. -->
+      <div v-if="showUrn && scoreSet.urn" class="mt-0.5 font-mono text-xs text-text-muted">{{ scoreSet.urn }}</div>
       <div v-if="geneName || scoreSet.numVariants" class="text-sm text-text-muted">
         <template v-if="geneName">{{ geneName }}</template>
         <template v-if="geneName && scoreSet.numVariants"> &middot; </template>
@@ -31,6 +33,7 @@
         :value="getKeyword('Phenotypic Assay Mechanism')"
       />
       <MvDetailRow fallback="Not specified" label="Model system" :value="getKeyword('Phenotypic Assay Model System')" />
+      <MvDetailRow fallback="Not mapped" label="Assay level" :value="assayLevelLabel" />
       <MvDetailRow fallback="Not specified" label="Detects splicing?">
         <span
           v-if="detectsSplicing != null"
@@ -80,6 +83,7 @@ import {
   getPrimaryCalibration
 } from '@/lib/calibrations'
 import {getExperimentKeyword} from '@/lib/experiments'
+import {ASSAY_LEVEL_LABELS} from '@/lib/measurement-types'
 import {getScoreSetShortName} from '@/lib/score-sets'
 import {components} from '@/schema/openapi'
 
@@ -97,16 +101,22 @@ export default defineComponent({
   },
 
   props: {
+    // The measured assay level (protein / cdna / genomic) — score-set-wide, shared across its variants.
+    assayLevel: {type: String as PropType<keyof typeof ASSAY_LEVEL_LABELS | null>, default: null},
     columns: {type: Number as PropType<1 | 2>, default: 2},
     linkTitle: {type: Boolean, default: true},
+    showUrn: {type: Boolean, default: false},
     scoreSet: {type: Object as PropType<ScoreSet>, default: null},
     variantUrn: {type: String, default: null}
   },
 
   computed: {
+    assayLevelLabel(): string | null {
+      return this.assayLevel ? (ASSAY_LEVEL_LABELS[this.assayLevel] ?? null) : null
+    },
     gridClass(): string {
       return this.columns === 2
-        ? 'assay-facts-grid grid grid-cols-1 gap-x-8 tablet:grid-cols-2'
+        ? 'assay-facts-grid assay-facts-grid--2col grid grid-cols-1 gap-x-8 tablet:grid-cols-2'
         : 'assay-facts-grid grid grid-cols-1 gap-x-8'
     },
     geneName(): string | null {
@@ -181,9 +191,10 @@ export default defineComponent({
 </script>
 
 <style scoped>
-/* In 2-col grid, the 2nd item is first in the right column — remove its inherited top border */
+/* In 2-col grid, the 2nd item is first in the right column — remove its inherited top border. Scoped to
+   the 2-col variant so the 1-col layout keeps its divider between every stacked row. */
 @media (min-width: 56rem) {
-  .assay-facts-grid > :nth-child(2) {
+  .assay-facts-grid--2col > :nth-child(2) {
     border-top: none;
   }
 }

From d39add0b63c6e433a3b47b86354359431ff9a72d Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 9 Jul 2026 11:35:44 -0700
Subject: [PATCH 09/84] perf(variant-preview): fetch only preview rows from the
 api

- Pass MAX_ROWS as a limit to the scores/counts preview requests
  instead of fetching the full dataset and slicing client-side
- Derive the "Showing X of Y" total from the score set's numVariants
  rather than the now-truncated fetched rows, since the fetch no
  longer returns the true total
---
 src/components/common/MvVariantPreview.vue | 21 +++++++++++----------
 1 file changed, 11 insertions(+), 10 deletions(-)

diff --git a/src/components/common/MvVariantPreview.vue b/src/components/common/MvVariantPreview.vue
index 85fd7762..6d1bf442 100644
--- a/src/components/common/MvVariantPreview.vue
+++ b/src/components/common/MvVariantPreview.vue
@@ -3,8 +3,8 @@
     <div class="flex flex-wrap items-center justify-between gap-3 border-b border-border-light px-4 py-3.5 tablet:px-5">
       <h3 class="mave-section-title">
         Variants preview
-        <span v-if="scoreSet.numVariants" class="font-normal text-text-muted">
-          ({{ scoreSet.numVariants.toLocaleString() }})
+        <span v-if="scoreSet.numVariants" class="font-normal text-xs text-text-muted lowercase">
+          ({{ scoreSet.numVariants.toLocaleString() }} total variants)
         </span>
       </h3>
       <div class="flex flex-wrap items-center gap-2">
@@ -54,9 +54,7 @@
       <div v-if="scoresRows.length > 0">
         <div class="flex items-center justify-between border-b border-border-light bg-bg px-4 py-2 tablet:px-5">
           <span class="text-xs font-semibold uppercase tracking-wider text-text-muted">Scores</span>
-          <span class="text-xs text-text-muted">
-            Showing {{ scoresRows.length }} of {{ scoresData.length.toLocaleString() }}
-          </span>
+          <span class="text-xs text-text-muted"> Showing {{ scoresRows.length }} of {{ totalLabel }} </span>
         </div>
         <div class="overflow-x-auto">
           <table class="variant-table w-full">
@@ -85,9 +83,7 @@
           class="flex items-center justify-between border-b border-border-light border-t bg-bg px-4 py-2 tablet:px-5"
         >
           <span class="text-xs font-semibold uppercase tracking-wider text-text-muted">Counts</span>
-          <span class="text-xs text-text-muted">
-            Showing {{ countsRows.length }} of {{ countsData.length.toLocaleString() }}
-          </span>
+          <span class="text-xs text-text-muted"> Showing {{ countsRows.length }} of {{ totalLabel }} </span>
         </div>
         <div class="overflow-x-auto">
           <table class="variant-table w-full">
@@ -187,6 +183,11 @@ export default defineComponent({
     hasCountData(): boolean {
       return this.countColumns.some((col) => !TEXT_COLUMNS.includes(col))
     },
+    // The preview fetches only MAX_ROWS, so the true total comes from the score set's variant count
+    // rather than the (truncated) fetched rows.
+    totalLabel(): string {
+      return (this.scoreSet.numVariants ?? this.scoresData.length).toLocaleString()
+    },
     scoresRows(): ScoresOrCountsRow[] {
       return this.scoresData.slice(0, MAX_ROWS)
     },
@@ -233,8 +234,8 @@ export default defineComponent({
       this.loading = true
       try {
         const [scoresRaw, countsRaw] = await Promise.all([
-          getScoreSetScoresPreview(this.scoreSet.urn),
-          getScoreSetCountsPreview(this.scoreSet.urn).catch(() => null)
+          getScoreSetScoresPreview(this.scoreSet.urn, MAX_ROWS),
+          getScoreSetCountsPreview(this.scoreSet.urn, MAX_ROWS).catch(() => null)
         ])
         this.scoresData = scoresRaw ? parseScoresOrCounts(scoresRaw, false) : []
         this.countsData = countsRaw ? parseScoresOrCounts(countsRaw, false) : []

From 7c93292d26803f102d5cc3ceb046aefe686659be Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 9 Jul 2026 11:41:00 -0700
Subject: [PATCH 10/84] fix(variants): use mapped protein hgvs instead of
 removed field

proteinConsequenceBlock referenced variant.proteinLevelHgvs, a field
that no longer exists on DisplayVariant; fall back through
variant.mapped.protein (the mapped protein representation) before
the submitted protein HGVS, matching the documented fallback order.
---
 src/lib/variants.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/lib/variants.ts b/src/lib/variants.ts
index 8e1c1ac3..5d057501 100644
--- a/src/lib/variants.ts
+++ b/src/lib/variants.ts
@@ -423,7 +423,7 @@ function translateSimpleCodingHgvsCVariant(
  * absent: the mapped protein representation preferred, falling back to the submitted protein HGVS.
  */
 function proteinConsequenceBlock(variant: DisplayVariant): HgvsField | null {
-  return variant.proteinLevelHgvs ?? variant.hgvsPro ?? null
+  return variant.mapped?.protein ?? variant.hgvsPro ?? null
 }
 
 /**

From 64b4c81fce73138d73f3c1c972def2c6a8e1e86f Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 9 Jul 2026 12:00:03 -0700
Subject: [PATCH 11/84] feat(measurement-types): add assay-level bucketing and
 rt labels

- Replace MeasurementType (nucleotide/protein/associatedNucleotide)
  with a two-way LevelBucket (nucleotide/protein) derived from the
  mapping record's AssayLevel, since cdna and genomic share one
  visual bucket
- Add assayLevelBucket() to bucket a raw assay level, and
  dominantAssayLevel() to pick the most common non-null level across
  a score set's variants
- Add ASSAY_LEVEL_LABELS for the three per-level labels and
  RELATIONSHIP_LABELS for the RT direct/protein_consequence/
  nucleotide_encoding relationship display strings
- Add unit tests covering bucketing and dominant-level selection,
  including ties and all-null/undefined inputs
---
 src/lib/measurement-types.test.ts | 55 +++++++++++++++++++++++++++++++
 src/lib/measurement-types.ts      | 54 ++++++++++++++++++++++++++----
 2 files changed, 102 insertions(+), 7 deletions(-)
 create mode 100644 src/lib/measurement-types.test.ts

diff --git a/src/lib/measurement-types.test.ts b/src/lib/measurement-types.test.ts
new file mode 100644
index 00000000..6c1f768c
--- /dev/null
+++ b/src/lib/measurement-types.test.ts
@@ -0,0 +1,55 @@
+import {describe, expect, it} from 'vitest'
+
+import {assayLevelBucket, dominantAssayLevel} from '@/lib/measurement-types'
+
+describe('assayLevelBucket', () => {
+  it('returns "protein" for protein', () => {
+    expect(assayLevelBucket('protein')).toBe('protein')
+  })
+
+  it('returns "nucleotide" for cdna', () => {
+    expect(assayLevelBucket('cdna')).toBe('nucleotide')
+  })
+
+  it('returns "nucleotide" for genomic', () => {
+    expect(assayLevelBucket('genomic')).toBe('nucleotide')
+  })
+
+  it('returns "nucleotide" for null', () => {
+    expect(assayLevelBucket(null)).toBe('nucleotide')
+  })
+
+  it('returns "nucleotide" for undefined', () => {
+    expect(assayLevelBucket(undefined)).toBe('nucleotide')
+  })
+})
+
+describe('dominantAssayLevel', () => {
+  it('returns the most common non-null level', () => {
+    expect(dominantAssayLevel(['cdna', 'protein', 'cdna'])).toBe('cdna')
+  })
+
+  it('returns the most common level when all levels are the same', () => {
+    expect(dominantAssayLevel(['protein', 'protein', 'protein'])).toBe('protein')
+  })
+
+  it('returns the first level when there is a tie', () => {
+    expect(dominantAssayLevel(['cdna', 'protein', 'cdna', 'protein'])).toBe('cdna')
+  })
+
+  it('returns null when no levels are provided', () => {
+    expect(dominantAssayLevel([])).toBeNull()
+  })
+
+  it('returns null when all levels are null', () => {
+    expect(dominantAssayLevel([null, null])).toBeNull()
+  })
+
+  it('returns null when all levels are undefined', () => {
+    expect(dominantAssayLevel([undefined, undefined])).toBeNull()
+  })
+
+  it('ignores null and undefined levels', () => {
+    expect(dominantAssayLevel(['cdna', null, 'protein', undefined, 'cdna'])).toBe('cdna')
+  })
+})
diff --git a/src/lib/measurement-types.ts b/src/lib/measurement-types.ts
index 2d41bf07..a271b6c7 100644
--- a/src/lib/measurement-types.ts
+++ b/src/lib/measurement-types.ts
@@ -1,13 +1,53 @@
-export type MeasurementType = 'nucleotide' | 'protein' | 'associatedNucleotide'
+import type {components} from '@/schema/openapi'
 
-export const MEASUREMENT_TYPE_LABELS: Record<MeasurementType, {full: string; short: string}> = {
+// The assayed level of a measurement (from the mapping record). The two nucleotide levels share one
+// visual bucket; protein is its own.
+export type AssayLevel = components['schemas']['AnnotationLayer'] // 'protein' | 'cdna' | 'genomic'
+export type MeasurementRelationship = components['schemas']['MeasurementRelationship']
+export type LevelBucket = 'nucleotide' | 'protein'
+
+export function assayLevelBucket(level: string | null | undefined): LevelBucket {
+  return level === 'protein' ? 'protein' : 'nucleotide'
+}
+
+// Per-level display labels for the three assay levels (distinct from the two-way bucket labels above).
+export const ASSAY_LEVEL_LABELS: Record<AssayLevel, string> = {
+  genomic: 'Genomic',
+  cdna: 'Coding',
+  protein: 'Protein'
+}
+
+// A score set's variants are all assayed at one level, but some may be unmapped (null). Return the most
+// common non-null level, or null when nothing is mapped.
+export function dominantAssayLevel(levels: Array<AssayLevel | null | undefined>): AssayLevel | null {
+  const counts = new Map<AssayLevel, number>()
+  for (const level of levels) {
+    if (level) counts.set(level, (counts.get(level) ?? 0) + 1)
+  }
+  let best: AssayLevel | null = null
+  let bestCount = 0
+  for (const [level, count] of counts) {
+    if (count > bestCount) {
+      best = level
+      bestCount = count
+    }
+  }
+  return best
+}
+
+export const LEVEL_BUCKET_LABELS: Record<LevelBucket, {full: string; short: string}> = {
   nucleotide: {full: 'Nucleotide level', short: 'Nucleotide'},
-  protein: {full: 'Protein level', short: 'Protein'},
-  associatedNucleotide: {full: 'Synonymous nucleotide', short: 'Synonymous'}
+  protein: {full: 'Protein level', short: 'Protein'}
 }
 
-export const MEASUREMENT_TYPE_CLASSES: Record<MeasurementType, string> = {
+export const LEVEL_BUCKET_CLASSES: Record<LevelBucket, string> = {
   nucleotide: 'bg-nucleotide-light text-nucleotide',
-  protein: 'bg-protein-light text-protein',
-  associatedNucleotide: 'bg-synonymous-nucleotide-light text-synonymous-nucleotide'
+  protein: 'bg-protein-light text-protein'
+}
+
+// How a measurement relates to the queried ClinGen allele — the RT asymmetry.
+export const RELATIONSHIP_LABELS: Record<MeasurementRelationship, string> = {
+  direct: 'Direct measurement',
+  protein_consequence: 'Protein consequence',
+  nucleotide_encoding: 'Nucleotide encoding'
 }

From e883e629fb029795f48f604e1ea001e6370c1a14 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 9 Jul 2026 15:46:06 -0700
Subject: [PATCH 12/84] feat(api): add ttl-cached read wrapper for deduped gets

Add memoizeRead, a p-memoize/expiry-map wrapper that dedupes
concurrent calls to the same idempotent GET and caches the result
for a short TTL. Read data can be rewritten underneath us at any
time by the mapping/annotation worker, so the cache is tuned to
collapse page-load request bursts rather than to reuse results
long-term; a 30s default TTL bounds staleness while composables
still handle same-page reuse via their own reactive caches.
---
 src/api/cache.ts | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100644 src/api/cache.ts

diff --git a/src/api/cache.ts b/src/api/cache.ts
new file mode 100644
index 00000000..56f97604
--- /dev/null
+++ b/src/api/cache.ts
@@ -0,0 +1,34 @@
+import pMemoize from 'p-memoize'
+import ExpiryMap from 'expiry-map'
+
+/**
+ * Default TTL for cached reads — deliberately short.
+ *
+ * Nearly all of our read data is mutable: the mapping/annotation worker rewrites the layer underneath even
+ * "published" score sets, variants, and allele equivalence classes, and it registers/enriches ClinGen
+ * alleles. So this cache is dedup-focused, not reuse-focused — its real job is collapsing the page-load
+ * request burst (the composables already handle same-page reuse via their own reactive caches). 30s covers
+ * that burst plus rapid interaction while bounding worker-driven staleness to well under a minute. Pass a
+ * longer `ttlMs` only for data that is genuinely immutable by cache key (e.g. content-addressed lookups).
+ */
+export const READ_CACHE_TTL_MS = 30 * 1000 // 30 seconds
+
+/**
+ * Wrap a promise-returning read with request deduplication + a TTL cache.
+ *
+ * Concurrent callers for the same key share one in-flight request; a resolved value is reused until it
+ * expires. Rejected requests are dropped from the cache (retried on the next call), so a transient failure
+ * never sticks. Only use for idempotent GETs whose results this client does not itself mutate — a resource
+ * edited through this app would serve stale data for up to the TTL.
+ */
+// eslint-disable-next-line @typescript-eslint/no-explicit-any -- mirror p-memoize's own function constraint; returning Fn verbatim preserves optional params
+export function memoizeRead<Fn extends (...args: any[]) => Promise<unknown>>(
+  fn: Fn,
+  cacheKey: (...args: Parameters<Fn>) => string,
+  ttlMs: number = READ_CACHE_TTL_MS
+): Fn {
+  return pMemoize(fn, {
+    cache: new ExpiryMap(ttlMs),
+    cacheKey: (args) => cacheKey(...args)
+  })
+}

From 5bd5e3b13e8974fd4cc405ec5822012d02463687 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 9 Jul 2026 15:46:42 -0700
Subject: [PATCH 13/84] fixup

---
 package-lock.json | 123 +++++++++++++++++++++++++++++++++++++++++++---
 package.json      |   3 ++
 2 files changed, 118 insertions(+), 8 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index d3fc69d7..174d8f9f 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -36,6 +36,7 @@
         "datatables.net-select": "1.4.0",
         "datatables.net-select-dt": "1.4.0",
         "dompurify": "^3.4.11",
+        "expiry-map": "^2.0.0",
         "fasta-js": "^1.0.1",
         "indefinite": "^2.4.3",
         "jquery": "^3.7.1",
@@ -48,6 +49,8 @@
         "lodash": "^4.18.1",
         "marked": "^11.1.0",
         "moment": "^2.29.4",
+        "p-limit": "^7.3.0",
+        "p-memoize": "^8.0.0",
         "papaparse": "^5.4.1",
         "pdbe-molstar": "^3.4.0",
         "pdfmake": "^0.2.8",
@@ -5085,6 +5088,18 @@
         "node": ">=12.0.0"
       }
     },
+    "node_modules/expiry-map": {
+      "version": "2.0.0",
+      "resolved": "https://registry.npmjs.org/expiry-map/-/expiry-map-2.0.0.tgz",
+      "integrity": "sha512-K1I5wJe2fiqjyUZf/xhxwTpaopw3F+19DsO7Oggl20+3SVTXDIevVRJav0aBMfposQdkl2E4+gnuOKd3j2X0sA==",
+      "license": "MIT",
+      "dependencies": {
+        "map-age-cleaner": "^0.2.0"
+      },
+      "engines": {
+        "node": ">=8"
+      }
+    },
     "node_modules/express": {
       "version": "4.22.2",
       "resolved": "https://registry.npmjs.org/express/-/express-4.22.2.tgz",
@@ -6876,6 +6891,18 @@
         "url": "https://github.com/sponsors/sindresorhus"
       }
     },
+    "node_modules/map-age-cleaner": {
+      "version": "0.2.0",
+      "resolved": "https://registry.npmjs.org/map-age-cleaner/-/map-age-cleaner-0.2.0.tgz",
+      "integrity": "sha512-AvxTC6id0fzSf6OyNBTp1syyCuKO7nOJvHgYlhT0Qkkjvk40zZo+av3ayVgXlxnF/DxEzEfY9mMdd7FHsd+wKQ==",
+      "license": "MIT",
+      "dependencies": {
+        "p-defer": "^1.0.0"
+      },
+      "engines": {
+        "node": ">=7.6"
+      }
+    },
     "node_modules/marked": {
       "version": "11.1.0",
       "license": "MIT",
@@ -7604,6 +7631,18 @@
         "node": ">= 0.6"
       }
     },
+    "node_modules/mimic-function": {
+      "version": "5.0.1",
+      "resolved": "https://registry.npmjs.org/mimic-function/-/mimic-function-5.0.1.tgz",
+      "integrity": "sha512-VP79XUPxV2CigYP3jWwAUFSku2aKqBH7uTAapFWCBqutsbmDo96KY5o8uh6U+/YSIn5OxJnXp73beVkpqMIGhA==",
+      "license": "MIT",
+      "engines": {
+        "node": ">=18"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/sindresorhus"
+      }
+    },
     "node_modules/minimalistic-assert": {
       "version": "1.0.1",
       "license": "ISC"
@@ -7974,15 +8013,25 @@
         "url": "https://github.com/sponsors/ljharb"
       }
     },
+    "node_modules/p-defer": {
+      "version": "1.0.0",
+      "resolved": "https://registry.npmjs.org/p-defer/-/p-defer-1.0.0.tgz",
+      "integrity": "sha512-wB3wfAxZpk2AzOfUMJNL+d36xothRSyj8EXOa4f6GMqYDN9BJaaSISbsk+wS9abmnebVw95C2Kb5t85UmpCxuw==",
+      "license": "MIT",
+      "engines": {
+        "node": ">=4"
+      }
+    },
     "node_modules/p-limit": {
-      "version": "3.1.0",
-      "dev": true,
+      "version": "7.3.0",
+      "resolved": "https://registry.npmjs.org/p-limit/-/p-limit-7.3.0.tgz",
+      "integrity": "sha512-7cIXg/Z0M5WZRblrsOla88S4wAK+zOQQWeBYfV3qJuJXMr+LnbYjaadrFaS0JILfEDPVqHyKnZ1Z/1d6J9VVUw==",
       "license": "MIT",
       "dependencies": {
-        "yocto-queue": "^0.1.0"
+        "yocto-queue": "^1.2.1"
       },
       "engines": {
-        "node": ">=10"
+        "node": ">=20"
       },
       "funding": {
         "url": "https://github.com/sponsors/sindresorhus"
@@ -8002,6 +8051,63 @@
         "url": "https://github.com/sponsors/sindresorhus"
       }
     },
+    "node_modules/p-locate/node_modules/p-limit": {
+      "version": "3.1.0",
+      "resolved": "https://registry.npmjs.org/p-limit/-/p-limit-3.1.0.tgz",
+      "integrity": "sha512-TYOanM3wGwNGsZN2cVTYPArw454xnXj5qmWF1bEoAc4+cU/ol7GVh7odevjp1FNHduHc3KZMcFduxU5Xc6uJRQ==",
+      "dev": true,
+      "license": "MIT",
+      "dependencies": {
+        "yocto-queue": "^0.1.0"
+      },
+      "engines": {
+        "node": ">=10"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/sindresorhus"
+      }
+    },
+    "node_modules/p-locate/node_modules/yocto-queue": {
+      "version": "0.1.0",
+      "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz",
+      "integrity": "sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q==",
+      "dev": true,
+      "license": "MIT",
+      "engines": {
+        "node": ">=10"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/sindresorhus"
+      }
+    },
+    "node_modules/p-memoize": {
+      "version": "8.0.0",
+      "resolved": "https://registry.npmjs.org/p-memoize/-/p-memoize-8.0.0.tgz",
+      "integrity": "sha512-jdZ10MCxavHoIHwJ5oweOtYy6ElPixEHaMkz0AuaEMovR1MRpVvYFzIEHRxgMEpXYzNpRVByFAniAzwmd1/uug==",
+      "license": "MIT",
+      "dependencies": {
+        "mimic-function": "^5.0.1",
+        "type-fest": "^4.41.0"
+      },
+      "engines": {
+        "node": ">=20"
+      },
+      "funding": {
+        "url": "https://github.com/sindresorhus/p-memoize?sponsor=1"
+      }
+    },
+    "node_modules/p-memoize/node_modules/type-fest": {
+      "version": "4.41.0",
+      "resolved": "https://registry.npmjs.org/type-fest/-/type-fest-4.41.0.tgz",
+      "integrity": "sha512-TeTSQ6H5YHvpqVwBRcnLDCBnDOHWYu7IvGbHT6N8AOymcr9PJGjc1GTtiWZTYg0NCgYwvnYWEkVChQAr9bjfwA==",
+      "license": "(MIT OR CC0-1.0)",
+      "engines": {
+        "node": ">=16"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/sindresorhus"
+      }
+    },
     "node_modules/package-json-from-dist": {
       "version": "1.0.1",
       "resolved": "https://registry.npmjs.org/package-json-from-dist/-/package-json-from-dist-1.0.1.tgz",
@@ -11081,11 +11187,12 @@
       }
     },
     "node_modules/yocto-queue": {
-      "version": "0.1.0",
-      "dev": true,
+      "version": "1.2.2",
+      "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-1.2.2.tgz",
+      "integrity": "sha512-4LCcse/U2MHZ63HAJVE+v71o7yOdIe4cZ70Wpf8D/IyjDKYQLV5GD46B+hSTjJsvV5PztjvHoU580EftxjDZFQ==",
       "license": "MIT",
       "engines": {
-        "node": ">=10"
+        "node": ">=12.20"
       },
       "funding": {
         "url": "https://github.com/sponsors/sindresorhus"
@@ -11122,4 +11229,4 @@
       }
     }
   }
-}
+}
\ No newline at end of file
diff --git a/package.json b/package.json
index 1a04a075..3baf1d53 100644
--- a/package.json
+++ b/package.json
@@ -40,6 +40,7 @@
     "datatables.net-select": "1.4.0",
     "datatables.net-select-dt": "1.4.0",
     "dompurify": "^3.4.11",
+    "expiry-map": "^2.0.0",
     "fasta-js": "^1.0.1",
     "indefinite": "^2.4.3",
     "jquery": "^3.7.1",
@@ -52,6 +53,8 @@
     "lodash": "^4.18.1",
     "marked": "^11.1.0",
     "moment": "^2.29.4",
+    "p-limit": "^7.3.0",
+    "p-memoize": "^8.0.0",
     "papaparse": "^5.4.1",
     "pdbe-molstar": "^3.4.0",
     "pdfmake": "^0.2.8",

From 6baf82935087210706bc2a74ef8176807a6a2efa Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 9 Jul 2026 15:47:14 -0700
Subject: [PATCH 14/84] refactor(api): wrap reads in ttl cache, retire clingen
 lookup endpoint

- Replace lookupVariantsByClingenId (POST clingen-allele-id-lookups)
  with getAlleleMeasurements (GET clingen-alleles/{id}/measurements),
  the new entrypoint for the ClinGen-allele-centric variant page;
  supports includeSuperseded, includeNucleotideSiblings, and asOf
- Wrap getAlleleByCaId, getScoreSet, getLeanScoreSetVariants, and
  getVariantDetail in memoizeRead so repeated reads for the same key
  dedupe and share a short-TTL cache instead of refetching
- Consolidate the duplicated getScoreSet into score-sets.ts and drop
  the copy from calibrations.ts
- Drop getHistogramVariantData now that its only caller is gone
---
 src/api/clingen/alleles.ts     | 13 +++++---
 src/api/mavedb/calibrations.ts |  9 ------
 src/api/mavedb/score-sets.ts   | 27 +++++++++++-----
 src/api/mavedb/variants.ts     | 57 ++++++++++++++++++++--------------
 4 files changed, 62 insertions(+), 44 deletions(-)

diff --git a/src/api/clingen/alleles.ts b/src/api/clingen/alleles.ts
index b67f4a68..23282a04 100644
--- a/src/api/clingen/alleles.ts
+++ b/src/api/clingen/alleles.ts
@@ -1,12 +1,17 @@
 import axios from 'axios'
+
+import {memoizeRead} from '@/api/cache'
 import type {ClinGenAllele, ClinGenGene} from './types'
 
 const CLINGEN_BASE_URL = 'https://reg.genome.network'
 
-export async function getAlleleByCaId(caId: string): Promise<ClinGenAllele> {
-  const response = await axios.get(`${CLINGEN_BASE_URL}/allele/${caId}`)
-  return response.data
-}
+export const getAlleleByCaId = memoizeRead(
+  async (caId: string): Promise<ClinGenAllele> => {
+    const response = await axios.get(`${CLINGEN_BASE_URL}/allele/${caId}`)
+    return response.data
+  },
+  (caId) => caId
+)
 
 export async function getAlleleByHgvs(hgvs: string): Promise<ClinGenAllele> {
   const response = await axios.get(`${CLINGEN_BASE_URL}/allele`, {
diff --git a/src/api/mavedb/calibrations.ts b/src/api/mavedb/calibrations.ts
index 8ebbf4f8..a80f64ca 100644
--- a/src/api/mavedb/calibrations.ts
+++ b/src/api/mavedb/calibrations.ts
@@ -5,7 +5,6 @@ import {components} from '@/schema/openapi'
 import type {MinimalScoreSet} from '@/lib/calibration-types'
 
 type ScoreCalibration = components['schemas']['ScoreCalibration']
-type ScoreSet = components['schemas']['ScoreSet']
 
 /**
  * Fetch a single score calibration by URN.
@@ -137,14 +136,6 @@ export async function searchEditableScoreSets(): Promise<MinimalScoreSet[]> {
   return response.data.scoreSets || []
 }
 
-/**
- * Fetch a single score set by URN (used as fallback when a score set isn't in the editable list).
- */
-export async function getScoreSetByUrn(urn: string): Promise<ScoreSet> {
-  const response = await axios.get(`${config.apiBaseUrl}/score-sets/${encodeURIComponent(urn)}`)
-  return response.data
-}
-
 export async function getMyCalibrations(): Promise<components['schemas']['ScoreCalibrationWithScoreSetUrn'][]> {
   const response = await axios.get(`${config.apiBaseUrl}/score-calibrations/me`, {
     headers: {accept: 'application/json'}
diff --git a/src/api/mavedb/score-sets.ts b/src/api/mavedb/score-sets.ts
index 8ecc0216..a7064211 100644
--- a/src/api/mavedb/score-sets.ts
+++ b/src/api/mavedb/score-sets.ts
@@ -1,13 +1,24 @@
 import axios from 'axios'
 
+import {memoizeRead} from '@/api/cache'
 import config from '@/config'
 import {components} from '@/schema/openapi'
 import type {LeanVariant} from '@/lib/variants'
 
+type ScoreSet = components['schemas']['ScoreSet']
 type ScoreSetSearch = components['schemas']['ScoreSetsSearch']
 type ScoreSetsSearchResponse = components['schemas']['ScoreSetsSearchResponse']
 export type ScoreSetsSearchFilterOptionsResponse = components['schemas']['ScoreSetsSearchFilterOptionsResponse']
 
+/** Fetch a single score set by URN. */
+export const getScoreSet = memoizeRead(
+  async (urn: string): Promise<ScoreSet> => {
+    const response = await axios.get(`${config.apiBaseUrl}/score-sets/${encodeURIComponent(urn)}`)
+    return response.data
+  },
+  (urn) => urn
+)
+
 function scoreSetVariantDataUrl(urn: string, params: URLSearchParams = new URLSearchParams()): string {
   const query = params.toString()
   const baseUrl = `${config.apiBaseUrl}/score-sets/${encodeURIComponent(urn)}/variants/data`
@@ -23,13 +34,15 @@ export function leanScoreSetVariantsUrl(urn: string): string {
 }
 
 /** Fetch the lean whole-set variant view for a score set — one pre-chewed record per variant. */
-export async function getLeanScoreSetVariants(urn: string, signal?: AbortSignal): Promise<LeanVariant[]> {
-  const response = await axios.get(leanScoreSetVariantsUrl(urn), {
-    headers: {accept: 'application/json'},
-    signal
-  })
-  return response.data || []
-}
+export const getLeanScoreSetVariants = memoizeRead(
+  async (urn: string): Promise<LeanVariant[]> => {
+    const response = await axios.get(leanScoreSetVariantsUrl(urn), {
+      headers: {accept: 'application/json'}
+    })
+    return response.data || []
+  },
+  (urn) => urn
+)
 
 // ---------------------------------------------------------------------------
 // Search
diff --git a/src/api/mavedb/variants.ts b/src/api/mavedb/variants.ts
index 1ecc9910..a0441483 100644
--- a/src/api/mavedb/variants.ts
+++ b/src/api/mavedb/variants.ts
@@ -1,22 +1,35 @@
 import axios from 'axios'
 
+import {memoizeRead} from '@/api/cache'
 import config from '@/config'
-import {histogramScoreSetVariantDataUrl} from '@/api/mavedb/score-sets'
 import {components} from '@/schema/openapi'
 
-type ScoreSet = components['schemas']['ScoreSet']
 type VariantDetail = components['schemas']['VariantDetail']
-type ClingenAlleleIdVariantLookupResponse = components['schemas']['ClingenAlleleIdVariantLookupResponse']
+type AlleleMeasurement = components['schemas']['AlleleMeasurement']
 type MappedVariant = components['schemas']['MappedVariant']
 
-export async function lookupVariantsByClingenId(
-  clingenAlleleIds: string[]
-): Promise<ClingenAlleleIdVariantLookupResponse[]> {
-  const response = await axios.post(`${config.apiBaseUrl}/variants/clingen-allele-id-lookups`, {
-    clingenAlleleIds
-  })
-  return response.data
-}
+// The ClinGen-allele-centric variant page's entrypoint: every measurement whose cross-layer
+// equivalence class touches this CAID/PAID, in the API's default order (direct-first). `includeSuperseded`
+// opts in to superseded score-set versions; `includeNucleotideSiblings` (CA only) widens a nucleotide
+// query through its protein consequence to the sibling nt changes — the search discovery path.
+export const getAlleleMeasurements = memoizeRead(
+  async (
+    clingenAlleleId: string,
+    options?: {includeSuperseded?: boolean; includeNucleotideSiblings?: boolean; asOf?: string}
+  ): Promise<AlleleMeasurement[]> => {
+    const params: Record<string, string | boolean> = {}
+    if (options?.includeSuperseded) params.include_superseded = true
+    if (options?.includeNucleotideSiblings) params.include_nucleotide_siblings = true
+    if (options?.asOf) params.as_of = options.asOf
+    const response = await axios.get(
+      `${config.apiBaseUrl}/clingen-alleles/${encodeURIComponent(clingenAlleleId)}/measurements`,
+      {params}
+    )
+    return response.data
+  },
+  (clingenAlleleId, options) =>
+    `${clingenAlleleId}|${options?.includeSuperseded ?? false}|${options?.includeNucleotideSiblings ?? false}|${options?.asOf ?? ''}`
+)
 
 export async function lookupVariantsByVrsDigest(identifier: string): Promise<MappedVariant[]> {
   const response = await axios.get(`${config.apiBaseUrl}/mapped-variants/vrs/${encodeURIComponent(identifier)}`, {
@@ -25,15 +38,15 @@ export async function lookupVariantsByVrsDigest(identifier: string): Promise<Map
   return response.data
 }
 
-export async function getVariantDetail(urn: string): Promise<VariantDetail> {
-  const response = await axios.get(`${config.apiBaseUrl}/variants/${encodeURIComponent(urn)}`)
-  return response.data
-}
-
-export async function getHistogramVariantData(scoreSetUrn: string): Promise<string> {
-  const response = await axios.get(histogramScoreSetVariantDataUrl(scoreSetUrn))
-  return response.data
-}
+export const getVariantDetail = memoizeRead(
+  async (urn: string, options?: {asOf?: string}): Promise<VariantDetail> => {
+    const params: Record<string, string> = {}
+    if (options?.asOf) params.as_of = options.asOf
+    const response = await axios.get(`${config.apiBaseUrl}/variants/${encodeURIComponent(urn)}`, {params})
+    return response.data
+  },
+  (urn, options) => `${urn}|${options?.asOf ?? ''}`
+)
 
 export async function getVariantAnnotation(variantUrn: string, annotationType: string): Promise<unknown> {
   const response = await axios.get(
@@ -43,7 +56,3 @@ export async function getVariantAnnotation(variantUrn: string, annotationType: s
   return response.data
 }
 
-export async function getScoreSet(urn: string): Promise<ScoreSet> {
-  const response = await axios.get(`${config.apiBaseUrl}/score-sets/${encodeURIComponent(urn)}`)
-  return response.data
-}

From 969dacab7822aee50ea9ecb0675459a834385974 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Fri, 10 Jul 2026 12:27:16 -0700
Subject: [PATCH 15/84] feat(allele-grouping): add projection-pair grouping for
 allele display

Add groupAlleles, which collapses a variant detail's allele sidecar
into rendered groups: each c<->g projection pair (linked by
projectionOf) folds into one entry with deduplicated annotations,
while the protein apex and projection-failed candidates stay as
one-member groups. Groups carry a measured/pageRoot/derivation
summary and sort measured-and-page-root entries first, then
bottom-up by level (genomic -> cdna -> protein), so the UI can
render one block per real allele instead of one per c/g/p record.

Add unit tests covering the nucleotide-assay and protein-assay
pairing shapes, divergent-annotation flagging, dangling projectionOf,
the measured-vs-null-relation distinction, and page-anchor CAID
exclusion from surfaced links.
---
 src/lib/allele-grouping.test.ts | 118 ++++++++++++++++++++++++++
 src/lib/allele-grouping.ts      | 141 ++++++++++++++++++++++++++++++++
 2 files changed, 259 insertions(+)
 create mode 100644 src/lib/allele-grouping.test.ts
 create mode 100644 src/lib/allele-grouping.ts

diff --git a/src/lib/allele-grouping.test.ts b/src/lib/allele-grouping.test.ts
new file mode 100644
index 00000000..e1e32aab
--- /dev/null
+++ b/src/lib/allele-grouping.test.ts
@@ -0,0 +1,118 @@
+import {describe, expect, it} from 'vitest'
+
+import {groupAlleles, type GroupAllelesInput} from '@/lib/allele-grouping'
+import type {components} from '@/schema/openapi'
+
+type AlleleIdentity = components['schemas']['AlleleIdentity']
+type AlleleAnnotations = components['schemas']['AlleleAnnotations']
+
+function vep(consequence: string): AlleleAnnotations {
+  return {vep: {consequence}} as AlleleAnnotations
+}
+
+function run(overrides: Partial<GroupAllelesInput>) {
+  return groupAlleles({
+    alleles: {},
+    annotations: {},
+    pageClingenAlleleId: null,
+    ...overrides
+  })
+}
+
+describe('groupAlleles — projection pairing + confidence', () => {
+  // Nucleotide (cdna) assay: the measured cdna folds into its pair's group with its genomic projection;
+  // the protein apex is a deterministic projection, unpaired.
+  const nucleotide: Record<string, AlleleIdentity> = {
+    c: {level: 'cdna', hgvs: 'NM_x:c.6C>T', relation: null, derivation: 'authoritative', projectionOf: 'g'},
+    g: {level: 'genomic', hgvs: 'NC_x:g.100C>T', relation: 'is_genomic_of', derivation: 'projection', projectionOf: 'c'},
+    p: {level: 'protein', hgvs: 'NP_x:p.Leu2Phe', relation: 'translation_of', derivation: 'projection'}
+  }
+
+  it('collapses the measured c↔g pair into one group and keeps the apex separate', () => {
+    const groups = run({alleles: nucleotide})
+    expect(groups).toHaveLength(2)
+
+    const [pair, apex] = groups
+    // Measured pair floats to the top, carries both levels, and is labeled by the authoritative member.
+    expect(pair.measured).toBe(true)
+    expect(pair.derivation).toBe('authoritative')
+    expect(pair.members.map((m) => m.level)).toEqual(['genomic', 'cdna'])
+
+    expect(apex.measured).toBe(false)
+    expect(apex.members).toHaveLength(1)
+    expect(apex.derivation).toBe('projection')
+  })
+
+  // Protein assay: the protein apex is authoritative/measured; the nucleotide fan-out is candidate pairs.
+  const protein: Record<string, AlleleIdentity> = {
+    p: {level: 'protein', hgvs: 'NP_x:p.Leu6Gly', relation: null, derivation: 'authoritative'},
+    c1: {level: 'cdna', hgvs: 'NM_x:c.16C>G', relation: 'encodes', derivation: 'candidate', projectionOf: 'g1'},
+    g1: {level: 'genomic', hgvs: 'NC_x:g.200C>G', relation: 'is_genomic_of', derivation: 'candidate', projectionOf: 'c1'},
+    c2: {level: 'cdna', hgvs: 'NM_x:c.16C>A', relation: 'encodes', derivation: 'candidate', projectionOf: 'g2'},
+    g2: {level: 'genomic', hgvs: 'NC_x:g.200C>A', relation: 'is_genomic_of', derivation: 'candidate', projectionOf: 'c2'}
+  }
+
+  it('keeps the apex measured and collapses each candidate hypothesis into one group', () => {
+    const groups = run({alleles: protein})
+    expect(groups).toHaveLength(3) // apex + 2 candidate pairs
+
+    expect(groups[0].measured).toBe(true) // apex pinned first
+    const candidates = groups.filter((g) => g.derivation === 'candidate')
+    expect(candidates).toHaveLength(2)
+    expect(candidates.every((g) => g.members.length === 2 && !g.measured)).toBe(true)
+  })
+
+  it('flags a projection pair whose annotations diverge instead of hiding the difference', () => {
+    const groups = run({
+      alleles: nucleotide,
+      annotations: {c: vep('missense_variant'), g: vep('intron_variant'), p: vep('missense_variant')}
+    })
+    const pair = groups.find((g) => g.members.length === 2)!
+    expect(pair.annotationsMatch).toBe(false)
+  })
+
+  it('treats a matching pair as one deduplicated block', () => {
+    const groups = run({
+      alleles: nucleotide,
+      annotations: {c: vep('missense_variant'), g: vep('missense_variant')}
+    })
+    const pair = groups.find((g) => g.members.length === 2)!
+    expect(pair.annotationsMatch).toBe(true)
+  })
+
+  it('leaves a projection-failed candidate (dangling projectionOf) as a one-member group', () => {
+    const groups = run({
+      alleles: {
+        p: {level: 'protein', hgvs: 'NP_x:p.Leu6Gly', relation: null, derivation: 'authoritative'},
+        c1: {level: 'cdna', hgvs: 'NM_x:c.16C>G', relation: 'encodes', derivation: 'candidate', projectionOf: 'missing'}
+      }
+    })
+    const candidate = groups.find((g) => g.derivation === 'candidate')!
+    expect(candidate.members).toHaveLength(1)
+  })
+
+  // `measured` keys off derivation === 'authoritative', not relation == null: the defining allele AND any
+  // non-member link both carry relation null, so a null-relation non-authoritative allele must NOT be pinned.
+  it('does not flag a null-relation non-authoritative allele as measured', () => {
+    const groups = run({
+      alleles: {
+        n: {level: 'protein', hgvs: 'NP_x:p.Leu6Gly', relation: null, derivation: 'projection'}
+      }
+    })
+    expect(groups).toHaveLength(1)
+    expect(groups[0].measured).toBe(false)
+  })
+
+  it('surfaces distinct linked CAIDs, excluding the page anchor', () => {
+    const groups = run({
+      alleles: {
+        c: {level: 'cdna', hgvs: 'NM_x:c.6C>T', relation: null, clingenAlleleId: 'CA1', derivation: 'authoritative', projectionOf: 'g'},
+        g: {level: 'genomic', hgvs: 'NC_x:g.100C>T', relation: 'is_genomic_of', clingenAlleleId: 'CA1', derivation: 'projection', projectionOf: 'c'}
+      },
+      pageClingenAlleleId: 'CA1'
+    })
+    // The shared CAID is the page anchor, so no outward link and the group is flagged page-root.
+    expect(groups[0].pageRoot).toBe(true)
+    expect(groups[0].clingenLinks).toEqual([])
+  })
+})
diff --git a/src/lib/allele-grouping.ts b/src/lib/allele-grouping.ts
new file mode 100644
index 00000000..82e58274
--- /dev/null
+++ b/src/lib/allele-grouping.ts
@@ -0,0 +1,141 @@
+import _ from 'lodash'
+
+import type {components} from '@/schema/openapi'
+
+type AlleleIdentity = components['schemas']['AlleleIdentity']
+type AlleleAnnotations = components['schemas']['AlleleAnnotations']
+
+/** Confidence/provenance axis (orthogonal to Cat-VRS `relation`); strongest first. */
+export type Derivation = 'authoritative' | 'projection' | 'candidate'
+const DERIVATION_RANK: Record<string, number> = {authoritative: 0, projection: 1, candidate: 2}
+
+// Level display order (genomic → coding → protein) so a group reads bottom-up through the layer stack.
+const LEVEL_ORDER: Record<string, number> = {genomic: 0, cdna: 1, protein: 2}
+
+export interface AlleleMember extends AlleleIdentity {
+  digest: string
+  annotations: AlleleAnnotations | null
+  /** This allele is the CAID/PAID the page is anchored on. */
+  pageRoot: boolean
+}
+
+/**
+ * A group of alleles rendered as one entry. Either a single allele (the protein apex, an unpaired
+ * measured allele, or a projection-failed one-member candidate) or a c↔g projection pair collapsed into
+ * one — the same change at two levels — with its annotations deduplicated.
+ */
+export interface AlleleGroup {
+  key: string
+  members: AlleleMember[]
+  /** Contains the measured (authoritative) allele. */
+  measured: boolean
+  /** Contains the page-anchor allele. */
+  pageRoot: boolean
+  /** Grouped confidence: the strongest derivation among the members. */
+  derivation: Derivation | null
+  /** Members share one annotation block, so it renders once; otherwise render each level's separately. */
+  annotationsMatch: boolean
+  /** Distinct linked CAIDs to surface, excluding the page anchor (which is this page). */
+  clingenLinks: string[]
+}
+
+export interface GroupAllelesInput {
+  alleles: Record<string, AlleleIdentity>
+  annotations: Record<string, AlleleAnnotations>
+  /** The ClinGen id the page is anchored on. */
+  pageClingenAlleleId: string | null
+}
+
+function pickDerivation(members: AlleleMember[]): Derivation | null {
+  let best: Derivation | null = null
+  let bestRank = Infinity
+  for (const m of members) {
+    const rank = m.derivation != null ? DERIVATION_RANK[m.derivation] : undefined
+    if (rank != null && rank < bestRank) {
+      bestRank = rank
+      best = m.derivation as Derivation
+    }
+  }
+  return best
+}
+
+// Mutual by construction, but honor a one-sided link too so a group is never split by iteration order.
+function buildPartnerMap(alleles: Record<string, AlleleIdentity>): Map<string, string> {
+  const partnerOf = new Map<string, string>()
+  for (const [digest, identity] of Object.entries(alleles)) {
+    const sibling = identity.projectionOf
+    if (sibling && sibling !== digest && alleles[sibling]) {
+      partnerOf.set(digest, sibling)
+      partnerOf.set(sibling, digest)
+    }
+  }
+  return partnerOf
+}
+
+function makeMember(
+  digest: string,
+  identity: AlleleIdentity,
+  annotations: Record<string, AlleleAnnotations>,
+  pageClingenAlleleId: string | null
+): AlleleMember {
+  return {
+    digest,
+    level: identity.level,
+    hgvs: identity.hgvs,
+    clingenAlleleId: identity.clingenAlleleId ?? null,
+    relation: identity.relation ?? null,
+    derivation: identity.derivation ?? null,
+    annotations: annotations[digest] ?? null,
+    pageRoot: identity.clingenAlleleId != null && identity.clingenAlleleId === pageClingenAlleleId
+  }
+}
+
+/**
+ * Collapse the detail envelope's `alleles` sidecar into rendered groups, pairing each c↔g projection
+ * (linked by `projectionOf`) into one entry and deduplicating its annotations. `derivation` labels the
+ * group's confidence — orthogonal to Cat-VRS `relation`, which stays per member. Groups are ordered
+ * measured/page-root first, then bottom-up by level.
+ */
+export function groupAlleles(input: GroupAllelesInput): AlleleGroup[] {
+  const {alleles, annotations, pageClingenAlleleId} = input
+  const partnerOf = buildPartnerMap(alleles)
+
+  // Pair-and-consume: each allele is visited once; its projection partner (if any) is pulled in immediately.
+  const done = new Set<string>()
+  const groups: AlleleGroup[] = []
+  for (const [digest, identity] of Object.entries(alleles)) {
+    if (done.has(digest)) continue
+    done.add(digest)
+    const members = [makeMember(digest, identity, annotations, pageClingenAlleleId)]
+    const sibling = partnerOf.get(digest)
+    if (sibling && !done.has(sibling)) {
+      done.add(sibling)
+      members.push(makeMember(sibling, alleles[sibling], annotations, pageClingenAlleleId))
+    }
+    // Sort members genomic → cDNA → protein so the group reads consistently regardless of input order.
+    members.sort((a, b) => (LEVEL_ORDER[a.level ?? ''] ?? 99) - (LEVEL_ORDER[b.level ?? ''] ?? 99))
+
+    groups.push({
+      key: members[0].digest,
+      members,
+      measured: members.some((m) => m.derivation === 'authoritative'),
+      pageRoot: members.some((m) => m.pageRoot),
+      derivation: pickDerivation(members),
+      // If both members carry identical annotations, the UI renders one shared block instead of two.
+      annotationsMatch: members.length < 2 || _.isEqual(members[0].annotations, members[1].annotations),
+      clingenLinks: _.uniq(
+        members.map((m) => m.clingenAlleleId).filter((id): id is string => id != null && id !== pageClingenAlleleId)
+      )
+    })
+  }
+
+  // Measured/page-root groups float to the top; within those, measured beats page-root-only.
+  // Remaining groups sort by their first member's level (genomic → cDNA → protein).
+  return groups.sort((a, b) => {
+    const aPinned = a.measured || a.pageRoot
+    const bPinned = b.measured || b.pageRoot
+    if (aPinned !== bPinned) return aPinned ? -1 : 1
+    if (a.measured !== b.measured) return a.measured ? -1 : 1
+    return (LEVEL_ORDER[a.members[0].level ?? ''] ?? 99) - (LEVEL_ORDER[b.members[0].level ?? ''] ?? 99)
+  })
+}

From 3673a6faf3ec995dc58a97ff195644e5483f2da3 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Fri, 10 Jul 2026 14:52:46 -0700
Subject: [PATCH 16/84] chore(entity-cache): remove stray debug log

Drop a leftover console.log(endpoint) call in useEntityCache's fetch
path.
---
 src/composables/entity-cache.ts | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/composables/entity-cache.ts b/src/composables/entity-cache.ts
index d1323eae..7e57a4bb 100644
--- a/src/composables/entity-cache.ts
+++ b/src/composables/entity-cache.ts
@@ -112,7 +112,6 @@ export function useEntityCache(): UseEntityCacheReturn {
         throw new Error(`Unknown entity type: ${entityType}`)
       }
 
-      console.log(endpoint)
       const data =
         endpoint === 'score-sets'
           ? await getBufferedScoreSet(urn)

From 94ea6b0f81abd10035ea5a7e9ddbfcadb4fd7d54 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Fri, 10 Jul 2026 14:53:18 -0700
Subject: [PATCH 17/84] refactor(variant-lookup): rebuild on the measurements
 endpoint

- Replace the retired lookupVariantsByClingenId flow with
  getAlleleMeasurements, consuming the API's own direct-first order
  instead of re-deriving nucleotide/protein/associatedNucleotide
  buckets from a nested exactMatch/equivalentAa/equivalentNt shape
- Extract per-URN detail/score-set/scores caching into
  useMeasurementCache, and selection + its derived state (score,
  calibration resolution, clingen id) into useMeasurementSelection,
  so useVariantLookup becomes an orchestrating facade over both plus
  useClingenAllele
- Add includeSuperseded and asOf query axes; any change to anchor,
  superseded scope, or as_of bumps a query epoch, clears the caches,
  and refetches, so a slower stale response can't clobber a newer one
- Add a one-shot citation fallback: an initial `?variant=` deep link
  to a superseded measurement enables includeSuperseded once so it
  resolves, without fighting a later manual toggle-off
- Cap background prefetch of non-selected measurement details at 4
  concurrent requests via p-limit, so a large equivalence class
  doesn't fire a request storm on load
---
 src/composables/use-measurement-cache.ts     |  78 ++++
 src/composables/use-measurement-selection.ts | 130 ++++++
 src/composables/use-variant-lookup.ts        | 447 ++++++-------------
 3 files changed, 336 insertions(+), 319 deletions(-)
 create mode 100644 src/composables/use-measurement-cache.ts
 create mode 100644 src/composables/use-measurement-selection.ts

diff --git a/src/composables/use-measurement-cache.ts b/src/composables/use-measurement-cache.ts
new file mode 100644
index 00000000..d38378cc
--- /dev/null
+++ b/src/composables/use-measurement-cache.ts
@@ -0,0 +1,78 @@
+import {shallowRef, type Ref} from 'vue'
+
+import {getVariantDetail} from '@/api/mavedb/variants'
+import {getLeanScoreSetVariants, getScoreSet} from '@/api/mavedb/score-sets'
+import type {DisplayVariant} from '@/lib/variants'
+import type {components} from '@/schema/openapi'
+
+type ScoreSet = components['schemas']['ScoreSet']
+type VariantDetail = components['schemas']['VariantDetail']
+
+// A variant URN is `<score-set-urn>#<n>`, so its score set is the URN's prefix — no extra lookup needed.
+export const scoreSetUrnOf = (variantUrn: string): string => variantUrn.split('#')[0]
+
+export interface UseMeasurementCacheReturn {
+  variantDetails: Ref<Record<string, VariantDetail>>
+  scoreSets: Ref<Record<string, ScoreSet>>
+  scores: Ref<Record<string, DisplayVariant[]>>
+  loadDetail: (variantUrn: string) => Promise<void>
+  clear: () => void
+}
+
+/**
+ * Per-URN cache for a measurement's detail envelope, its score set, and its lean score distribution.
+ *
+ * `loadDetail` resolves all three for a variant URN — the score set (calibrations, target, experiment)
+ * and scores are keyed by the URN's score-set prefix and shared across measurements from the same assay.
+ * Request dedup + reads are memoized in the api layer (@/api/cache); these Records are just the reactive
+ * projection the template renders. `clear()` drops everything for a new query epoch (a changed `as_of`
+ * must re-resolve the molecular/annotation layer).
+ *
+ * Used by: useVariantLookup, useMeasurementSelection
+ */
+export function useMeasurementCache(asOf: Ref<string | null>): UseMeasurementCacheReturn {
+  const variantDetails = shallowRef<Record<string, VariantDetail>>({})
+  const scoreSets = shallowRef<Record<string, ScoreSet>>({})
+  const scores = shallowRef<Record<string, DisplayVariant[]>>({})
+
+  async function loadScoreSet(scoreSetUrn: string) {
+    if (scoreSets.value[scoreSetUrn]) return
+    try {
+      scoreSets.value = {...scoreSets.value, [scoreSetUrn]: await getScoreSet(scoreSetUrn)}
+    } catch (error) {
+      console.error(`Error fetching score set "${scoreSetUrn}"`, error)
+    }
+  }
+
+  async function loadScores(scoreSetUrn: string) {
+    if (scores.value[scoreSetUrn]) return
+    try {
+      scores.value = {...scores.value, [scoreSetUrn]: await getLeanScoreSetVariants(scoreSetUrn)}
+    } catch (error) {
+      console.error(`Error fetching scores for score set "${scoreSetUrn}"`, error)
+    }
+  }
+
+  async function loadDetail(variantUrn: string) {
+    const scoreSetUrn = scoreSetUrnOf(variantUrn)
+    // The score set and lean scores are needed regardless of whether the envelope is cached, so kick
+    // those off first.
+    loadScoreSet(scoreSetUrn)
+    loadScores(scoreSetUrn)
+    if (variantDetails.value[variantUrn]) return
+    try {
+      const detail = await getVariantDetail(variantUrn, {asOf: asOf.value ?? undefined})
+      variantDetails.value = {...variantDetails.value, [variantUrn]: detail}
+    } catch (error) {
+      console.error(`Error fetching variant detail for "${variantUrn}"`, error)
+    }
+  }
+
+  function clear() {
+    variantDetails.value = {}
+    scoreSets.value = {}
+    scores.value = {}
+  }
+
+  return {variantDetails, scoreSets, scores, loadDetail, clear}
+}
diff --git a/src/composables/use-measurement-selection.ts b/src/composables/use-measurement-selection.ts
new file mode 100644
index 00000000..c8e00a86
--- /dev/null
+++ b/src/composables/use-measurement-selection.ts
@@ -0,0 +1,130 @@
+import {computed, ref, watch, type ComputedRef, type Ref} from 'vue'
+
+import {useCalibrationResolution, type UseCalibrationResolutionReturn} from '@/composables/use-calibration-resolution'
+import {scoreSetUrnOf, type UseMeasurementCacheReturn} from '@/composables/use-measurement-cache'
+import type {DisplayVariant} from '@/lib/variants'
+import type {components} from '@/schema/openapi'
+
+type ScoreCalibration = components['schemas']['ScoreCalibration']
+type ScoreSet = components['schemas']['ScoreSet']
+type AlleleMeasurement = components['schemas']['AlleleMeasurement']
+type VariantDetail = components['schemas']['VariantDetail']
+
+export interface UseMeasurementSelectionReturn {
+  selectedVariantUrn: Ref<string | null>
+  selectVariant: (urn: string | null | undefined) => void
+  selectedVariant: ComputedRef<AlleleMeasurement | undefined>
+  selectedVariantDetail: ComputedRef<VariantDetail | null>
+  selectedVariantName: ComputedRef<string | null>
+  selectedClingenAlleleId: ComputedRef<string | null>
+  selectedScoreSet: ComputedRef<ScoreSet | null>
+  selectedScoreSetUrn: ComputedRef<string | null>
+  scores: ComputedRef<DisplayVariant[] | null>
+  variantScoreRow: ComputedRef<DisplayVariant | undefined>
+  selectedVariantScore: ComputedRef<number | null>
+  selectedCalibration: Ref<string | null>
+  selectedCalibrationObject: ComputedRef<ScoreCalibration | null>
+  calibrationResolution: UseCalibrationResolutionReturn
+}
+
+/**
+ * Selection state for the measurements list: which measurement is active and everything derived from it
+ * (detail envelope, score set, score distribution, calibration resolution).
+ *
+ * Reconciles the selection against list changes — honors the `?variant=` highlight, falls back to the
+ * first visible measurement when a filter hides the active one, and loads the selected measurement's
+ * detail on change. Reads cached detail/score-set/scores from {@link useMeasurementCache}; the caller
+ * owns the list and seeds the initial selection by writing `selectedVariantUrn` after a fetch.
+ *
+ * Used by: useVariantLookup
+ */
+export function useMeasurementSelection(
+  variants: Ref<AlleleMeasurement[]>,
+  filteredVariants: ComputedRef<AlleleMeasurement[]>,
+  highlightUrn: Ref<string | null>,
+  cache: UseMeasurementCacheReturn
+): UseMeasurementSelectionReturn {
+  const selectedVariantUrn = ref<string | null>(null)
+  const selectedCalibration = ref<string | null>(null)
+
+  const selectedVariant = computed(() => variants.value.find((m) => m.variantUrn === selectedVariantUrn.value))
+  const selectedVariantDetail = computed<VariantDetail | null>(() => {
+    if (!selectedVariantUrn.value) return null
+    return cache.variantDetails.value[selectedVariantUrn.value] || null
+  })
+  const selectedScoreSet = computed<ScoreSet | null>(() => {
+    if (!selectedVariantUrn.value) return null
+    return cache.scoreSets.value[scoreSetUrnOf(selectedVariantUrn.value)] || null
+  })
+  const selectedVariantName = computed(() => {
+    const m = selectedVariant.value
+    if (m) return m.assayLevelHgvs || m.submittedHgvs || null
+    const detail = selectedVariantDetail.value
+    return detail?.referenceHgvs || detail?.targetHgvs || null
+  })
+  // The detail envelope carries the measured allele's ClinGen id as a flat field (centers the measured
+  // level — a related measurement shows its OWN CAID/PAID, not the queried anchor's).
+  const selectedClingenAlleleId = computed(() => selectedVariantDetail.value?.clingenAlleleId || null)
+
+  const selectedScoreSetUrn = computed(() => selectedScoreSet.value?.urn || null)
+  const scores = computed(() => {
+    if (!selectedScoreSetUrn.value) return null
+    return cache.scores.value[selectedScoreSetUrn.value] || null
+  })
+  const variantScoreRow = computed(() => (scores.value || []).find((s) => s.variantUrn === selectedVariantUrn.value))
+  const selectedVariantScore = computed(() => variantScoreRow.value?.score ?? null)
+
+  const selectedCalibrationObject = computed<ScoreCalibration | null>(() => {
+    if (!selectedCalibration.value || !selectedScoreSet.value?.scoreCalibrations) return null
+    return (
+      selectedScoreSet.value.scoreCalibrations.find((c: ScoreCalibration) => c.urn === selectedCalibration.value) ||
+      null
+    )
+  })
+
+  const calibrationResolution = useCalibrationResolution(
+    selectedCalibrationObject,
+    selectedVariantUrn,
+    selectedVariantScore
+  )
+
+  function selectVariant(urn: string | null | undefined) {
+    selectedVariantUrn.value = urn ?? null
+  }
+
+  // The `?variant=` highlight can change without the CAID changing (e.g. arriving from a redirect).
+  watch(highlightUrn, (urn) => {
+    if (urn && variants.value.some((m) => m.variantUrn === urn)) {
+      selectedVariantUrn.value = urn
+    }
+  })
+
+  // When filters hide the currently selected measurement, fall back to the first visible one.
+  watch(filteredVariants, (visible) => {
+    if (selectedVariantUrn.value && !visible.some((m) => m.variantUrn === selectedVariantUrn.value)) {
+      selectedVariantUrn.value = visible[0]?.variantUrn ?? null
+    }
+  })
+
+  watch(selectedVariantUrn, async (newUrn) => {
+    selectedCalibration.value = null
+    if (newUrn) await cache.loadDetail(newUrn)
+  })
+
+  return {
+    selectedVariantUrn,
+    selectVariant,
+    selectedVariant,
+    selectedVariantDetail,
+    selectedVariantName,
+    selectedClingenAlleleId,
+    selectedScoreSet,
+    selectedScoreSetUrn,
+    scores,
+    variantScoreRow,
+    selectedVariantScore,
+    selectedCalibration,
+    selectedCalibrationObject,
+    calibrationResolution
+  }
+}
diff --git a/src/composables/use-variant-lookup.ts b/src/composables/use-variant-lookup.ts
index 9cd152de..cb05650e 100644
--- a/src/composables/use-variant-lookup.ts
+++ b/src/composables/use-variant-lookup.ts
@@ -1,80 +1,45 @@
 import axios from 'axios'
-import {computed, ref, shallowRef, watch, type ComputedRef, type Ref} from 'vue'
+import pLimit from 'p-limit'
+import {computed, ref, type ComputedRef, type Ref, watch} from 'vue'
 
-import {getScoreSet, getVariantAnnotation, getVariantDetail, lookupVariantsByClingenId} from '@/api/mavedb/variants'
-import {getLeanScoreSetVariants} from '@/api/mavedb/score-sets'
-import {useCalibrationResolution, type UseCalibrationResolutionReturn} from '@/composables/use-calibration-resolution'
+import {getAlleleMeasurements, getVariantAnnotation} from '@/api/mavedb/variants'
 import {useClingenAllele, type UseClingenAlleleReturn} from '@/composables/use-clingen-allele'
+import {scoreSetUrnOf, useMeasurementCache} from '@/composables/use-measurement-cache'
+import {useMeasurementSelection, type UseMeasurementSelectionReturn} from '@/composables/use-measurement-selection'
 
-import {
-  formatEvidenceCode,
-  functionalClassificationContainsVariant,
-  getClassificationOddsPath,
-  getPrimaryCalibration
-} from '@/lib/calibrations'
 import {triggerDownload} from '@/lib/downloads'
 import {getExperimentKeyword} from '@/lib/experiments'
-import type {DisplayVariant} from '@/lib/variants'
-import type {MeasurementType} from '@/lib/measurement-types'
+import {assayLevelBucket} from '@/lib/measurement-types'
 import type {components} from '@/schema/openapi'
 
-export type {MeasurementType}
+type AlleleMeasurement = components['schemas']['AlleleMeasurement']
 
-type ScoreCalibration = components['schemas']['ScoreCalibration']
-type ScoreSet = components['schemas']['ScoreSet']
-type VariantEffectMeasurementWithShortScoreSet = components['schemas']['VariantEffectMeasurementWithShortScoreSet']
-type VariantDetail = components['schemas']['VariantDetail']
-type AlleleAnnotations = components['schemas']['AlleleAnnotations']
-type FunctionalClassification =
-  components['schemas']['mavedb__view_models__score_calibration__FunctionalClassification']
+export type {AlleleMeasurement}
 
-export type VariantEntry = {content: VariantEffectMeasurementWithShortScoreSet; type: MeasurementType}
+// Cap concurrent background prefetches so a large equivalence class doesn't fire a request storm on load.
+const PREFETCH_CONCURRENCY = 4
 
-export interface UseVariantLookupReturn {
+export interface UseVariantLookupReturn extends UseMeasurementSelectionReturn {
   // ClinGen allele (delegated)
   clingenAllele: UseClingenAlleleReturn
 
-  // Variant list
-  variants: Ref<VariantEntry[]>
+  // Measurements list
+  variants: Ref<AlleleMeasurement[]>
   variantsStatus: Ref<'NotLoaded' | 'Loading' | 'Loaded' | 'Error'>
   fetchVariants: () => Promise<void>
 
-  // Filters
+  // Filters (by assayed level)
   showNucleotide: Ref<boolean>
   showProtein: Ref<boolean>
-  showAssociatedNucleotide: Ref<boolean>
+  includeSuperseded: Ref<boolean>
+  // Content valid-time — null = current; reconstructs the molecular/annotation layer as of an instant.
+  asOf: Ref<string | null>
   nucleotideCount: ComputedRef<number>
   proteinCount: ComputedRef<number>
-  associatedNucleotideCount: ComputedRef<number>
-  filteredVariants: ComputedRef<VariantEntry[]>
+  filteredVariants: ComputedRef<AlleleMeasurement[]>
 
-  // Selection
-  selectedVariantUrn: Ref<string | null>
-  selectVariant: (urn: string | null | undefined) => void
-  selectedVariant: ComputedRef<VariantEntry | undefined>
-  selectedVariantDetail: ComputedRef<VariantDetail | null>
-  selectedVariantName: ComputedRef<string | null>
-  selectedClingenAlleleId: ComputedRef<string | null>
-  selectedGnomad: ComputedRef<AlleleAnnotations['gnomad'] | null>
-
-  // Scores
-  selectedScoreSet: ComputedRef<ScoreSet | null>
-  selectedScoreSetUrn: ComputedRef<string | null>
-  scores: ComputedRef<DisplayVariant[] | null>
-  variantScoreRow: ComputedRef<DisplayVariant | undefined>
-  selectedVariantScore: ComputedRef<number | null>
-
-  // Calibration
-  selectedCalibration: Ref<string | null>
-  selectedCalibrationObject: ComputedRef<ScoreCalibration | null>
-  calibrationResolution: UseCalibrationResolutionReturn
-
-  // Per-variant helpers
-  getAbnormalOddsPath: (urn: string | null | undefined) => string | null
-  getNormalOddsPath: (urn: string | null | undefined) => string | null
-  getVariantClassification: (urn: string | null | undefined) => string | null
-  getVariantEvidenceCode: (urn: string | null | undefined) => string | null
-  getKeyword: (variantContent: VariantEffectMeasurementWithShortScoreSet, key: string) => string | null
+  // Per-measurement helpers (for measurement cards)
+  getKeyword: (scoreSetUrn: string | null | undefined, key: string) => string | null
 
   // Page-level
   geneName: ComputedRef<string | null>
@@ -85,214 +50,143 @@ export interface UseVariantLookupReturn {
 }
 
 /**
- * Variant lookup composable for the VariantScreen.
+ * Variant lookup composable for the ClinGen-allele-centric VariantScreen.
  *
- * Given a ClinGen allele ID, fetches all matching variant effect measurements
- * (nucleotide and protein level), manages measurement-type filters, and drives
- * the selected variant's detail panel, score distribution chart, and calibration
- * resolution.
+ * Given a ClinGen allele ID (a nucleotide `CA` or protein `PA`), fetches its cross-layer equivalence
+ * class of measurements from `GET /clingen-alleles/{caid}/measurements`, in the API's default order.
+ * Manages assay-level filters and drives the selected measurement's detail panel, score distribution
+ * chart, and calibration resolution.
+ *
+ * This is the orchestrating facade: it owns the measurements list, the query-axis controls, and the
+ * fetch flow, and composes the per-URN cache ({@link useMeasurementCache}), selection + its derivations
+ * ({@link useMeasurementSelection}), and allele metadata ({@link useClingenAllele}) into one flat return.
  *
  * Key behaviors:
- * - Variant details and score data are cached per-URN to avoid redundant fetches
- *   when switching between measurement cards.
- * - When filters hide the currently selected variant, the selection auto-falls
- *   back to the first visible measurement.
- * - Delegates to {@link useClingenAllele} for allele metadata and
- *   {@link useCalibrationResolution} for classification resolution.
+ * - The measurements list order is authoritative; the default selection is simply the first entry (or
+ *   the `?variant=` highlight when present).
+ * - Details, score sets, and score data are cached per-URN to avoid redundant fetches when switching
+ *   between measurement cards.
+ * - Any query-axis change (anchor, superseded scope, content valid-time) refetches and clears the caches.
  *
  * Used by: VariantScreen.vue
  */
 export function useVariantLookup(
   clingenAlleleId: Ref<string>,
-  options?: {toast?: {add: (opts: {severity: string; summary: string; detail: string; life: number}) => void}}
+  options?: {
+    highlightUrn?: Ref<string | null>
+    // Seeded from the URL so a shared `?include_superseded=`/`?as_of=` link loads in one fetch.
+    initialIncludeSuperseded?: boolean
+    initialAsOf?: string | null
+    toast?: {add: (opts: {severity: string; summary: string; detail: string; life: number}) => void}
+  }
 ): UseVariantLookupReturn {
-  // ── Leaf composables ──────────────────────────────────────
   const clingenAllele = useClingenAllele(clingenAlleleId)
+  const highlightUrn = options?.highlightUrn ?? ref<string | null>(null)
 
-  // ── Reactive state ────────────────────────────────────────
-  const variants = ref<VariantEntry[]>([])
+  // ── Measurements list + query axes ────────────────────────
+  const variants = ref<AlleleMeasurement[]>([])
   const variantsStatus = ref<'NotLoaded' | 'Loading' | 'Loaded' | 'Error'>('NotLoaded')
-  const selectedVariantUrn = ref<string | null>(null)
   const showNucleotide = ref(true)
   const showProtein = ref(true)
-  const showAssociatedNucleotide = ref(true)
-  const variantDetailCache = ref<Record<string, VariantDetail>>({})
-  const scoreSetCache = shallowRef<Record<string, ScoreSet>>({})
-  const scoresCache = shallowRef<Record<string, DisplayVariant[]>>({})
-  const selectedCalibration = ref<string | null>(null)
-
-  // A variant URN is `<score-set-urn>#<n>`, so its score set is the URN's prefix — no extra lookup
-  // needed. The detail envelope deliberately doesn't embed the score set (it's its own resource), so
-  // score-set metadata (calibrations, target, experiment) is fetched separately and cached per URN.
-  const scoreSetUrnOf = (variantUrn: string): string => variantUrn.split('#')[0]
-
-  // ── Filters ───────────────────────────────────────────────
-  const nucleotideCount = computed(() => variants.value.filter((v) => v.type === 'nucleotide').length)
-  const proteinCount = computed(() => variants.value.filter((v) => v.type === 'protein').length)
-  const associatedNucleotideCount = computed(
-    () => variants.value.filter((v) => v.type === 'associatedNucleotide').length
+  const includeSuperseded = ref(options?.initialIncludeSuperseded ?? false)
+  const asOf = ref<string | null>(options?.initialAsOf ?? null)
+
+  const prefetchLimit = pLimit(PREFETCH_CONCURRENCY)
+  // Bumped each fetch so stale-epoch prefetches (and a slower in-flight list response) bail instead of
+  // repopulating the just-cleared caches.
+  let queryEpoch = 0
+  // One-shot guard: honor an initial `?variant=` deep link that points at a superseded measurement exactly
+  // once (enable superseded so it resolves). After the first fetch, user toggles are always respected —
+  // toggling superseded off never re-enables itself just because the selected variant left the list.
+  let honoredInitialHighlight = false
+
+  // ── Filters (by assayed level) ────────────────────────────
+  const nucleotideCount = computed(
+    () => variants.value.filter((m) => assayLevelBucket(m.assayLevel) === 'nucleotide').length
   )
+  const proteinCount = computed(() => variants.value.filter((m) => assayLevelBucket(m.assayLevel) === 'protein').length)
   const filteredVariants = computed(() =>
-    variants.value.filter((v) => {
-      if (v.type === 'nucleotide') return showNucleotide.value
-      if (v.type === 'protein') return showProtein.value
-      if (v.type === 'associatedNucleotide') return showAssociatedNucleotide.value
-      return true
+    variants.value.filter((m) => {
+      const bucket = assayLevelBucket(m.assayLevel)
+      return bucket === 'protein' ? showProtein.value : showNucleotide.value
     })
   )
 
-  // ── Selection ─────────────────────────────────────────────
-  const selectedVariant = computed(() => variants.value.find((v) => v.content.urn === selectedVariantUrn.value))
-  const selectedVariantDetail = computed<VariantDetail | null>(() => {
-    if (!selectedVariantUrn.value) return null
-    return variantDetailCache.value[selectedVariantUrn.value] || null
-  })
-  const selectedScoreSet = computed<ScoreSet | null>(() => {
-    if (!selectedVariantUrn.value) return null
-    return scoreSetCache.value[scoreSetUrnOf(selectedVariantUrn.value)] || null
-  })
-  const selectedVariantName = computed(() => {
-    if (!selectedVariant.value) return null
-    const v = selectedVariant.value.content
-    const mapped = v.mappedVariants.find((m) => m.current)
-    // postMapped is typed as `unknown` in the schema — cast to access VRS expression fields
-    const postMapped = mapped?.postMapped as {expressions?: {value?: string}[]} | undefined
-    return postMapped?.expressions?.[0]?.value || v.hgvsNt || v.hgvsPro || v.hgvsSplice || null
-  })
-  // The detail envelope carries the assay-level ClinGen id as a flat field (the URN→allele bridge).
-  const selectedClingenAlleleId = computed(() => selectedVariantDetail.value?.clingenAlleleId || null)
-  // Population frequency for the assay-level allele, from the envelope's digest-keyed annotation map.
-  const selectedGnomad = computed<AlleleAnnotations['gnomad'] | null>(() => {
-    const detail = selectedVariantDetail.value
-    const digest = detail?.assayLevelDigest
-    if (!detail?.annotations || !digest) return null
-    return detail.annotations[digest]?.gnomad ?? null
-  })
-
-  // ── Scores ────────────────────────────────────────────────
-  const selectedScoreSetUrn = computed(() => selectedScoreSet.value?.urn || null)
-  const scores = computed(() => {
-    if (!selectedScoreSetUrn.value) return null
-    return scoresCache.value[selectedScoreSetUrn.value] || null
-  })
-  const variantScoreRow = computed(() => (scores.value || []).find((s) => s.variantUrn === selectedVariantUrn.value))
-  const selectedVariantScore = computed(() => variantScoreRow.value?.score ?? null)
-
-  // ── Calibration ───────────────────────────────────────────
-  const selectedCalibrationObject = computed<ScoreCalibration | null>(() => {
-    if (!selectedCalibration.value || !selectedScoreSet.value?.scoreCalibrations) return null
-    return (
-      selectedScoreSet.value.scoreCalibrations.find((c: ScoreCalibration) => c.urn === selectedCalibration.value) ||
-      null
-    )
-  })
-
-  const selectedVariantScoreAsNumber = computed<number | null>(() => selectedVariantScore.value)
-
-  const calibrationResolution = useCalibrationResolution(
-    selectedCalibrationObject,
-    selectedVariantUrn,
-    selectedVariantScoreAsNumber
-  )
+  // ── Composed sub-domains ──────────────────────────────────
+  const cache = useMeasurementCache(asOf)
+  const selection = useMeasurementSelection(variants, filteredVariants, highlightUrn, cache)
 
   // ── Page-level ────────────────────────────────────────────
   const geneName = computed(() => {
-    const firstVariant = variants.value[0]?.content
-    const targets = firstVariant?.scoreSet?.targetGenes
-    return targets?.length > 0 ? targets[0].name || null : null
-  })
-  const uniqueAssayCount = computed(() => {
-    const urns = new Set(variants.value.map((v) => v.content.scoreSet?.urn).filter(Boolean))
-    return urns.size
+    const firstUrn = variants.value[0]?.variantUrn
+    if (!firstUrn) return null
+    const targets = cache.scoreSets.value[scoreSetUrnOf(firstUrn)]?.targetGenes
+    return targets && targets.length > 0 ? targets[0].name || null : null
   })
+  const uniqueAssayCount = computed(() => new Set(variants.value.map((m) => m.scoreSetUrn)).size)
 
-  // ── Data fetching ─────────────────────────────────────────
-  async function fetchVariantDetail(variantUrn: string) {
-    const scoreSetUrn = scoreSetUrnOf(variantUrn)
-    // The score set (calibrations, target, experiment) and lean scores are needed regardless of
-    // whether the envelope is already cached, so kick those off first.
-    fetchScoreSet(scoreSetUrn)
-    fetchScores(scoreSetUrn)
-    if (variantDetailCache.value[variantUrn]) return
-    try {
-      variantDetailCache.value[variantUrn] = await getVariantDetail(variantUrn)
-    } catch (error) {
-      console.error(`Error fetching variant detail for "${variantUrn}"`, error)
-    }
-  }
-
-  async function fetchScoreSet(scoreSetUrn: string) {
-    if (scoreSetCache.value[scoreSetUrn]) return
-    try {
-      const scoreSet = await getScoreSet(scoreSetUrn)
-      scoreSetCache.value = {...scoreSetCache.value, [scoreSetUrn]: scoreSet}
-    } catch (error) {
-      console.error(`Error fetching score set "${scoreSetUrn}"`, error)
-    }
-  }
-
-  async function fetchScores(scoreSetUrn: string) {
-    if (scoresCache.value[scoreSetUrn]) return
-    try {
-      const data = await getLeanScoreSetVariants(scoreSetUrn)
-      scoresCache.value = {
-        ...scoresCache.value,
-        [scoreSetUrn]: data
-      }
-    } catch (error) {
-      console.error(`Error fetching scores for score set "${scoreSetUrn}"`, error)
-    }
+  function getKeyword(scoreSetUrn: string | null | undefined, key: string): string | null {
+    if (!scoreSetUrn) return null
+    return getExperimentKeyword(cache.scoreSets.value[scoreSetUrn]?.experiment, key)
   }
 
+  // ── Data fetching ─────────────────────────────────────────
   async function fetchVariants() {
     variants.value = []
-    variantDetailCache.value = {}
-    scoreSetCache.value = {}
-    scoresCache.value = {}
+    cache.clear()
+    // New query epoch (anchor / as_of / superseded changed). Fresh reads are keyed by as_of/superseded in
+    // the memoized api layer, so a changed axis always misses the cache and hits the network.
+    const epoch = ++queryEpoch
     variantsStatus.value = 'Loading'
+    if (!clingenAlleleId.value) {
+      variantsStatus.value = 'Loaded'
+      return
+    }
+
     try {
-      const results = await lookupVariantsByClingenId([clingenAlleleId.value])
-      const lookup = results[0]
+      // The API order IS the default (direct-first, strongest-evidence) — never re-ranked here.
+      const measurements = await getAlleleMeasurements(clingenAlleleId.value, {
+        includeSuperseded: includeSuperseded.value,
+        asOf: asOf.value ?? undefined
+      })
 
-      if (clingenAlleleId.value.startsWith('CA')) {
-        const nucleotideVariants = (lookup?.exactMatch?.variantEffectMeasurements || []).map((entry) => ({
-          content: entry,
-          type: 'nucleotide' as const
-        }))
-        const proteinVariants = (
-          lookup?.equivalentAa?.flatMap((entry) => entry.variantEffectMeasurements || []) || []
-        ).map((entry) => ({content: entry, type: 'protein' as const}))
-        const associatedNucleotideVariants = (
-          lookup?.equivalentNt?.flatMap((entry) => entry.variantEffectMeasurements || []) || []
-        ).map((entry) => ({content: entry, type: 'associatedNucleotide' as const}))
-        variants.value = [...nucleotideVariants, ...proteinVariants, ...associatedNucleotideVariants]
-      } else if (clingenAlleleId.value.startsWith('PA')) {
-        const proteinVariants = (lookup?.exactMatch?.variantEffectMeasurements || []).map((entry) => ({
-          content: entry,
-          type: 'protein' as const
-        }))
-        const nucleotideVariants = (
-          lookup?.equivalentNt?.flatMap((entry) => entry.variantEffectMeasurements || []) || []
-        ).map((entry) => ({content: entry, type: 'nucleotide' as const}))
-        variants.value = [...proteinVariants, ...nucleotideVariants]
+      // A newer query axis changed while this was in flight; let that fetch own the state so this slower
+      // stale response can't overwrite it.
+      if (epoch !== queryEpoch) return
+      variants.value = measurements
+
+      // Citation path, initial load ONLY: if the page opened on a `?variant=` deep link absent from the
+      // current-only list (e.g. a cited *superseded* measurement), enable superseded once so it resolves and its
+      // banner shows. The watcher refetches. Guarded by the one-shot flag so a later manual toggle-off is
+      // honored (switches to a current variant below) instead of flipping superseded back on.
+      const shouldHonorCitation =
+        !honoredInitialHighlight &&
+        highlightUrn.value &&
+        !includeSuperseded.value &&
+        !variants.value.some((m) => m.variantUrn === highlightUrn.value)
+      honoredInitialHighlight = true
+      if (shouldHonorCitation) {
+        // Stay 'Loading' through the handoff — the watcher's refetch owns the terminal status, so we skip
+        // the transient 'Loaded' that would otherwise flicker Loaded→Loading→Loaded.
+        includeSuperseded.value = true
+        return
       }
 
       variantsStatus.value = 'Loaded'
-
       if (variants.value.length === 0) return
 
-      const firstUrn = variants.value[0].content.urn
-      if (!firstUrn) return
-      await fetchVariantDetail(firstUrn)
-      selectedVariantUrn.value = firstUrn
-
-      // Background-fetch remaining variant details
-      const remainingUrns = variants.value
-        .slice(1)
-        .map((v) => v.content.urn)
-        .filter((urn): urn is string => urn != null)
-      for (const urn of remainingUrns) {
-        fetchVariantDetail(urn)
+      // Default selection = the `?variant=` highlight if it's in the list, else the first measurement.
+      // Writing the selection triggers useMeasurementSelection's watcher to load the selected detail.
+      const highlighted = highlightUrn.value && variants.value.find((m) => m.variantUrn === highlightUrn.value)
+      const selected = highlighted ? highlightUrn.value! : variants.value[0].variantUrn
+      selection.selectedVariantUrn.value = selected
+
+      // Background-fetch the rest (details + their score sets, which back the cards' assay facts), capped so
+      // a large equivalence class doesn't fire a request storm. Skip if a newer query epoch has started.
+      for (const m of variants.value) {
+        if (m.variantUrn !== selected) {
+          prefetchLimit(() => (epoch === queryEpoch ? cache.loadDetail(m.variantUrn) : Promise.resolve()))
+        }
       }
     } catch (error) {
       console.error('Error while loading variants', error)
@@ -301,7 +195,7 @@ export function useVariantLookup(
   }
 
   async function fetchVariantAnnotations(annotationType: string) {
-    const activeVariant = selectedVariantDetail.value
+    const activeVariant = selection.selectedVariantDetail.value
     if (!activeVariant?.urn) return
 
     try {
@@ -326,108 +220,23 @@ export function useVariantLookup(
     }
   }
 
-  function selectVariant(urn: string | null | undefined) {
-    selectedVariantUrn.value = urn ?? null
-  }
-
-  // ── Per-variant helpers (for measurement cards) ───────────
-  function getKeyword(variantContent: VariantEffectMeasurementWithShortScoreSet, key: string): string | null {
-    return getExperimentKeyword(variantContent?.scoreSet?.experiment, key)
-  }
-
-  function getAbnormalOddsPath(urn: string | null | undefined): string | null {
-    if (!urn) return null
-    return getClassificationOddsPath(getPrimaryCalibration(scoreSetCache.value[scoreSetUrnOf(urn)]), 'abnormal')
-  }
-
-  function getNormalOddsPath(urn: string | null | undefined): string | null {
-    if (!urn) return null
-    return getClassificationOddsPath(getPrimaryCalibration(scoreSetCache.value[scoreSetUrnOf(urn)]), 'normal')
-  }
-
-  function getVariantScoreRange(variantUrn: string | null | undefined): FunctionalClassification | null {
-    if (!variantUrn) return null
-    const scoreSetUrn = scoreSetUrnOf(variantUrn)
-    const scoreSet = scoreSetCache.value[scoreSetUrn]
-    if (!scoreSet) return null
-
-    const cachedScores = scoresCache.value[scoreSetUrn]
-    if (!cachedScores) return null
-
-    const scoreRow = cachedScores.find((s) => s.variantUrn === variantUrn)
-    const score = scoreRow?.score
-    if (score == null) return null
-
-    const cal = getPrimaryCalibration(scoreSet)
-    if (!cal?.functionalClassifications) return null
-
-    return cal.functionalClassifications.find((r) => functionalClassificationContainsVariant(r, score)) || null
-  }
-
-  function getVariantClassification(variantUrn: string | null | undefined): string | null {
-    return getVariantScoreRange(variantUrn)?.functionalClassification || null
-  }
-
-  function getVariantEvidenceCode(variantUrn: string | null | undefined): string | null {
-    return formatEvidenceCode(getVariantScoreRange(variantUrn)) || null
-  }
-
-  // ── Watchers ──────────────────────────────────────────────
-  watch(
-    clingenAlleleId,
-    async (newValue, oldValue) => {
-      if (newValue !== oldValue) {
-        await fetchVariants()
-      }
-    },
-    {immediate: true}
-  )
-
-  // When filters hide the currently selected variant, fall back to the first visible one.
-  watch(filteredVariants, (visible) => {
-    if (selectedVariantUrn.value && !visible.some((v) => v.content.urn === selectedVariantUrn.value)) {
-      selectedVariantUrn.value = visible[0]?.content.urn ?? null
-    }
-  })
-
-  watch(selectedVariantUrn, async (newUrn) => {
-    selectedCalibration.value = null
-    if (newUrn) {
-      await fetchVariantDetail(newUrn)
-    }
-  })
+  // Any query-axis change (anchor, superseded scope, content valid-time) refetches; fetchVariants clears
+  // the per-URN caches so detail/scores re-resolve under the new as_of.
+  watch([clingenAlleleId, includeSuperseded, asOf], fetchVariants, {immediate: true})
 
   return {
+    ...selection,
     clingenAllele,
     variants,
     variantsStatus,
     fetchVariants,
     showNucleotide,
     showProtein,
-    showAssociatedNucleotide,
+    includeSuperseded,
+    asOf,
     nucleotideCount,
     proteinCount,
-    associatedNucleotideCount,
     filteredVariants,
-    selectedVariantUrn,
-    selectVariant,
-    selectedVariant,
-    selectedVariantDetail,
-    selectedVariantName,
-    selectedClingenAlleleId,
-    selectedGnomad,
-    selectedScoreSet,
-    selectedScoreSetUrn,
-    scores,
-    variantScoreRow,
-    selectedVariantScore,
-    selectedCalibration,
-    selectedCalibrationObject,
-    calibrationResolution,
-    getAbnormalOddsPath,
-    getNormalOddsPath,
-    getVariantClassification,
-    getVariantEvidenceCode,
     getKeyword,
     geneName,
     uniqueAssayCount,

From c9ac5300223808506f745f634ea3824e9604538d Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Fri, 10 Jul 2026 14:53:51 -0700
Subject: [PATCH 18/84] refactor(variant-coordinates): split dna level into
 cdna and genomic

- Widen SequenceLevel from 'dna'|'protein' to 'cdna'|'genomic'|
  'protein', mirroring the backend's AnnotationLayer enum, and route
  the mapped frame through the new mapped.{cdna,genomic,protein}
  triple instead of the removed assayLevelHgvs/proteinLevelHgvs
  fields
- In the raw frame, cdna and genomic both alias hgvsNt since the
  submitted string is target-relative and the level split only
  exists post-mapping; sequenceTypeOptions collapses them into one
  "Nucleotide" option keyed by the variant's assayLevel
- Make getHgvsNt in the mapped frame prefer the coding (cdna)
  coordinate over genomic, falling back to genomic only when there
  is no coding projection, so it pairs naturally with the protein
  change in labels and tooltips
- Update tests for the three-level split, the raw-frame NT aliasing,
  the coding-preferred mapped fallback, and the existing protein-only
  no-fabricated-coding guarantee (#784)
---
 .../use-variant-coordinates.test.ts           | 136 ++++++++++++++----
 src/composables/use-variant-coordinates.ts    |  99 +++++++++----
 2 files changed, 176 insertions(+), 59 deletions(-)

diff --git a/src/composables/use-variant-coordinates.test.ts b/src/composables/use-variant-coordinates.test.ts
index cdf6fa6a..2b8fab4f 100644
--- a/src/composables/use-variant-coordinates.test.ts
+++ b/src/composables/use-variant-coordinates.test.ts
@@ -3,8 +3,15 @@ import {describe, expect, it} from 'vitest'
 import {useVariantCoordinates} from '@/composables/use-variant-coordinates'
 import type {HgvsField, LeanVariant} from '@/lib/variants'
 
-const {coordinateFor, getHgvsNt, getHgvsPro, labelForVariant, levelAvailable, sequenceTypeOptions, resolveLevel} =
-  useVariantCoordinates()
+const {
+  coordinateFor,
+  getHgvsNt,
+  getHgvsPro,
+  labelForVariant,
+  levelAvailable,
+  sequenceTypeOptions,
+  resolveLevel
+} = useVariantCoordinates()
 
 function field(hgvs: string, position?: number, ref?: string, alt?: string): HgvsField {
   return {hgvs, position, ref, alt}
@@ -14,54 +21,98 @@ function variant(overrides: Partial<LeanVariant>): LeanVariant {
   return {variantUrn: 'urn:mavedb:00000001-a-1#1', ...overrides} as LeanVariant
 }
 
-// A coding/genomic assay: measured at the nucleotide level, mapped up to protein.
+// A coding assay: measured at the cdna level, projected up to protein and down to genomic.
 const dnaAssay = variant({
   variantUrn: 'urn:dna#1',
   hgvsNt: field('c.6C>T', 6, 'C', 'T'),
   hgvsPro: field('p.Leu2Phe', 2, 'Leu', 'Phe'),
-  assayLevelHgvs: field('NM_x:c.6C>T', 6, 'C', 'T'),
-  proteinLevelHgvs: field('NP_x:p.Leu2Phe', 2, 'Leu', 'Phe')
+  assayLevel: 'cdna',
+  mapped: {
+    genomic: field('NC_x:g.100C>T', 100, 'C', 'T'),
+    cdna: field('NM_x:c.6C>T', 6, 'C', 'T'),
+    protein: field('NP_x:p.Leu2Phe', 2, 'Leu', 'Phe')
+  }
 })
 
-// A protein assay: measured at the protein level; there is no mapped coding (mavedb-api#784).
+// A genomic assay: measured at the genomic level; cdna is still present as the coding search key.
+const genomicAssay = variant({
+  variantUrn: 'urn:g#1',
+  hgvsNt: field('g.100C>T', 100, 'C', 'T'),
+  assayLevel: 'genomic',
+  mapped: {
+    genomic: field('NC_x:g.100C>T', 100, 'C', 'T'),
+    cdna: field('NM_x:c.6C>T', 6, 'C', 'T'),
+    protein: field('NP_x:p.Leu2Phe', 2, 'Leu', 'Phe')
+  }
+})
+
+// A protein assay: measured at the protein level; the c/g fan-out is ambiguous, so only protein is
+// filled (mavedb-api#784).
 const proteinAssay = variant({
   variantUrn: 'urn:pro#1',
   hgvsPro: field('p.Leu6Gly', 6, 'Leu', 'Gly'),
-  assayLevelHgvs: field('NP_x:p.Leu6Gly', 6, 'Leu', 'Gly'),
-  proteinLevelHgvs: field('NP_x:p.Leu6Gly', 6, 'Leu', 'Gly')
+  assayLevel: 'protein',
+  mapped: {protein: field('NP_x:p.Leu6Gly', 6, 'Leu', 'Gly')}
 })
 
-describe('coordinateFor — the 2×2 (level, frame) resolution', () => {
-  it('raw frame reads the submitted slots', () => {
-    expect(coordinateFor(dnaAssay, 'dna', 'raw')).toBe(dnaAssay.hgvsNt)
-    expect(coordinateFor(dnaAssay, 'protein', 'raw')).toBe(dnaAssay.hgvsPro)
+describe('coordinateFor — (level, frame) resolution', () => {
+  it('raw frame: cdna and genomic both alias hgvsNt regardless of assayLevel', () => {
+    // The cdna/genomic distinction only exists in mapped frame; raw frame has one NT field.
+    expect(coordinateFor(dnaAssay, 'cdna', 'raw')).toBe(dnaAssay.hgvsNt)
+    expect(coordinateFor(dnaAssay, 'genomic', 'raw')).toBe(dnaAssay.hgvsNt)
+    expect(coordinateFor(genomicAssay, 'cdna', 'raw')).toBe(genomicAssay.hgvsNt)
+    expect(coordinateFor(genomicAssay, 'genomic', 'raw')).toBe(genomicAssay.hgvsNt)
   })
 
-  it('mapped protein reads proteinLevelHgvs for either assay type', () => {
-    expect(coordinateFor(dnaAssay, 'protein', 'mapped')).toBe(dnaAssay.proteinLevelHgvs)
-    expect(coordinateFor(proteinAssay, 'protein', 'mapped')).toBe(proteinAssay.proteinLevelHgvs)
+  it('raw frame: protein reads hgvsPro', () => {
+    expect(coordinateFor(dnaAssay, 'protein', 'raw')).toBe(dnaAssay.hgvsPro)
+    expect(coordinateFor(proteinAssay, 'protein', 'raw')).toBe(proteinAssay.hgvsPro)
   })
 
-  it('mapped dna reads assayLevelHgvs only when it is nucleotide (coding/genomic assay)', () => {
-    expect(coordinateFor(dnaAssay, 'dna', 'mapped')).toBe(dnaAssay.assayLevelHgvs)
+  it('mapped frame: each level routes directly to its MappedTriple slot', () => {
+    expect(coordinateFor(dnaAssay, 'cdna', 'mapped')).toBe(dnaAssay.mapped!.cdna)
+    expect(coordinateFor(dnaAssay, 'genomic', 'mapped')).toBe(dnaAssay.mapped!.genomic)
+    expect(coordinateFor(dnaAssay, 'protein', 'mapped')).toBe(dnaAssay.mapped!.protein)
+    expect(coordinateFor(genomicAssay, 'genomic', 'mapped')).toBe(genomicAssay.mapped!.genomic)
+    expect(coordinateFor(genomicAssay, 'cdna', 'mapped')).toBe(genomicAssay.mapped!.cdna)
+    expect(coordinateFor(proteinAssay, 'protein', 'mapped')).toBe(proteinAssay.mapped!.protein)
   })
 
-  it('mapped dna is null for a protein assay — never fabricates a coding coordinate (#784)', () => {
-    expect(coordinateFor(proteinAssay, 'dna', 'mapped')).toBeNull()
+  it('mapped cdna/genomic are null for a protein assay — never fabricates a coding coordinate (#784)', () => {
+    expect(coordinateFor(proteinAssay, 'cdna', 'mapped')).toBeNull()
+    expect(coordinateFor(proteinAssay, 'genomic', 'mapped')).toBeNull()
   })
 
   it('returns null for an absent slot', () => {
-    expect(coordinateFor(proteinAssay, 'dna', 'raw')).toBeNull() // protein assay has no submitted nt
+    expect(coordinateFor(proteinAssay, 'cdna', 'raw')).toBeNull()
     expect(coordinateFor(variant({}), 'protein', 'raw')).toBeNull()
+    expect(coordinateFor(variant({}), 'cdna', 'mapped')).toBeNull()
   })
 })
 
 describe('getHgvsNt / getHgvsPro — string convenience over coordinateFor', () => {
-  it('return the resolved hgvs string or undefined', () => {
+  it('getHgvsNt returns hgvsNt directly in raw frame, coding-preferred in mapped frame', () => {
     expect(getHgvsNt(dnaAssay, 'raw')).toBe('c.6C>T')
+    expect(getHgvsNt(genomicAssay, 'raw')).toBe('g.100C>T')
     expect(getHgvsNt(dnaAssay, 'mapped')).toBe('NM_x:c.6C>T')
+    // Coding-preferred: a genomic-measured variant surfaces its NM_:c. coding key, not the NC_:g. one.
+    expect(getHgvsNt(genomicAssay, 'mapped')).toBe('NM_x:c.6C>T')
     expect(getHgvsNt(proteinAssay, 'mapped')).toBeUndefined()
+  })
+
+  it('getHgvsNt falls back to genomic when a genomic assay has no coding projection', () => {
+    // Deep intronic / intergenic in a genomic set: no cdna slot, so NC_:g. is the sole nucleotide identity.
+    const genomicOnly = variant({
+      variantUrn: 'urn:g-only#1',
+      assayLevel: 'genomic',
+      mapped: {genomic: field('NC_x:g.100C>T', 100, 'C', 'T')}
+    })
+    expect(getHgvsNt(genomicOnly, 'mapped')).toBe('NC_x:g.100C>T')
+  })
+
+  it('getHgvsPro returns the resolved protein hgvs string or undefined', () => {
     expect(getHgvsPro(proteinAssay, 'raw')).toBe('p.Leu6Gly')
+    expect(getHgvsPro(dnaAssay, 'mapped')).toBe('NP_x:p.Leu2Phe')
   })
 })
 
@@ -77,7 +128,6 @@ describe('labelForVariant — frame coords → submitted HGVS → URN', () => {
   })
 
   it('in the mapped frame, an unmapped variant falls back to its submitted HGVS, not the URN', () => {
-    // No mapped coordinates (unmapped), but a submitted intronic nucleotide string is present.
     const unmappedIntronic = variant({variantUrn: 'urn:intron', hgvsNt: field('c.122-6T>A')})
     expect(labelForVariant(unmappedIntronic, 'mapped')).toBe('c.122-6T>A')
   })
@@ -101,26 +151,50 @@ describe('labelForVariant — frame coords → submitted HGVS → URN', () => {
 })
 
 describe('levelAvailable / sequenceTypeOptions — availability per frame', () => {
-  it('a coding assay offers both levels in both frames', () => {
+  it('in raw frame levelAvailable returns true for both cdna and genomic when hgvsNt is present', () => {
+    // cdna and genomic alias hgvsNt in raw frame — both are technically available.
+    // sequenceTypeOptions collapses them into one option using assayLevel as a label hint.
+    expect(levelAvailable([dnaAssay], 'cdna', 'raw')).toBe(true)
+    expect(levelAvailable([dnaAssay], 'genomic', 'raw')).toBe(true)
+    expect(levelAvailable([genomicAssay], 'cdna', 'raw')).toBe(true)
+    expect(levelAvailable([genomicAssay], 'genomic', 'raw')).toBe(true)
+  })
+
+  it('sequenceTypeOptions offers one NT option in raw frame labelled Nucleotide, value keyed by assayLevel', () => {
     expect(sequenceTypeOptions([dnaAssay], 'raw')).toEqual([
-      {title: 'DNA', value: 'dna'},
+      {title: 'Nucleotide', value: 'cdna'},
       {title: 'Protein', value: 'protein'}
     ])
+    expect(sequenceTypeOptions([genomicAssay], 'raw')).toEqual([{title: 'Nucleotide', value: 'genomic'}])
+  })
+
+  it('a cdna assay with all mapped slots offers cdna, genomic, protein in mapped frame', () => {
     expect(sequenceTypeOptions([dnaAssay], 'mapped')).toEqual([
-      {title: 'DNA', value: 'dna'},
+      {title: 'cDNA', value: 'cdna'},
+      {title: 'Genomic', value: 'genomic'},
+      {title: 'Protein', value: 'protein'}
+    ])
+  })
+
+  it('a genomic assay offers cdna, genomic, protein in mapped frame', () => {
+    expect(sequenceTypeOptions([genomicAssay], 'mapped')).toEqual([
+      {title: 'cDNA', value: 'cdna'},
+      {title: 'Genomic', value: 'genomic'},
       {title: 'Protein', value: 'protein'}
     ])
   })
 
-  it('a protein assay never offers DNA — in either frame (#784)', () => {
+  it('a protein assay never offers cdna or genomic — in either frame (#784)', () => {
     expect(sequenceTypeOptions([proteinAssay], 'raw')).toEqual([{title: 'Protein', value: 'protein'}])
     expect(sequenceTypeOptions([proteinAssay], 'mapped')).toEqual([{title: 'Protein', value: 'protein'}])
-    expect(levelAvailable([proteinAssay], 'dna', 'mapped')).toBe(false)
+    expect(levelAvailable([proteinAssay], 'cdna', 'mapped')).toBe(false)
+    expect(levelAvailable([proteinAssay], 'genomic', 'mapped')).toBe(false)
   })
 
   it('availability is a set-wide OR across variants', () => {
     expect(sequenceTypeOptions([dnaAssay, proteinAssay], 'mapped')).toEqual([
-      {title: 'DNA', value: 'dna'},
+      {title: 'cDNA', value: 'cdna'},
+      {title: 'Genomic', value: 'genomic'},
       {title: 'Protein', value: 'protein'}
     ])
   })
@@ -129,12 +203,12 @@ describe('levelAvailable / sequenceTypeOptions — availability per frame', () =
 describe('resolveLevel — explicit frame→level coupling', () => {
   it('keeps the desired level when available', () => {
     expect(resolveLevel([dnaAssay], 'protein', 'mapped')).toBe('protein')
-    expect(resolveLevel([dnaAssay], 'dna', 'mapped')).toBe('dna')
+    expect(resolveLevel([dnaAssay], 'cdna', 'mapped')).toBe('cdna')
+    expect(resolveLevel([dnaAssay], 'genomic', 'mapped')).toBe('genomic')
   })
 
   it('falls back deterministically when the desired level is stranded', () => {
-    // Protein assay: desiring DNA in mapped frame falls back to the only available level.
-    expect(resolveLevel([proteinAssay], 'dna', 'mapped')).toBe('protein')
+    expect(resolveLevel([proteinAssay], 'cdna', 'mapped')).toBe('protein')
   })
 
   it('returns null when no level is available', () => {
diff --git a/src/composables/use-variant-coordinates.ts b/src/composables/use-variant-coordinates.ts
index aae4a52f..a08f4747 100644
--- a/src/composables/use-variant-coordinates.ts
+++ b/src/composables/use-variant-coordinates.ts
@@ -1,15 +1,14 @@
-import {isNucleotideHgvs} from '@/lib/mave-hgvs'
 import type {HgvsField, LeanVariant} from '@/lib/variants'
 
-/** The sequence level a coordinate is expressed in. */
-export type SequenceLevel = 'dna' | 'protein'
+/** The sequence level a coordinate is expressed in, mirroring the backend's AnnotationLayer enum. */
+export type SequenceLevel = 'cdna' | 'genomic' | 'protein'
 
 /** The coordinate frame: `raw` = submitted/target numbering, `mapped` = reference numbering. */
 export type CoordinateFrame = 'raw' | 'mapped'
 
 /**
  * Stateless resolution of a variant's HGVS coordinate across two orthogonal axes — sequence
- * **level** (dna ↔ protein) and **frame** (raw/submitted ↔ mapped/reference).
+ * **level** (cdna / genomic / protein) and **frame** (raw/submitted ↔ mapped/reference).
  *
  * `coordinateFor` is the single source of truth: every downstream derivation (heatmap x/y,
  * axis availability, labels, tooltips) resolves through it, so the (level, frame) → coordinate
@@ -23,31 +22,49 @@ export function useVariantCoordinates() {
    * Resolve the HGVS coordinate for a variant at a given level and frame, or `null` when that
    * cell does not exist for the variant.
    *
-   * The 2×2 mapping onto the lean record's slots:
+   * In the **mapped** frame each level routes directly to its `MappedTriple` slot:
    *
-   * |         | raw       | mapped                                |
-   * | ------- | --------- | ------------------------------------- |
-   * | dna     | `hgvsNt`  | `assayLevelHgvs` iff it is nucleotide |
-   * | protein | `hgvsPro` | `proteinLevelHgvs`                    |
+   * | level   | mapped slot       |
+   * | ------- | ----------------- |
+   * | cdna    | `mapped.cdna`     |
+   * | genomic | `mapped.genomic`  |
+   * | protein | `mapped.protein`  |
    *
-   * The (mapped, dna) cell is `null` for a protein assay: a protein measurement has no mapped
-   * coding representation (mavedb-api#784), so we never fabricate one from a degenerate sibling.
+   * In the **raw** frame `cdna` and `genomic` both alias `hgvsNt` — the depositor submitted one
+   * nucleotide string and the schema has a single field for it. The cdna/genomic distinction is a
+   * post-mapping conclusion, since raw submitted HGVS strings only have meaning relative to the submitted
+   * sequence. Both levels therefore return `hgvsNt` and `levelAvailable` will report both as true whenever
+   * `hgvsNt` is present. `sequenceTypeOptions` handles the display concern of offering only one NT option
+   * in raw frame.
    */
   function coordinateFor(variant: LeanVariant, level: SequenceLevel, frame: CoordinateFrame): HgvsField | null {
     if (frame === 'raw') {
-      return (level === 'dna' ? variant.hgvsNt : variant.hgvsPro) ?? null
+      if (level === 'protein') return variant.hgvsPro ?? null
+      return variant.hgvsNt ?? null
     }
-    if (level === 'protein') {
-      return variant.proteinLevelHgvs ?? null
-    }
-    // mapped + dna: only when the assay-level mapped representation is itself nucleotide.
-    const assayLevel = variant.assayLevelHgvs
-    return assayLevel && isNucleotideHgvs(assayLevel.hgvs) ? assayLevel : null
+    // mapped: direct slot lookup — no assayLevel indirection needed.
+    return variant.mapped?.[level] ?? null
   }
 
-  /** The nucleotide HGVS string for a variant in the given frame, if any. */
+  /**
+   * The canonical nucleotide HGVS string for a variant in the given frame, if any — the single
+   * nucleotide coordinate a compact surface (label pair, tooltip note, search chip) should show.
+   *
+   * In the raw frame reads `hgvsNt` directly — no level discrimination, since the submitted string is
+   * a single field. In the mapped frame the ordering is prescriptive: **coding (`cdna`) preferred,
+   * genomic fallback.** The coding `NM_:c.` string is the natural pair of the protein `NP_:p.` change
+   * (same transcript, same frame, the conventional `c. (p.)` citation), so a genomic-*measured* variant
+   * surfaces its coding coordinate here rather than the `NC_:g.` one. It becomes the string only when
+   * there is no coding projection.
+   *
+   * The plotted-axis coordinate is a different concern: when a surface has a user-selected level (the
+   * heatmap axis) it should read `coordinateFor(variant, level, frame)` directly, not this.
+   *
+   * Returns `undefined` for protein assays or unmapped variants in the mapped frame.
+   */
   function getHgvsNt(variant: LeanVariant, frame: CoordinateFrame): string | undefined {
-    return coordinateFor(variant, 'dna', frame)?.hgvs
+    if (frame === 'raw') return variant.hgvsNt?.hgvs
+    return (variant.mapped?.cdna ?? variant.mapped?.genomic)?.hgvs
   }
 
   /** The protein HGVS string for a variant in the given frame, if any. */
@@ -56,8 +73,9 @@ export function useVariantCoordinates() {
   }
 
   /**
-   * Preferred display label in the given frame, most to least specific:
-   *   frame protein → frame nucleotide → submitted protein → submitted nucleotide → submitted splice → URN.
+   * Preferred display label in the given frame, following the prescriptive identity order
+   * protein > coding > genomic (the last two via `getHgvsNt`), then submitted-string fallbacks:
+   *   frame protein → frame nucleotide (coding-preferred) → submitted protein → submitted nucleotide → submitted splice → URN.
    *
    * The mapped frame has no coordinate for an unmapped variant, so before giving up to the bare URN we
    * fall back to the variant's submitted (target-frame) HGVS: an unmapped intronic variant still carries
@@ -68,7 +86,7 @@ export function useVariantCoordinates() {
   function labelForVariant(variant: LeanVariant, frame: CoordinateFrame): string {
     return (
       coordinateFor(variant, 'protein', frame)?.hgvs ??
-      coordinateFor(variant, 'dna', frame)?.hgvs ??
+      getHgvsNt(variant, frame) ??
       variant.hgvsPro?.hgvs ??
       variant.hgvsNt?.hgvs ??
       variant.hgvsSplice?.hgvs ??
@@ -81,15 +99,40 @@ export function useVariantCoordinates() {
     return variants.some((v) => coordinateFor(v, level, frame) != null)
   }
 
-  /** The level options to offer for the given frame, in display order (DNA before Protein). */
+  const LEVEL_LABELS: Record<SequenceLevel, string> = {cdna: 'cDNA', genomic: 'Genomic', protein: 'Protein'}
+  const LEVEL_ORDER: SequenceLevel[] = ['cdna', 'genomic', 'protein']
+
+  /**
+   * The level options to offer for the given frame, in display order.
+   *
+   * In the **mapped** frame returns whichever of cDNA / Genomic / Protein have data (up to all three
+   * for a nucleotide assay). In the **raw** frame cdna and genomic both alias `hgvsNt`, so the
+   * distinction is meaningless — the submitted string is target-relative and its level is only
+   * determined after mapping. A single "Nucleotide" option is returned instead, with the `value`
+   * keyed to `assayLevel` so that a frame switch routes to the right mapped slot.
+   */
   function sequenceTypeOptions(
     variants: LeanVariant[],
     frame: CoordinateFrame
   ): Array<{title: string; value: SequenceLevel}> {
-    const options: Array<{title: string; value: SequenceLevel}> = []
-    if (levelAvailable(variants, 'dna', frame)) options.push({title: 'DNA', value: 'dna'})
-    if (levelAvailable(variants, 'protein', frame)) options.push({title: 'Protein', value: 'protein'})
-    return options
+    if (frame === 'raw') {
+      const options: Array<{title: string; value: SequenceLevel}> = []
+
+      if (variants.some((v) => v.hgvsNt != null)) {
+        const ntLevel =
+          (variants.find((v) => v.assayLevel === 'cdna' || v.assayLevel === 'genomic')?.assayLevel as SequenceLevel) ??
+          'cdna'
+        options.push({title: 'Nucleotide', value: ntLevel})
+      }
+
+      if (variants.some((v) => v.hgvsPro != null)) options.push({title: 'Protein', value: 'protein'})
+      return options
+    }
+
+    return LEVEL_ORDER.filter((level) => levelAvailable(variants, level, frame)).map((level) => ({
+      title: LEVEL_LABELS[level],
+      value: level
+    }))
   }
 
   /**

From 8906f9aca6498f017188d40f70bc3f1c461a1bf0 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Fri, 10 Jul 2026 14:54:22 -0700
Subject: [PATCH 19/84] feat(measurement-aggregation): add per-study
 aggregation for rt evidence
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Reverse translation expands a change into many redundant equivalence-
class representations (a protein consequence plus its sibling
nucleotide encodings). Add aggregateByStudy to collapse those back
into one entry per study — measurement count, assay level(s)
(protein/nucleotide/mixed), distinct functional classifications, and
functional score range — so search can surface per-study evidence
instead of a row per representation. Studies with more corroborating
measurements sort first, ties broken by title.

Add unit tests covering single- and multi-study collapsing, the
mixed-level flag with internal disagreement, and a null score range
when no measurement carries a score.
---
 src/lib/measurement-aggregation.test.ts | 61 ++++++++++++++++++++
 src/lib/measurement-aggregation.ts      | 76 +++++++++++++++++++++++++
 2 files changed, 137 insertions(+)
 create mode 100644 src/lib/measurement-aggregation.test.ts
 create mode 100644 src/lib/measurement-aggregation.ts

diff --git a/src/lib/measurement-aggregation.test.ts b/src/lib/measurement-aggregation.test.ts
new file mode 100644
index 00000000..37f0142f
--- /dev/null
+++ b/src/lib/measurement-aggregation.test.ts
@@ -0,0 +1,61 @@
+import {describe, expect, it} from 'vitest'
+
+import {aggregateByStudy} from '@/lib/measurement-aggregation'
+import type {components} from '@/schema/openapi'
+
+type AlleleMeasurement = components['schemas']['AlleleMeasurement']
+
+function m(overrides: Partial<AlleleMeasurement>): AlleleMeasurement {
+  return {
+    variantUrn: 'urn:mavedb:x#1',
+    relationship: 'nucleotide_encoding',
+    assayLevel: 'cdna',
+    scoreSetUrn: 'urn:mavedb:x',
+    scoreSetTitle: 'Study X',
+    ...overrides
+  } as AlleleMeasurement
+}
+
+function classified(fc: string): AlleleMeasurement['primaryClassification'] {
+  return {functionalClassification: fc} as AlleleMeasurement['primaryClassification']
+}
+
+describe('aggregateByStudy', () => {
+  it('collapses a study’s many nucleotide encodings into one entry with a score range', () => {
+    const result = aggregateByStudy([
+      m({scoreSetUrn: 'urn:s1', scoreSetTitle: 'Findlay', score: -2.0, primaryClassification: classified('abnormal')}),
+      m({scoreSetUrn: 'urn:s1', scoreSetTitle: 'Findlay', score: -1.7, primaryClassification: classified('abnormal')}),
+      m({scoreSetUrn: 'urn:s1', scoreSetTitle: 'Findlay', score: -1.9, primaryClassification: classified('abnormal')})
+    ])
+    expect(result).toHaveLength(1)
+    expect(result[0].measurements).toHaveLength(3)
+    expect(result[0].level).toBe('nucleotide')
+    expect(result[0].classifications).toEqual(['abnormal'])
+    expect(result[0].scoreRange).toEqual({min: -2.0, max: -1.7})
+  })
+
+  it('separates distinct studies and sorts the more-corroborated one first', () => {
+    const result = aggregateByStudy([
+      m({scoreSetUrn: 'urn:solo', scoreSetTitle: 'Giacomelli', assayLevel: 'protein', score: -2.1}),
+      m({scoreSetUrn: 'urn:many', scoreSetTitle: 'Findlay', score: -2.0}),
+      m({scoreSetUrn: 'urn:many', scoreSetTitle: 'Findlay', score: -1.8})
+    ])
+    expect(result.map((s) => s.scoreSetTitle)).toEqual(['Findlay', 'Giacomelli'])
+    expect(result[0].measurements).toHaveLength(2)
+    expect(result[1].level).toBe('protein')
+  })
+
+  it('flags a study that assayed both levels as mixed and surfaces internal disagreement', () => {
+    const result = aggregateByStudy([
+      m({scoreSetUrn: 'urn:s', assayLevel: 'protein', primaryClassification: classified('abnormal')}),
+      m({scoreSetUrn: 'urn:s', assayLevel: 'cdna', primaryClassification: classified('normal')})
+    ])
+    expect(result[0].level).toBe('mixed')
+    expect(new Set(result[0].classifications)).toEqual(new Set(['abnormal', 'normal']))
+  })
+
+  it('returns a null score range when no measurement carries a score', () => {
+    const result = aggregateByStudy([m({scoreSetUrn: 'urn:s', score: null})])
+    expect(result[0].scoreRange).toBeNull()
+  })
+})
diff --git a/src/lib/measurement-aggregation.ts b/src/lib/measurement-aggregation.ts
new file mode 100644
index 00000000..33cf8130
--- /dev/null
+++ b/src/lib/measurement-aggregation.ts
@@ -0,0 +1,76 @@
+import type {components} from '@/schema/openapi'
+
+type AlleleMeasurement = components['schemas']['AlleleMeasurement']
+type FunctionalClassification = NonNullable<
+  NonNullable<AlleleMeasurement['primaryClassification']>['functionalClassification']
+>
+
+export type EvidenceLevel = 'protein' | 'nucleotide' | 'mixed'
+
+/** One study's evidence for a change, collapsed from however many equivalence-class representations it assayed. */
+export interface StudyEvidence {
+  scoreSetUrn: string
+  scoreSetTitle: string
+  /** The underlying measurements, revealed on expand (a saturation screen may hold many). */
+  measurements: AlleleMeasurement[]
+  /** The assay level(s) this study contributed: all-protein, all-nucleotide, or both. */
+  level: EvidenceLevel
+  /** Distinct functional classifications present — one value = concordant, several = the study disagrees internally. */
+  classifications: FunctionalClassification[]
+  /** Span of functional scores, or null when none carry a score. `min === max` for a single value. */
+  scoreRange: {min: number; max: number} | null
+}
+
+function levelOf(measurements: AlleleMeasurement[]): EvidenceLevel {
+  let protein = false
+  let nucleotide = false
+  for (const m of measurements) {
+    if (m.assayLevel === 'protein') protein = true
+    else if (m.assayLevel === 'cdna' || m.assayLevel === 'genomic') nucleotide = true
+
+    if (protein && nucleotide) break
+  }
+
+  if (protein && nucleotide) return 'mixed'
+  else if (protein) return 'protein'
+  else return 'nucleotide'
+}
+
+/**
+ * Collapse a closed equivalence set (a change's protein-consequence assays + its sibling nucleotide
+ * encodings) into one entry per study. Reverse translation makes the individual members redundant — they
+ * re-encode the same functional change — so search shows per-study evidence (level, call, score range)
+ * rather than a row per representation. Studies with more corroborating measurements sort first.
+ */
+export function aggregateByStudy(measurements: AlleleMeasurement[]): StudyEvidence[] {
+  const byStudy = new Map<string, AlleleMeasurement[]>()
+  for (const m of measurements) {
+    const existing = byStudy.get(m.scoreSetUrn)
+    if (existing) existing.push(m)
+    else byStudy.set(m.scoreSetUrn, [m])
+  }
+
+  const studies: StudyEvidence[] = []
+  for (const [scoreSetUrn, list] of byStudy) {
+    const scores = list.map((m) => m.score).filter((s): s is number => s != null)
+    const classifications = [
+      ...new Set(
+        list
+          .map((m) => m.primaryClassification?.functionalClassification)
+          .filter((c): c is FunctionalClassification => c != null)
+      )
+    ]
+    studies.push({
+      scoreSetUrn,
+      scoreSetTitle: list[0].scoreSetTitle,
+      measurements: list,
+      level: levelOf(list),
+      classifications,
+      scoreRange: scores.length ? {min: Math.min(...scores), max: Math.max(...scores)} : null
+    })
+  }
+
+  return studies.sort(
+    (a, b) => b.measurements.length - a.measurements.length || a.scoreSetTitle.localeCompare(b.scoreSetTitle)
+  )
+}

From 3b2acfa796ea583246144f39dec03e4ca41b0710 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Fri, 10 Jul 2026 14:54:58 -0700
Subject: [PATCH 20/84] feat(mavemd): add mergeAlleleSpellings, rebucket
 variants by relationship

- Rename AlleleResult.variants from nucleotide/protein/
  associatedNucleotide to direct/proteinConsequence/nucleotideEncoding,
  mirroring the API's AlleleMeasurement.relationship, and switch its
  entries from VariantEffectMeasurementWithShortScoreSet to
  AlleleMeasurement
- Add mergeAlleleSpellings to fold one allele's transcript/genomic/MANE
  coordinates into another, deduplicating shared MANE entries, so a
  protein change's several registered transcript alleles collapse into
  one search result instead of several
- Drop the unused `m` regex flag from clinGenAlleleIdRegex/
  clinVarVariationIdRegex/rsIdRegex, switch `||` defaults to `??`, and
  replace a for-in loop with Object.entries in the MANE coordinate walk

Add unit tests for mergeAlleleSpellings covering coordinate folding,
MANE coordinate dedup, and fill-without-overwrite of genome-build HGVS.
---
 src/lib/mavemd.test.ts | 49 ++++++++++++++++++++++++++++++++++++++++
 src/lib/mavemd.ts      | 51 ++++++++++++++++++++++++++++++------------
 2 files changed, 86 insertions(+), 14 deletions(-)
 create mode 100644 src/lib/mavemd.test.ts

diff --git a/src/lib/mavemd.test.ts b/src/lib/mavemd.test.ts
new file mode 100644
index 00000000..e8b2d79e
--- /dev/null
+++ b/src/lib/mavemd.test.ts
@@ -0,0 +1,49 @@
+import {describe, expect, it} from 'vitest'
+
+import {mergeAlleleSpellings, type AlleleResult} from '@/lib/mavemd'
+
+function result(overrides: Partial<AlleleResult>): AlleleResult {
+  return {
+    clingenAlleleUrl: undefined,
+    clingenAlleleId: undefined,
+    canonicalAlleleName: undefined,
+    maneStatus: null,
+    genomicAlleles: [],
+    grch38Hgvs: null,
+    grch37Hgvs: null,
+    transcriptAlleles: [],
+    maneCoordinates: [],
+    variantsStatus: 'NotLoaded',
+    variants: {direct: [], proteinConsequence: [], nucleotideEncoding: []},
+    ...overrides
+  }
+}
+
+describe('mergeAlleleSpellings', () => {
+  it('folds a transcript spelling onto the target and keeps distinct MANE coordinates', () => {
+    const target = result({
+      clingenAlleleId: 'PA9',
+      maneCoordinates: [{sequenceType: 'protein', database: 'RefSeq', hgvs: 'NP_x:p.Arg273His'}]
+    })
+    mergeAlleleSpellings(
+      target,
+      result({maneCoordinates: [{sequenceType: 'nucleotide', database: 'RefSeq', hgvs: 'NM_x:c.818G>A'}]})
+    )
+    expect(target.clingenAlleleId).toBe('PA9') // anchor unchanged
+    expect(target.maneCoordinates.map((c) => c.hgvs)).toEqual(['NP_x:p.Arg273His', 'NM_x:c.818G>A'])
+  })
+
+  it('deduplicates a coordinate shared across transcripts', () => {
+    const coord = {sequenceType: 'nucleotide', database: 'RefSeq', hgvs: 'NM_x:c.818G>A'}
+    const target = result({maneCoordinates: [coord]})
+    mergeAlleleSpellings(target, result({maneCoordinates: [{...coord}]}))
+    expect(target.maneCoordinates).toHaveLength(1)
+  })
+
+  it('fills a missing genome-build HGVS from the source without overwriting a present one', () => {
+    const target = result({grch38Hgvs: 'NC_x:g.100A>T', grch37Hgvs: null})
+    mergeAlleleSpellings(target, result({grch38Hgvs: 'other', grch37Hgvs: 'NC_y:g.200A>T'}))
+    expect(target.grch38Hgvs).toBe('NC_x:g.100A>T') // kept
+    expect(target.grch37Hgvs).toBe('NC_y:g.200A>T') // filled
+  })
+})
diff --git a/src/lib/mavemd.ts b/src/lib/mavemd.ts
index f945e25c..65ddc693 100644
--- a/src/lib/mavemd.ts
+++ b/src/lib/mavemd.ts
@@ -1,12 +1,12 @@
 import type {ClinGenAllele, ClinGenGenomicAllele, ClinGenTranscriptAllele} from '@/api/clingen'
 import type {components} from '@/schema/openapi'
 
-type VariantMeasurement = components['schemas']['VariantEffectMeasurementWithShortScoreSet']
+type AlleleMeasurement = components['schemas']['AlleleMeasurement']
 
 /**
  * Regular expression for valid CA or PA ids that can be used in ClinGen searches.
  */
-export const clinGenAlleleIdRegex = /^(CA|PA)[0-9]+$/im
+export const clinGenAlleleIdRegex = /^(CA|PA)[0-9]+$/i
 
 /**
  * Regular expression for GA4GH VRS identifiers: ga4gh:<type>.<32-char base64url digest>.
@@ -26,12 +26,12 @@ export function scoreSetUrnFromVariantUrn(variantUrn: string): string | null {
 /**
  * Regular expression for valid ClinVar Variation IDs that can be used in ClinGen searches.
  */
-export const clinVarVariationIdRegex = /^[0-9]+$/m
+export const clinVarVariationIdRegex = /^[0-9]+$/
 
 /**
  * Regular expression for valid Reference SNP cluster IDs that can be used in ClinGen searches.
  */
-export const rsIdRegex = /^rs[0-9]+$/im
+export const rsIdRegex = /^rs[0-9]+$/i
 
 /** A single MANE coordinate extracted from a ClinGen transcript allele. */
 export interface ManeCoordinate {
@@ -52,13 +52,36 @@ export interface AlleleResult {
   transcriptAlleles: ClinGenTranscriptAllele[]
   maneCoordinates: ManeCoordinate[]
   variantsStatus: string
+  // Measurements of this allele's equivalence class, bucketed by each one's relationship to the searched
+  // change (mirrors the API `AlleleMeasurement.relationship`).
   variants: {
-    nucleotide: VariantMeasurement[]
-    protein: VariantMeasurement[]
-    associatedNucleotide: VariantMeasurement[]
+    direct: AlleleMeasurement[]
+    proteinConsequence: AlleleMeasurement[]
+    nucleotideEncoding: AlleleMeasurement[]
   }
   /** MaveDB variant URN — present when a VRS digest search resolves to a variant without a ClinGen Allele ID. */
-  variantUrn?: string | null
+  variantUrn?: string
+}
+
+/**
+ * Fold one allele's spellings (transcript / genomic / MANE coordinates) into another. Used to collapse a
+ * protein change's several registered transcript alleles onto ONE search result — the change is a single
+ * finding, and its transcript spellings are representations to list, not separate hits. MANE coordinates
+ * are deduplicated so shared entries aren't repeated.
+ */
+export function mergeAlleleSpellings(target: AlleleResult, source: AlleleResult): void {
+  const seen = new Set(target.maneCoordinates.map((c) => `${c.sequenceType}|${c.database}|${c.hgvs}`))
+  for (const coord of source.maneCoordinates) {
+    const key = `${coord.sequenceType}|${coord.database}|${coord.hgvs}`
+    if (!seen.has(key)) {
+      seen.add(key)
+      target.maneCoordinates.push(coord)
+    }
+  }
+  target.transcriptAlleles.push(...source.transcriptAlleles)
+  target.genomicAlleles.push(...source.genomicAlleles)
+  target.grch38Hgvs ??= source.grch38Hgvs
+  target.grch37Hgvs ??= source.grch37Hgvs
 }
 
 /** Extract the trailing path segment from a URL (e.g. ClinGen allele ID from its URL). */
@@ -75,13 +98,13 @@ export function createAlleleResult(data: ClinGenAllele, maneStatus: string | nul
     clingenAlleleId: extractIdFromUrl(data['@id']),
     canonicalAlleleName: data.communityStandardTitle?.[0],
     maneStatus,
-    genomicAlleles: data.genomicAlleles || [],
+    genomicAlleles: data.genomicAlleles ?? [],
     grch38Hgvs: null,
     grch37Hgvs: null,
-    transcriptAlleles: data.transcriptAlleles || [],
+    transcriptAlleles: data.transcriptAlleles ?? [],
     maneCoordinates: [],
     variantsStatus: 'NotLoaded',
-    variants: {nucleotide: [], protein: [], associatedNucleotide: []}
+    variants: {direct: [], proteinConsequence: [], nucleotideEncoding: []}
   }
 
   for (const genomicAllele of allele.genomicAlleles) {
@@ -98,16 +121,16 @@ export function createAlleleResult(data: ClinGenAllele, maneStatus: string | nul
       for (const sequenceType of ['nucleotide', 'protein'] as const) {
         const records = mane[sequenceType]
         if (records) {
-          for (const database in records) {
+          for (const [database, record] of Object.entries(records)) {
             allele.maneCoordinates.push({
               sequenceType,
               database,
-              hgvs: records[database].hgvs
+              hgvs: record.hgvs
             })
           }
         }
       }
-      // Assuming all MANE transcripts have the same MANE status, we can set it from the first one we encounter.
+      // All MANE statuses should be identical, use the first.
       break
     }
   }

From 6f9547cbf80ae5c121c7a580b933ea2dfe1b2639 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Fri, 10 Jul 2026 14:55:25 -0700
Subject: [PATCH 21/84] chore(schema): regenerate openapi types for
 measurements endpoint

Regenerate src/schema/openapi.d.ts against the API's new GET
/clingen-alleles/{id}/measurements endpoint and its supporting
AlleleIdentity/AlleleMeasurement/SequenceLevel/MeasurementRelationship
schemas, and drop the retired clingen-allele-id-lookups endpoint and
its ClingenAlleleIdVariantLookup*/ClingenAlleleVariants types.
---
 src/schema/openapi.d.ts | 359 ++++++++++++++++++++++------------------
 1 file changed, 195 insertions(+), 164 deletions(-)

diff --git a/src/schema/openapi.d.ts b/src/schema/openapi.d.ts
index 89c11931..c20348e9 100644
--- a/src/schema/openapi.d.ts
+++ b/src/schema/openapi.d.ts
@@ -38,6 +38,17 @@ export interface paths {
      */
     get: operations["show_version_api_v1_api_version_get"];
   };
+  "/api/v1/clingen-alleles/{clingen_allele_id}/measurements": {
+    /**
+     * List measurements for a ClinGen allele's equivalence class
+     * @description List every measurement whose cross-layer equivalence class touches this ClinGen allele (a ``CA`` or
+     * ``PA``) — the direct measurements assayed at this change plus the reverse-translation-related ones,
+     * each labeled by its assayed level and relationship. This is the ClinGen-allele-centric variant page's
+     * entrypoint. A private score set's measurement is never included; its inline classification is withheld
+     * where the calibration is unreadable while the measurement still shows.
+     */
+    get: operations["get_clingen_allele_measurements_api_v1_clingen_alleles__clingen_allele_id__measurements_get"];
+  };
   "/api/v1/users/me/collections": {
     /**
      * List my collections
@@ -1328,13 +1339,6 @@ export interface paths {
      */
     put: operations["update_user_api_v1_users___id__put"];
   };
-  "/api/v1/variants/clingen-allele-id-lookups": {
-    /**
-     * Lookup variants by ClinGen Allele IDs
-     * @description Lookup variants by ClinGen Allele IDs.
-     */
-    post: operations["lookup_variants_api_v1_variants_clingen_allele_id_lookups_post"];
-  };
   "/api/v1/variants/{urn}": {
     /**
      * Fetch assayed variant detail by URN
@@ -1642,16 +1646,69 @@ export interface components {
       clinvar?: components["schemas"]["ClinvarAnnotation"][];
     };
     /**
-     * AnnotationLayer
-     * @description Annotation layer for a variant mapping result.
+     * AlleleIdentity
+     * @description The MaveDB molecular-identity facts for one of the variant's linked alleles.
      *
-     * Mirrors the ``AnnotationLayer`` enum produced by the dcd-mapping QC API.
-     * Values use full names so they round-trip readably through the database
-     * column; the dcd-mapping payload uses short single-character codes
-     * (``p`` / ``c`` / ``g``) which the worker translates via :func:`from_wire`.
-     * @enum {string}
-     */
-    AnnotationLayer: "protein" | "cdna" | "genomic";
+     * An entry of the ``alleles`` sidecar, keyed by VRS digest. ``level`` + ``hgvs`` (the reference-frame
+     * HGVS) are what the UI labels the per-level annotation panel by — never the digest.
+     *
+     * Three independent axes:
+     * - ``relation`` (Cat-VRS, structural): member→defining relation; ``null`` when it *is* the measured
+     *   allele, or when the allele is not a Cat-VRS member.
+     * - ``derivation`` (provenance): ``authoritative`` (measured) / ``projection`` (deterministic,
+     *   precise) / ``candidate`` (reverse-translation, ambiguous). Orthogonal to ``relation`` — never
+     *   conflate them.
+     * - ``projectionOf`` (provenance): the VRS digest of this allele's projection sibling (the paired c↔g member of
+     *   its projection pair group); ``null`` for the protein apex and pre-reverse-translation data.
+     */
+    AlleleIdentity: {
+      /** Level */
+      level?: string | null;
+      /** Hgvs */
+      hgvs?: string | null;
+      /** Clingenalleleid */
+      clingenAlleleId?: string | null;
+      /** Relation */
+      relation?: string | null;
+      /** Derivation */
+      derivation?: string | null;
+      /** Projectionof */
+      projectionOf?: string | null;
+    };
+    /**
+     * AlleleMeasurement
+     * @description One measurement in the queried ClinGen allele's cross-layer equivalence class.
+     *
+     * ``assayLevel`` is the level at which this measurement was actually assayed (``protein`` / ``cdna`` /
+     * ``genomic``) — always shown, since the measured level is the clinically load-bearing fact.
+     * ``relationship`` says how the measurement relates to the queried ClinGen id: ``direct`` (assayed at
+     * this allele), ``protein_consequence`` (a protein measurement of a nt query's consequence), or
+     * ``nucleotide_encoding`` (a nt measurement encoding a protein query). ``primaryClassification`` is the
+     * primary readable functional classification, omitted when absent or gated. ``isCurrent`` /
+     * ``supersededByScoreSet`` let a superseded measurement (surfaced only under ``include_superseded``)
+     * self-describe; ``supersededByScoreSet`` is the superseding *score set*'s URN.
+     */
+    AlleleMeasurement: {
+      /** Varianturn */
+      variantUrn: string;
+      /** Score */
+      score?: number | null;
+      assayLevel?: components["schemas"]["SequenceLevel"] | null;
+      relationship: components["schemas"]["MeasurementRelationship"];
+      /** Assaylevelhgvs */
+      assayLevelHgvs?: string | null;
+      /** Submittedhgvs */
+      submittedHgvs?: string | null;
+      /** Scoreseturn */
+      scoreSetUrn: string;
+      /** Scoresettitle */
+      scoreSetTitle: string;
+      primaryClassification?: components["schemas"]["SavedFunctionalClassification"] | null;
+      /** Iscurrent */
+      isCurrent: boolean;
+      /** Supersededbyscoreset */
+      supersededByScoreSet?: string | null;
+    };
     /** ApiVersion */
     ApiVersion: {
       /** Name */
@@ -1804,46 +1861,6 @@ export interface components {
       /** @description An optional Sequence Reference on which all of the in-cis Alleles are found. When defined, this may be used to implicitly define the `sequenceReference` attribute for each of the CisPhasedBlock member Alleles. */
       sequenceReference?: components["schemas"]["SequenceReference"] | null;
     };
-    /**
-     * ClingenAlleleIdVariantLookupResponse
-     * @description Response model for a variant lookup by ClinGen allele ID
-     */
-    ClingenAlleleIdVariantLookupResponse: {
-      /** Clingenalleleid */
-      clingenAlleleId: string;
-      exactMatch?: components["schemas"]["ClingenAlleleVariants"] | null;
-      /**
-       * Equivalentnt
-       * @default []
-       */
-      equivalentNt?: components["schemas"]["ClingenAlleleVariants"][];
-      /**
-       * Equivalentaa
-       * @default []
-       */
-      equivalentAa?: components["schemas"]["ClingenAlleleVariants"][];
-    };
-    /**
-     * ClingenAlleleIdVariantLookupsRequest
-     * @description A request to search for variants matching a list of ClinGen allele IDs
-     */
-    ClingenAlleleIdVariantLookupsRequest: {
-      /** Clingenalleleids */
-      clingenAlleleIds: string[];
-    };
-    /**
-     * ClingenAlleleVariants
-     * @description The assayed variants sharing one ClinGen allele id, with their variant effect measurements.
-     *
-     * An allele-side grouping (keyed by ClinGen allele id), it is the mapped-allele view of "which
-     * measurements share this molecular identity," not the assayed variant itself.
-     */
-    ClingenAlleleVariants: {
-      /** Clingenalleleid */
-      clingenAlleleId: string;
-      /** Varianteffectmeasurements */
-      variantEffectMeasurements: components["schemas"]["VariantEffectMeasurementWithShortScoreSet"][];
-    };
     /** ClinicalControlOptions */
     ClinicalControlOptions: {
       /** Dbname */
@@ -3589,11 +3606,11 @@ export interface components {
      * @description One pre-chewed per-variant record feeding the score-set table, heatmap, and histograms.
      *
      * ``variantUrn`` is the universal selection key; ``assayLevelDigest`` bridges into the digest-keyed
-     * annotation dimensions. The submitted HGVS (``hgvsNt``/``hgvsPro``/``hgvsSplice``, target frame) and
-     * the mapped ``assayLevelHgvs`` (reference frame) carry both sides of the heatmap's frame toggle, each
-     * with an optional parsed block for the level toggle. ``proteinLevelHgvs`` is the mapped protein
-     * representation (distinct from the *submitted* ``hgvsPro``); for a protein assay it coincides with
-     * ``assayLevelHgvs``. Fields are omitted when null.
+     * annotation dimensions. The submitted HGVS (``hgvsNt``/``hgvsPro``/``hgvsSplice``, target frame) carry
+     * the depositor's frame for the heatmap's raw↔mapped toggle. The mapped (reference) frame is the
+     * ``mapped`` :class:`MappedTriple` plus the ``assayLevel`` pointer (an ``SequenceLevel`` value) naming
+     * the measured/canonical slot: ``mapped[assayLevel]`` is the measured representation and ``mapped.cdna``
+     * the level-invariant search key. Fields are omitted when null.
      */
     LeanVariant: {
       /** Varianturn */
@@ -3609,8 +3626,9 @@ export interface components {
       hgvsNt?: components["schemas"]["HgvsField"] | null;
       hgvsPro?: components["schemas"]["HgvsField"] | null;
       hgvsSplice?: components["schemas"]["HgvsField"] | null;
-      assayLevelHgvs?: components["schemas"]["HgvsField"] | null;
-      proteinLevelHgvs?: components["schemas"]["HgvsField"] | null;
+      assayLevel?: components["schemas"]["SequenceLevel"] | null;
+      /** @default {} */
+      mapped?: components["schemas"]["MappedTriple"];
     };
     /**
      * LengthExpression
@@ -3760,6 +3778,20 @@ export interface components {
        */
       mappings?: components["schemas"]["ConceptMapping"][] | null;
     };
+    /**
+     * MappedTriple
+     * @description The mapped (reference-frame) HGVS keyed by level — the canonical projection of the measured change.
+     *
+     * One slot per level. A nucleotide assay populates all three (``mapped[assayLevel]`` is the measured
+     * slot; ``cdna`` is the level-invariant search key, present even when ``assayLevel`` is ``genomic``); a
+     * protein assay populates only ``protein`` (the ambiguous c/g fan-out is not fabricated). Null slots are
+     * omitted under ``response_model_exclude_none``.
+     */
+    MappedTriple: {
+      genomic?: components["schemas"]["HgvsField"] | null;
+      cdna?: components["schemas"]["HgvsField"] | null;
+      protein?: components["schemas"]["HgvsField"] | null;
+    };
     /** MappedVariant */
     MappedVariant: {
       /** Premapped */
@@ -3784,7 +3816,7 @@ export interface components {
       mappingApiVersion: string;
       /** Current */
       current: boolean;
-      alignmentLevel?: components["schemas"]["AnnotationLayer"] | null;
+      alignmentLevel?: components["schemas"]["SequenceLevel"] | null;
       /** Atmismatchedlocus */
       atMismatchedLocus?: boolean | null;
       /** Neargap */
@@ -3830,7 +3862,7 @@ export interface components {
       mappingApiVersion: string;
       /** Current */
       current: boolean;
-      alignmentLevel?: components["schemas"]["AnnotationLayer"] | null;
+      alignmentLevel?: components["schemas"]["SequenceLevel"] | null;
       /** Atmismatchedlocus */
       atMismatchedLocus?: boolean | null;
       /** Neargap */
@@ -3850,6 +3882,14 @@ export interface components {
      * @enum {string}
      */
     MappingState: "incomplete" | "processing" | "failed" | "complete" | "pending_variant_processing" | "not_attempted" | "queued";
+    /**
+     * MeasurementRelationship
+     * @description The relationship of a measurement to the queried ClinGen allele. ``direct`` = the measurement was
+     * assayed *at* this allele; the other two are the RT-related measurements, named for how they relate
+     * to the query.
+     * @enum {string}
+     */
+    MeasurementRelationship: "direct" | "protein_consequence" | "nucleotide_encoding";
     /**
      * MembershipOperator
      * @description The logical relationship between members of the set, that indicates how they
@@ -5005,6 +5045,20 @@ export interface components {
        */
       seqrepo_dependency_version: string;
     };
+    /**
+     * SequenceLevel
+     * @description The molecular sequence level of a variant representation: genomic DNA, coding DNA, or protein.
+     *
+     * A single, duty-neutral closed set reused across several columns that each carry a different
+     * semantic meaning: the level a variant was *assayed* at (``assay_level``), the level dcd-mapping
+     * *aligned* it at (``alignment_level``), and the level of a stored allele (``level``).
+     *
+     * Values use full names so they round-trip readably through the database column; the dcd-mapping
+     * payload uses short single-character codes (``p`` / ``c`` / ``g``) which the worker translates via
+     * :func:`from_wire`.
+     * @enum {string}
+     */
+    SequenceLevel: "protein" | "cdna" | "genomic";
     /**
      * SequenceLocation
      * @description A `Location` defined by an interval on a `Sequence`.
@@ -5478,7 +5532,7 @@ export interface components {
     };
     /** TargetGeneMapping */
     TargetGeneMapping: {
-      alignmentLevel: components["schemas"]["AnnotationLayer"];
+      alignmentLevel: components["schemas"]["SequenceLevel"];
       /**
        * Preferred
        * @default false
@@ -5805,17 +5859,18 @@ export interface components {
     };
     /**
      * VariantDetail
-     * @description The assayed variant-detail envelope (``GET /variants/{urn}``, design §7.1).
+     * @description The assayed variant-detail envelope (``GET /variants/{urn}``).
      *
      * Two tiers: flat, UI-ergonomic assay fields (the ``targetHgvs``/``referenceHgvs`` coordinate pair
      * is a client-side toggle, no refetch) plus the spec-pure GA4GH ``molecularRepresentation``
-     * (``CategoricalVariant``, no MaveDB fields inside). The MaveDB layer rides alongside keyed by VRS
-     * digest: ``memberRelations`` (member→defining relation) and the ``annotations`` map. ``isCurrent``
-     * /``supersededByScoreSet`` let a superseded variant self-describe: ``supersededByScoreSet`` is the
-     * superseding *score set*'s URN, not a variant URN. Supersession is versioned at the score-set level,
-     * and a newer version may add, drop, or renumber variants — so there is no stable
-     * superseding-*variant* pointer to hand back; a consumer resolves the current measurement by looking
-     * this variant up within that score set. Absent fields are omitted.
+     * (``CategoricalVariant``, no MaveDB fields inside). The MaveDB layer rides alongside, keyed by VRS
+     * digest: the ``alleles`` identity sidecar (per-allele ``level`` / ``hgvs`` / ``clingenAlleleId`` /
+     * ``relation`` — one entry per linked allele, sharing keys with ``annotations``) and the
+     * ``annotations`` map. ``isCurrent``/``supersededByScoreSet`` let a superseded variant self-describe:
+     * ``supersededByScoreSet`` is the superseding *score set*'s URN, not a variant URN. Supersession is
+     * versioned at the score-set level, and a newer version may add, drop, or renumber variants — so there
+     * is no stable superseding-*variant* pointer to hand back; a consumer resolves the current measurement
+     * by looking this variant up within that score set. Absent fields are omitted.
      */
     VariantDetail: {
       /** Urn */
@@ -5829,8 +5884,7 @@ export interface components {
        * @default []
        */
       classifications?: components["schemas"]["VariantClassification"][];
-      /** Assaylevel */
-      assayLevel?: string | null;
+      assayLevel?: components["schemas"]["SequenceLevel"] | null;
       /** Targethgvs */
       targetHgvs?: string | null;
       /** Referencehgvs */
@@ -5844,11 +5898,11 @@ export interface components {
       /** Mode */
       mode?: string | null;
       /**
-       * Memberrelations
+       * Alleles
        * @default {}
        */
-      memberRelations?: {
-        [key: string]: string;
+      alleles?: {
+        [key: string]: components["schemas"]["AlleleIdentity"];
       };
       /**
        * Annotations
@@ -5957,41 +6011,6 @@ export interface components {
       /** Recordtype */
       recordType?: string;
     };
-    /**
-     * VariantEffectMeasurementWithShortScoreSet
-     * @description Variant effect measurement view model with mapped variants and a limited set of score set details
-     */
-    VariantEffectMeasurementWithShortScoreSet: {
-      /** Urn */
-      urn?: string | null;
-      /** Data */
-      data: unknown;
-      /** Scoresetid */
-      scoreSetId: number;
-      /** Hgvsnt */
-      hgvsNt?: string | null;
-      /** Hgvspro */
-      hgvsPro?: string | null;
-      /** Hgvssplice */
-      hgvsSplice?: string | null;
-      /**
-       * Creationdate
-       * Format: date
-       */
-      creationDate: string;
-      /**
-       * Modificationdate
-       * Format: date
-       */
-      modificationDate: string;
-      /** Id */
-      id: number;
-      /** Recordtype */
-      recordType?: string;
-      scoreSet: components["schemas"]["ShortScoreSet"];
-      /** Mappedvariants */
-      mappedVariants: components["schemas"]["MappedVariant"][];
-    };
     /**
      * VariantOncogenicityProposition
      * @description A proposition describing the role of a variant in causing a tumor type.
@@ -6723,6 +6742,62 @@ export interface operations {
       };
     };
   };
+  /**
+   * List measurements for a ClinGen allele's equivalence class
+   * @description List every measurement whose cross-layer equivalence class touches this ClinGen allele (a ``CA`` or
+   * ``PA``) — the direct measurements assayed at this change plus the reverse-translation-related ones,
+   * each labeled by its assayed level and relationship. This is the ClinGen-allele-centric variant page's
+   * entrypoint. A private score set's measurement is never included; its inline classification is withheld
+   * where the calibration is unreadable while the measurement still shows.
+   */
+  get_clingen_allele_measurements_api_v1_clingen_alleles__clingen_allele_id__measurements_get: {
+    parameters: {
+      query?: {
+        /** @description Include measurements from superseded score-set versions. Default false — superseded measurements are a deliberate power-user / citation path, never surfaced by discovery. */
+        include_superseded?: boolean;
+        /** @description For a nucleotide (CA) query only: also return sibling nucleotide changes — other DNA variants encoding the same protein consequence that were themselves assayed at the nucleotide level (relationship 'nucleotide_encoding'). Default false: the variant page anchors strictly on the queried allele. Discovery surfaces (search) set it to surface all evidence bearing on the consequence. No-op for a protein (PA) query. */
+        include_nucleotide_siblings?: boolean;
+        /** @description Reconstruct the equivalence class (which mapping records / allele links are live) as it stood at this instant. ISO 8601, ideally timezone-aware. Scores and classifications are as-of-invariant. Defaults to current. */
+        as_of?: string | null;
+      };
+      header?: {
+        "x-active-roles"?: string | null;
+      };
+      path: {
+        clingen_allele_id: string;
+      };
+    };
+    responses: {
+      /** @description Successful Response */
+      200: {
+        content: {
+          "application/json": components["schemas"]["AlleleMeasurement"][];
+        };
+      };
+      /** @description Authentication required. */
+      401: {
+        content: never;
+      };
+      /** @description Forbidden. Insufficient permissions. */
+      403: {
+        content: never;
+      };
+      /** @description Resource not found. */
+      404: {
+        content: never;
+      };
+      /** @description Validation Error */
+      422: {
+        content: {
+          "application/json": components["schemas"]["HTTPValidationError"];
+        };
+      };
+      /** @description Internal server error. */
+      500: {
+        content: never;
+      };
+    };
+  };
   /**
    * List my collections
    * @description List the current user's collections. These are all the collections the user either owns or
@@ -11018,6 +11093,8 @@ export interface operations {
   get_clinical_controls_for_score_set_api_v1_score_sets__urn__clinical_controls_get: {
     parameters: {
       query?: {
+        /** @description Reconstruct the allele → ClinVar link state as it stood at this instant. ISO 8601, ideally timezone-aware. Defaults to current. */
+        as_of?: string | null;
         db?: string | null;
         version?: string | null;
       };
@@ -11065,6 +11142,10 @@ export interface operations {
    */
   get_clinical_controls_options_for_score_set_api_v1_score_sets__urn__clinical_controls_options_get: {
     parameters: {
+      query?: {
+        /** @description Reconstruct the allele → ClinVar link state as it stood at this instant. ISO 8601, ideally timezone-aware. Defaults to current. */
+        as_of?: string | null;
+      };
       header?: {
         "x-active-roles"?: string | null;
       };
@@ -12590,56 +12671,6 @@ export interface operations {
       };
     };
   };
-  /**
-   * Lookup variants by ClinGen Allele IDs
-   * @description Lookup variants by ClinGen Allele IDs.
-   */
-  lookup_variants_api_v1_variants_clingen_allele_id_lookups_post: {
-    parameters: {
-      header?: {
-        "x-active-roles"?: string | null;
-      };
-    };
-    requestBody: {
-      content: {
-        "application/json": components["schemas"]["ClingenAlleleIdVariantLookupsRequest"];
-      };
-    };
-    responses: {
-      /** @description Successful Response */
-      200: {
-        content: {
-          "application/json": components["schemas"]["ClingenAlleleIdVariantLookupResponse"][];
-        };
-      };
-      /** @description Bad request. Check parameters and payload. */
-      400: {
-        content: never;
-      };
-      /** @description Authentication required. */
-      401: {
-        content: never;
-      };
-      /** @description Forbidden. Insufficient permissions. */
-      403: {
-        content: never;
-      };
-      /** @description Resource not found. */
-      404: {
-        content: never;
-      };
-      /** @description Validation Error */
-      422: {
-        content: {
-          "application/json": components["schemas"]["HTTPValidationError"];
-        };
-      };
-      /** @description Internal server error. */
-      500: {
-        content: never;
-      };
-    };
-  };
   /**
    * Fetch assayed variant detail by URN
    * @description Fetch the two-tier detail envelope for a single assayed variant by URN.

From 6b2701928ec9441b32418609409722a4c026c9d0 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Fri, 10 Jul 2026 14:56:04 -0700
Subject: [PATCH 22/84] feat(router): carry variant urn as ?variant= highlight
 param

- Read `?variant=` off the variant route and pass it through as
  highlightVariantUrn, so VariantScreen can highlight one specific
  measurement without changing the CAID/PAID anchor
- Preserve it through the legacy variant-URN redirect: the resolved
  allele page now carries `?variant=<urn>` so the redirect still
  points at the cited measurement instead of just its allele
---
 src/router/index.ts | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/src/router/index.ts b/src/router/index.ts
index 97437a42..60d46513 100644
--- a/src/router/index.ts
+++ b/src/router/index.ts
@@ -178,7 +178,9 @@ const routes: RouteRecordRaw[] = [
     name: 'variant',
     component: VariantScreen,
     props: (route) => ({
-      clingenAlleleId: route.params.clingenAlleleId
+      clingenAlleleId: route.params.clingenAlleleId,
+      // `?variant=` highlights a specific measurement without changing the CAID/PAID anchor.
+      highlightVariantUrn: (Array.isArray(route.query.variant) ? route.query.variant[0] : route.query.variant) || null
     })
   },
   {
@@ -193,8 +195,11 @@ const routes: RouteRecordRaw[] = [
         // The detail envelope carries the assay-level ClinGen id as a flat field (the URN→allele
         // bridge), so resolving a legacy measurement URN to its allele page is a direct read.
         const detail = await getVariantDetail(urn)
+
+        // Carry the measurement URN as the `?variant=` highlight so the redirect preserves which
+        // measurement the cited link pointed at.
         if (detail.clingenAlleleId) {
-          return {name: 'variant', params: {clingenAlleleId: detail.clingenAlleleId}}
+          return {name: 'variant', params: {clingenAlleleId: detail.clingenAlleleId}, query: {variant: urn}}
         }
       } catch {
         // Fall through to 404 if the variant can't be resolved

From a5eee860278926a3aea8d6b6809ade53a53012be Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Mon, 13 Jul 2026 13:55:07 -0700
Subject: [PATCH 23/84] chore(schema): regenerate openapi types + tooling

---
 package-lock.json       |  2 +-
 src/schema/openapi.d.ts | 32 +++++++++++++++++++-------------
 2 files changed, 20 insertions(+), 14 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index 174d8f9f..1b25d5c4 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -11229,4 +11229,4 @@
       }
     }
   }
-}
\ No newline at end of file
+}
diff --git a/src/schema/openapi.d.ts b/src/schema/openapi.d.ts
index c20348e9..a8164365 100644
--- a/src/schema/openapi.d.ts
+++ b/src/schema/openapi.d.ts
@@ -1683,8 +1683,9 @@ export interface components {
      * ``genomic``) — always shown, since the measured level is the clinically load-bearing fact.
      * ``relationship`` says how the measurement relates to the queried ClinGen id: ``direct`` (assayed at
      * this allele), ``protein_consequence`` (a protein measurement of a nt query's consequence), or
-     * ``nucleotide_encoding`` (a nt measurement encoding a protein query). ``primaryClassification`` is the
-     * primary readable functional classification, omitted when absent or gated. ``isCurrent`` /
+     * ``nucleotide_encoding`` (a nt measurement encoding a protein query). ``preferredClassification`` is the
+     * readable functional classification the UI defaults to (primary-first cascade, RUO excluded), omitted
+     * when absent or gated. ``isCurrent`` /
      * ``supersededByScoreSet`` let a superseded measurement (surfaced only under ``include_superseded``)
      * self-describe; ``supersededByScoreSet`` is the superseding *score set*'s URN.
      */
@@ -1703,7 +1704,7 @@ export interface components {
       scoreSetUrn: string;
       /** Scoresettitle */
       scoreSetTitle: string;
-      primaryClassification?: components["schemas"]["SavedFunctionalClassification"] | null;
+      preferredClassification?: components["schemas"]["SavedFunctionalClassification"] | null;
       /** Iscurrent */
       isCurrent: boolean;
       /** Supersededbyscoreset */
@@ -1868,8 +1869,8 @@ export interface components {
       /** Availableversions */
       availableVersions: string[];
     };
-    /** ClinicalControlWithMappedVariants */
-    ClinicalControlWithMappedVariants: {
+    /** ClinicalControlWithClinvarLinks */
+    ClinicalControlWithClinvarLinks: {
       /** Dbidentifier */
       dbIdentifier: string;
       /** Genesymbol */
@@ -1896,8 +1897,8 @@ export interface components {
       creationDate: string;
       /** Recordtype */
       recordType?: string;
-      /** Mappedvariants */
-      mappedVariants: components["schemas"]["MappedVariantForClinicalControl"][];
+      /** Clinvarlinks */
+      clinvarLinks: components["schemas"]["ClinvarVariantLink"][];
     };
     /**
      * ClinvarAnnotation
@@ -1915,6 +1916,16 @@ export interface components {
       /** Dbversion */
       dbVersion: string;
     };
+    /**
+     * ClinvarVariantLink
+     * @description One score-set variant a ClinVar control reaches, tagged with the annotated allele's digest.
+     */
+    ClinvarVariantLink: {
+      /** Varianturn */
+      variantUrn: string;
+      /** Alleledigest */
+      alleleDigest?: string | null;
+    };
     /**
      * Coding
      * @description A structured representation of a code for a defined concept in a terminology or
@@ -3830,11 +3841,6 @@ export interface components {
       /** Recordtype */
       recordType?: string;
     };
-    /** MappedVariantForClinicalControl */
-    MappedVariantForClinicalControl: {
-      /** Varianturn */
-      variantUrn: string;
-    };
     /**
      * MappedVariantWithMappingDetails
      * @description Client-facing variant of :class:`SavedMappedVariantWithMappingDetails`.
@@ -11109,7 +11115,7 @@ export interface operations {
       /** @description Successful Response */
       200: {
         content: {
-          "application/json": components["schemas"]["ClinicalControlWithMappedVariants"][];
+          "application/json": components["schemas"]["ClinicalControlWithClinvarLinks"][];
         };
       };
       /** @description Authentication required. */

From 284da17e34070d3a41be119833261cd49ee7dcbe Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Mon, 13 Jul 2026 13:58:07 -0700
Subject: [PATCH 24/84] refactor(api): consolidate score-set fetchers on
 score-sets module

- rename getScoreSetByUrn to getScoreSet at its call site
- import getScoreSet from @/api/mavedb/score-sets instead of the
  variants module
- rename getScoreSetClinicalControlOptions to
  getScoreSetClinvarControlOptions to match the ClinVar naming
---
 src/api/mavedb/score-sets.ts                          | 2 +-
 src/components/calibration/CalibrationEditor.vue      | 4 ++--
 src/components/collection/CollectionDataSetEditor.vue | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/api/mavedb/score-sets.ts b/src/api/mavedb/score-sets.ts
index a7064211..9a7f0b78 100644
--- a/src/api/mavedb/score-sets.ts
+++ b/src/api/mavedb/score-sets.ts
@@ -115,7 +115,7 @@ export async function publishScoreSet(urn: string) {
   return response.data
 }
 
-export async function getScoreSetClinicalControlOptions(urn: string) {
+export async function getScoreSetClinvarControlOptions(urn: string) {
   const response = await axios.get(
     `${config.apiBaseUrl}/score-sets/${encodeURIComponent(urn)}/clinical-controls/options`
   )
diff --git a/src/components/calibration/CalibrationEditor.vue b/src/components/calibration/CalibrationEditor.vue
index cab2aaae..87101f05 100644
--- a/src/components/calibration/CalibrationEditor.vue
+++ b/src/components/calibration/CalibrationEditor.vue
@@ -59,7 +59,7 @@ import {
   type DraftFunctionalClassification,
   type DraftAcmgClassification
 } from '@/composables/use-calibration-editor'
-import {searchEditableScoreSets, getScoreSetByUrn} from '@/api/mavedb'
+import {searchEditableScoreSets, getScoreSet} from '@/api/mavedb'
 import {acceptNewPublicationIdentifier} from '@/lib/form-helpers'
 import {EVIDENCE_STRENGTH, BENIGN_CRITERION, PATHOGENIC_CRITERION} from '@/lib/calibrations'
 import {
@@ -218,7 +218,7 @@ export default defineComponent({
       if (scoreSet) {
         this.selectedScoreSet = scoreSet
       } else {
-        getScoreSetByUrn(urn)
+        getScoreSet(urn)
           .then((data) => {
             this.selectedScoreSet = data as unknown as MinimalScoreSet
             this.editableScoreSets.push(data as unknown as MinimalScoreSet)
diff --git a/src/components/collection/CollectionDataSetEditor.vue b/src/components/collection/CollectionDataSetEditor.vue
index 5e962885..f93bfd94 100644
--- a/src/components/collection/CollectionDataSetEditor.vue
+++ b/src/components/collection/CollectionDataSetEditor.vue
@@ -99,7 +99,7 @@ import Message from 'primevue/message'
 
 import useItem from '@/composition/item.ts'
 import {addCollectionScoreSet, addCollectionExperiment} from '@/api/mavedb/collections'
-import {getScoreSet} from '@/api/mavedb/variants'
+import {getScoreSet} from '@/api/mavedb/score-sets'
 import {getExperiment} from '@/api/mavedb/experiments'
 import {getErrorResponse} from '@/api/mavedb'
 import {type DataSetType, DATA_SET_TYPE_LABELS} from '@/lib/collections'

From a08092ef5ed09e5b7924863b3996068bf34703b5 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Mon, 13 Jul 2026 14:02:25 -0700
Subject: [PATCH 25/84] chore(ui): tokenize nav height and thin out
 gradient-bar accents

- add a --nav-height token and have MvNavBar reference it instead of a
  hard-coded 58px, giving full-height panels a single source of truth
- drop the mave-gradient-bar accent from the external identifiers,
  targets, score-set metadata, and experiment keyword/metadata cards
- move the gradient-bar accent from the abstract to the citation card
  on the publication identifier view
---
 src/assets/app.css                                   | 5 +++++
 src/components/common/MvExternalIdentifiersCard.vue  | 2 +-
 src/components/common/MvTargetsAccordion.vue         | 2 +-
 src/components/layout/MvNavBar.vue                   | 2 +-
 src/components/score-set/ScoreSetMetadataCard.vue    | 2 +-
 src/components/screens/ExperimentView.vue            | 4 ++--
 src/components/screens/PublicationIdentifierView.vue | 7 ++-----
 7 files changed, 13 insertions(+), 11 deletions(-)

diff --git a/src/assets/app.css b/src/assets/app.css
index 49b1e8b6..197e89ad 100644
--- a/src/assets/app.css
+++ b/src/assets/app.css
@@ -164,6 +164,11 @@
 
   /* ── Custom breakpoints ────────────────────────────────────── */
   --breakpoint-tablet: 56rem; /* 896px — between md (768) and lg (1024) */
+
+  /* ── Layout ──────────────────────────────────────────────────── */
+  /* Height of the sticky global nav (MvNavBar). Single source of truth: anything that must sit below
+     the nav (e.g. full-height side panels) offsets by var(--nav-height) instead of a hard-coded px. */
+  --nav-height: 58px;
 }
 
 /* ── Base Styles ───────────────────────────────────────────────── */
diff --git a/src/components/common/MvExternalIdentifiersCard.vue b/src/components/common/MvExternalIdentifiersCard.vue
index 7747159f..c4fee147 100644
--- a/src/components/common/MvExternalIdentifiersCard.vue
+++ b/src/components/common/MvExternalIdentifiersCard.vue
@@ -1,5 +1,5 @@
 <template>
-  <div class="mave-gradient-bar relative overflow-hidden rounded-lg border border-border bg-white p-5">
+  <div class="relative overflow-hidden rounded-lg border border-border bg-white p-5">
     <h3 class="mave-section-title">External Identifiers</h3>
     <div class="flex flex-col gap-3">
       <div>
diff --git a/src/components/common/MvTargetsAccordion.vue b/src/components/common/MvTargetsAccordion.vue
index 79f69b5b..896e814b 100644
--- a/src/components/common/MvTargetsAccordion.vue
+++ b/src/components/common/MvTargetsAccordion.vue
@@ -1,5 +1,5 @@
 <template>
-  <div class="mave-gradient-bar relative overflow-hidden rounded-lg border border-border bg-white">
+  <div class="relative overflow-hidden rounded-lg border border-border bg-white">
     <div class="border-b border-border-light px-5 py-3.5">
       <span class="text-xs font-bold uppercase tracking-wider text-text-dark">Targets</span>
     </div>
diff --git a/src/components/layout/MvNavBar.vue b/src/components/layout/MvNavBar.vue
index 540cc793..a04b2dd7 100644
--- a/src/components/layout/MvNavBar.vue
+++ b/src/components/layout/MvNavBar.vue
@@ -17,7 +17,7 @@
 
   <!-- Main nav -->
   <nav aria-label="Main navigation" class="sticky top-0 z-100 border-b border-border bg-white">
-    <div class="mx-auto flex h-[58px] max-w-screen-xl items-center gap-6 px-6">
+    <div class="mx-auto flex h-[var(--nav-height)] max-w-screen-xl items-center gap-6 px-6">
       <!-- Logo -->
       <router-link class="shrink-0" to="/">
         <img
diff --git a/src/components/score-set/ScoreSetMetadataCard.vue b/src/components/score-set/ScoreSetMetadataCard.vue
index 7aea5199..19e64440 100644
--- a/src/components/score-set/ScoreSetMetadataCard.vue
+++ b/src/components/score-set/ScoreSetMetadataCard.vue
@@ -1,5 +1,5 @@
 <template>
-  <div class="mave-gradient-bar relative overflow-hidden rounded-lg border border-border bg-white p-6">
+  <div class="relative overflow-hidden rounded-lg border border-border bg-white p-6">
     <h3 class="mave-section-title">Metadata</h3>
     <div class="border-b border-border-light pb-4">
       <h3 class="mb-3 text-[15px] font-bold text-text-dark">Abstract</h3>
diff --git a/src/components/screens/ExperimentView.vue b/src/components/screens/ExperimentView.vue
index 962b4f84..634258ea 100644
--- a/src/components/screens/ExperimentView.vue
+++ b/src/components/screens/ExperimentView.vue
@@ -88,7 +88,7 @@
         />
 
         <!-- Keywords -->
-        <div class="mave-gradient-bar relative mt-4 overflow-hidden rounded-lg border border-border bg-white p-5">
+        <div class="relative mt-4 overflow-hidden rounded-lg border border-border bg-white p-5">
           <h3 class="mb-3 text-xs font-bold uppercase tracking-wider text-text-dark">Keywords</h3>
           <template v-if="item.keywords && item.keywords.length > 0">
             <div v-for="(kw, i) in item.keywords" :key="i" class="border-b border-border-light py-2.5 last:border-b-0">
@@ -120,7 +120,7 @@
         </div>
 
         <!-- Metadata card (abstract, method, publications) -->
-        <div class="mave-gradient-bar relative mt-4 overflow-hidden rounded-lg border border-border bg-white p-6">
+        <div class="relative mt-4 overflow-hidden rounded-lg border border-border bg-white p-6">
           <div class="border-b border-border-light pb-4">
             <h3 class="mb-3 text-[15px] font-bold text-text-dark">Abstract</h3>
             <!-- eslint-disable vue/no-v-html -->
diff --git a/src/components/screens/PublicationIdentifierView.vue b/src/components/screens/PublicationIdentifierView.vue
index 7428bc34..9aaaf0ca 100644
--- a/src/components/screens/PublicationIdentifierView.vue
+++ b/src/components/screens/PublicationIdentifierView.vue
@@ -39,17 +39,14 @@
       style="max-width: 850px"
     >
       <!-- Reference -->
-      <div v-if="item.referenceHtml" class="mb-6 rounded-lg border border-border bg-white p-5">
+      <div v-if="item.referenceHtml" class="mave-gradient-bar mb-6 rounded-lg border border-border bg-white p-5">
         <h3 class="mb-3 text-xs font-bold uppercase tracking-wider text-text-dark">Citation</h3>
         <!-- eslint-disable-next-line vue/no-v-html -->
         <div class="text-sm leading-relaxed text-text-secondary" v-html="item.referenceHtml"></div>
       </div>
 
       <!-- Abstract -->
-      <div
-        v-if="item.abstract"
-        class="mave-gradient-bar relative mb-6 overflow-hidden rounded-lg border border-border bg-white p-6"
-      >
+      <div v-if="item.abstract" class="relative mb-6 overflow-hidden rounded-lg border border-border bg-white p-6">
         <h3 class="mb-3 text-[15px] font-bold text-text-dark">Abstract</h3>
         <!-- eslint-disable-next-line vue/no-v-html -->
         <div class="pl-4 text-sm leading-relaxed text-text-secondary" v-html="markdownToHtml(item.abstract)"></div>

From c6c8c55408ee97b1cb6666434824e494869205a6 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Mon, 13 Jul 2026 14:05:13 -0700
Subject: [PATCH 26/84] fix(measurement-cache): await reads before spreading
 into the cache

Writing `{...cache.value, [urn]: await fetch()}` snapshots the spread
baseline before the await resolves, so two concurrent loaders (the
selected measurement plus a prefetch) both capture the same pre-write
map and the later write clobbers the earlier key. Await into a local
first, then spread, in both loadScoreSet and loadScores.

- note in use-variant-lookup that the citation-honoring path triggers a
  redundant second fetch cycle, to be deduped by a future query cache
---
 src/composables/use-measurement-cache.ts | 12 ++++++++++--
 src/composables/use-variant-lookup.ts    |  4 ++++
 2 files changed, 14 insertions(+), 2 deletions(-)

diff --git a/src/composables/use-measurement-cache.ts b/src/composables/use-measurement-cache.ts
index d38378cc..b9b76ba0 100644
--- a/src/composables/use-measurement-cache.ts
+++ b/src/composables/use-measurement-cache.ts
@@ -38,7 +38,12 @@ export function useMeasurementCache(asOf: Ref<string | null>): UseMeasurementCac
   async function loadScoreSet(scoreSetUrn: string) {
     if (scoreSets.value[scoreSetUrn]) return
     try {
-      scoreSets.value = {...scoreSets.value, [scoreSetUrn]: await getScoreSet(scoreSetUrn)}
+      // Await into a local first, then spread — writing `{...scoreSets.value, [k]: await …}` would
+      // capture the spread baseline before the await resolves, so two concurrent loaders (the selected
+      // measurement + a prefetch) both snapshot the same pre-write map and the later write clobbers the
+      // earlier key.
+      const scoreSet = await getScoreSet(scoreSetUrn)
+      scoreSets.value = {...scoreSets.value, [scoreSetUrn]: scoreSet}
     } catch (error) {
       console.error(`Error fetching score set "${scoreSetUrn}"`, error)
     }
@@ -47,7 +52,10 @@ export function useMeasurementCache(asOf: Ref<string | null>): UseMeasurementCac
   async function loadScores(scoreSetUrn: string) {
     if (scores.value[scoreSetUrn]) return
     try {
-      scores.value = {...scores.value, [scoreSetUrn]: await getLeanScoreSetVariants(scoreSetUrn)}
+      // Await into a local before spreading — see loadScoreSet for why an inline `await` in the spread
+      // literal races and drops keys under concurrent loads.
+      const leanVariants = await getLeanScoreSetVariants(scoreSetUrn)
+      scores.value = {...scores.value, [scoreSetUrn]: leanVariants}
     } catch (error) {
       console.error(`Error fetching scores for score set "${scoreSetUrn}"`, error)
     }
diff --git a/src/composables/use-variant-lookup.ts b/src/composables/use-variant-lookup.ts
index cb05650e..77f1d42d 100644
--- a/src/composables/use-variant-lookup.ts
+++ b/src/composables/use-variant-lookup.ts
@@ -159,6 +159,10 @@ export function useVariantLookup(
       // current-only list (e.g. a cited *superseded* measurement), enable superseded once so it resolves and its
       // banner shows. The watcher refetches. Guarded by the one-shot flag so a later manual toggle-off is
       // honored (switches to a current variant below) instead of flipping superseded back on.
+      //
+      // NOTE: this deliberately triggers a second full fetch/clear cycle on load (current-only, then
+      // superseded). It's correct but redundant — a proper query cache would dedup the shared
+      // reads for free. Not worth hand-collapsing before such a migration.
       const shouldHonorCitation =
         !honoredInitialHighlight &&
         highlightUrn.value &&

From 9eb3384e7b202a47e0e56aa59522b09a71e9be7f Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Mon, 13 Jul 2026 14:09:18 -0700
Subject: [PATCH 27/84] refactor(coordinates): rename raw/mapped frames to
 submitted/reference

Rename the two coordinate frames throughout the resolver and heatmap:
raw -> submitted (target numbering), mapped -> reference. The names now
say what the frames mean rather than how they were produced.

- alias SequenceLevel to the backend enum so genomic is a first-class
  level distinct from cdna, not folded into a single "dna" case
- rework the heatmap tooltip to pair by level: protein <-> coding share
  a transcript, genomic stands alone with no coding pair
- pass the variant URN to the tooltip details link
- drop the now-dead codon-translation helpers and genetic-codes import
- relabel the "Mapped HGVS" download option to "Reference-frame HGVS"
---
 src/components/common/MvVariantPreview.vue    |   2 +-
 src/components/score-set/ScoreSetHeatmap.vue  |  88 ++++++------
 .../score-set/ScoreSetVisualizer.vue          |   2 +-
 src/composables/use-score-set-downloads.ts    |   2 +-
 .../use-variant-coordinates.test.ts           | 128 +++++++++---------
 src/composables/use-variant-coordinates.ts    |  59 ++++----
 6 files changed, 136 insertions(+), 145 deletions(-)

diff --git a/src/components/common/MvVariantPreview.vue b/src/components/common/MvVariantPreview.vue
index 6d1bf442..0e023829 100644
--- a/src/components/common/MvVariantPreview.vue
+++ b/src/components/common/MvVariantPreview.vue
@@ -197,7 +197,7 @@ export default defineComponent({
     dataTypeOptions(): Array<{label: string; value: string}> {
       const options = [
         {label: 'Scores', value: 'scores'},
-        {label: 'Mapped HGVS', value: 'mappedHgvs'},
+        {label: 'Reference-frame HGVS', value: 'mappedHgvs'},
         {label: 'Custom columns', value: 'includeCustomColumns'},
         {label: 'Without NA columns', value: 'dropNaColumns'}
       ]
diff --git a/src/components/score-set/ScoreSetHeatmap.vue b/src/components/score-set/ScoreSetHeatmap.vue
index a083f9ff..4753edf4 100644
--- a/src/components/score-set/ScoreSetHeatmap.vue
+++ b/src/components/score-set/ScoreSetHeatmap.vue
@@ -37,7 +37,7 @@
           <span
             >{{ notShownCounts.noCoordinate }}
             {{ notShownCounts.noCoordinate === 1 ? 'variant has' : 'variants have' }} no
-            {{ sequenceType === 'protein' ? 'protein' : 'DNA' }} representation in this view.</span
+            {{ sequenceType === 'protein' ? 'protein' : 'nucleotide' }} representation in this view.</span
           >
         </div>
         <div v-if="notShownCounts.complex > 0" class="flex items-center gap-1.5">
@@ -66,7 +66,6 @@ import type {PropType} from 'vue'
 
 import {AMINO_ACIDS, AMINO_ACIDS_WITH_TER, singleLetterAminoAcidOrHgvsCode} from '@/lib/amino-acids'
 import {saveChartAsSvg, saveChartAsPng} from '@/lib/chart-export'
-import geneticCodes from '@/lib/genetic-codes'
 import makeHeatmap from '@/lib/heatmap'
 import type {Heatmap, HeatmapDatum, HeatmapRowSpecification} from '@/lib/heatmap'
 import {NUCLEOTIDE_BASES} from '@/lib/nucleotides'
@@ -79,7 +78,7 @@ import {
   tooltipVariantDetailsLink
 } from '@/lib/tooltips'
 import {inferReferenceSequenceFromBlocks, isStartOrStopLoss, type DisplayVariant, type HgvsField} from '@/lib/variants'
-import {useVariantCoordinates} from '@/composables/use-variant-coordinates'
+import {useVariantCoordinates, type SequenceLevel} from '@/composables/use-variant-coordinates'
 import {components} from '@/schema/openapi'
 
 interface VariantHeatmapDatum {
@@ -178,8 +177,8 @@ export default defineComponent({
 
   props: {
     coordinates: {
-      type: String as PropType<'raw' | 'mapped'>,
-      default: 'raw'
+      type: String as PropType<'submitted' | 'reference'>,
+      default: 'submitted'
     },
     externalSelection: {
       type: Object as PropType<DisplayVariant | null>,
@@ -211,7 +210,7 @@ export default defineComponent({
       default: 'standard'
     },
     allowedSequenceTypes: {
-      type: Array as PropType<('dna' | 'protein')[] | undefined>,
+      type: Array as PropType<SequenceLevel[] | undefined>,
       default: undefined
     },
     variants: {
@@ -223,7 +222,7 @@ export default defineComponent({
       default: false
     },
     sequenceType: {
-      type: String as PropType<'dna' | 'protein'>,
+      type: String as PropType<SequenceLevel>,
       default: 'protein'
     },
     layout: {
@@ -346,10 +345,12 @@ export default defineComponent({
 
     inferredTargetSequenceAndOffset: function () {
       // Accession targets have no stored sequence; infer it from the submitted (raw) blocks.
-      const level = this.targetResidueType == 'aa' ? 'protein' : 'dna'
+      // Use the first variant's assayLevel to pick cdna vs genomic — accession assays are uniform.
+      const ntLevel: SequenceLevel = this.variants[0]?.assayLevel === 'genomic' ? 'genomic' : 'cdna'
+      const level: SequenceLevel = this.targetResidueType === 'aa' ? 'protein' : ntLevel
       const {referenceSequence, referenceSequenceRange} = inferReferenceSequenceFromBlocks(
         this.variants,
-        (v) => this.coordinateFor(v, level, 'raw'),
+        (v) => this.coordinateFor(v, level, 'submitted'),
         this.targetResidueType == 'aa' ? 'aa' : 'nt'
       )
       return {
@@ -371,15 +372,15 @@ export default defineComponent({
     ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
 
     wtResidueType: function () {
-      return this.sequenceType == 'dna' ? 'nt' : 'aa'
+      return this.sequenceType !== 'protein' ? 'nt' : 'aa'
     },
 
     wtSequenceAndOffset: function () {
       // Option A: the WT sequence is expressed in the same coordinate system as the plotted cells.
-      // In the raw frame with a target sequence of the matching residue type, that sequence is the
-      // authoritative WT in target coordinates. Otherwise (mapped frame, or a residue type the target
+      // In the submitted frame with a target sequence of the matching residue type, that sequence is the
+      // authoritative WT in target coordinates. Otherwise (reference frame, or a residue type the target
       // sequence doesn't provide) infer the WT from the plotted blocks in the current (level, frame).
-      if (this.coordinates == 'raw' && this.wtResidueType == this.targetResidueType && this.targetSequence) {
+      if (this.coordinates == 'submitted' && this.wtResidueType == this.targetResidueType && this.targetSequence) {
         return {
           wtSequence: this.targetSequence,
           wtSequenceOffset: this.targetSequenceOffset
@@ -510,11 +511,11 @@ export default defineComponent({
     ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
 
     heatmapRows: function () {
-      return this.sequenceType == 'dna' ? HEATMAP_NUCLEOTIDE_ROWS : HEATMAP_AMINO_ACID_ROWS
+      return this.sequenceType !== 'protein' ? HEATMAP_NUCLEOTIDE_ROWS : HEATMAP_AMINO_ACID_ROWS
     },
 
     heatmapRowForSubstitution: function () {
-      return this.sequenceType == 'dna' ? heatmapRowForNucleotideVariant : heatmapRowForProteinVariant
+      return this.sequenceType !== 'protein' ? heatmapRowForNucleotideVariant : heatmapRowForProteinVariant
     },
 
     ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
@@ -1044,30 +1045,40 @@ export default defineComponent({
     },
 
     tooltipHtmlGetter: function (v: VariantClassHeatmapDatum) {
-      // Identity: WT flag plus the variant's identifiers, resolved in the current coordinate frame.
-      // Prefers the HGVS in the coordinate frame of the current heatmap display, with HGVS in the
-      // non-displayed frame displayed as the secondary HGVS label when they differ.
+      // Identity: WT flag plus the variant's identifiers. The primary line leads with the plotted
+      // axis's representation; the secondary line is that level's natural pair, which is transcript-
+      // specific: protein `NP_:p.` and coding `NM_:c.` are the same transcript in two registers, so
+      // each pairs with the other. The genomic `NC_:g.` axis stands alone — a genomic position spans
+      // transcripts and its intronic/UTR positions have no coding equivalent, so no pair is shown.
+      // Unmapped variants have no mapped coordinate, so fall back to labelForVariant.
       const identity = []
       if (v.wt) {
         identity.push(tooltipTitle('Wild-type'))
       }
       const instance = v.instance
       if (instance) {
-        const ntHgvs = this.getHgvsNt(instance, this.coordinates)
-        const primaryLabel =
-          this.sequenceType === 'dna'
-            ? (ntHgvs ?? this.labelForVariant(instance, this.coordinates))
-            : this.labelForVariant(instance, this.coordinates)
+        let primaryHgvs: string | undefined
+        let pairHgvs: string | undefined
+        if (this.sequenceType === 'protein') {
+          primaryHgvs = this.getHgvsPro(instance, this.coordinates)
+          pairHgvs = this.getHgvsNt(instance, this.coordinates)
+        } else if (this.sequenceType === 'genomic') {
+          primaryHgvs = this.coordinateFor(instance, 'genomic', this.coordinates)?.hgvs
+          pairHgvs = undefined
+        } else {
+          primaryHgvs = this.getHgvsNt(instance, this.coordinates)
+          pairHgvs = this.getHgvsPro(instance, this.coordinates)
+        }
+        const primaryLabel = primaryHgvs ?? this.labelForVariant(instance, this.coordinates)
         if (primaryLabel) {
           identity.push(tooltipTitle(primaryLabel))
         }
-        const underlyingLabel = this.sequenceType === 'dna' ? this.getHgvsPro(instance, this.coordinates) : ntHgvs
-        if (underlyingLabel && underlyingLabel !== primaryLabel) {
-          identity.push(tooltipNote(underlyingLabel))
+        if (pairHgvs && pairHgvs !== primaryLabel) {
+          identity.push(tooltipNote(pairHgvs))
         }
       }
       if (instance?.clingenAlleleId) {
-        identity.push(tooltipVariantDetailsLink(instance.clingenAlleleId))
+        identity.push(tooltipVariantDetailsLink(instance.clingenAlleleId, instance.variantUrn))
       }
 
       // Aggregate score statistics for the cell.
@@ -1260,29 +1271,6 @@ export default defineComponent({
       this.proteinStructureVisible = true
     },
 
-    translateDnaToAminoAcids1Char: function (dna) {
-      const triplets = this.dnaToTriplets(dna)
-      return triplets.map((triplet) => this.translateCodon(triplet))
-    },
-
-    dnaToTriplets: function (dna) {
-      if (_.isArray(dna)) {
-        dna = dna.join('')
-      }
-      return _.words(dna, /.../g)
-    },
-
-    dnaToSingletons: function (dna) {
-      if (_.isArray(dna)) {
-        dna = dna.join('')
-      }
-      return _.words(dna, /./g)
-    },
-
-    translateCodon: function (codon) {
-      return geneticCodes.standard.dna.codonToAa[codon]
-    },
-
     variantSelected: function (v: VariantClassHeatmapDatum) {
       if (v === null) {
         this.$emit('variantSelected', null)
diff --git a/src/components/score-set/ScoreSetVisualizer.vue b/src/components/score-set/ScoreSetVisualizer.vue
index b5f136a1..052b0122 100644
--- a/src/components/score-set/ScoreSetVisualizer.vue
+++ b/src/components/score-set/ScoreSetVisualizer.vue
@@ -5,7 +5,7 @@
         <ScoreSetHeatmap
           ref="scoreSetHeatmap"
           :allowed-sequence-types="['protein']"
-          coordinates="mapped"
+          coordinates="reference"
           mode="protein-viz"
           :score-set="scoreSet"
           :show-protein-structure-button="false"
diff --git a/src/composables/use-score-set-downloads.ts b/src/composables/use-score-set-downloads.ts
index 44385d67..c1b95e93 100644
--- a/src/composables/use-score-set-downloads.ts
+++ b/src/composables/use-score-set-downloads.ts
@@ -24,7 +24,7 @@ export function useScoreSetDownloads({scoreSet, hasCounts}: UseScoreSetDownloads
   const dataTypeOptions = computed(() => {
     const options = [
       {label: 'Scores', value: 'scores'},
-      {label: 'Mapped HGVS', value: 'mappedHgvs'},
+      {label: 'Reference-frame HGVS', value: 'mappedHgvs'},
       {label: 'Custom columns', value: 'includeCustomColumns'},
       {label: 'Without NA columns', value: 'dropNaColumns'}
     ]
diff --git a/src/composables/use-variant-coordinates.test.ts b/src/composables/use-variant-coordinates.test.ts
index 2b8fab4f..5640601c 100644
--- a/src/composables/use-variant-coordinates.test.ts
+++ b/src/composables/use-variant-coordinates.test.ts
@@ -56,48 +56,48 @@ const proteinAssay = variant({
 })
 
 describe('coordinateFor — (level, frame) resolution', () => {
-  it('raw frame: cdna and genomic both alias hgvsNt regardless of assayLevel', () => {
-    // The cdna/genomic distinction only exists in mapped frame; raw frame has one NT field.
-    expect(coordinateFor(dnaAssay, 'cdna', 'raw')).toBe(dnaAssay.hgvsNt)
-    expect(coordinateFor(dnaAssay, 'genomic', 'raw')).toBe(dnaAssay.hgvsNt)
-    expect(coordinateFor(genomicAssay, 'cdna', 'raw')).toBe(genomicAssay.hgvsNt)
-    expect(coordinateFor(genomicAssay, 'genomic', 'raw')).toBe(genomicAssay.hgvsNt)
+  it('submitted frame: cdna and genomic both alias hgvsNt regardless of assayLevel', () => {
+    // The cdna/genomic distinction only exists in reference frame; submitted frame has one NT field.
+    expect(coordinateFor(dnaAssay, 'cdna', 'submitted')).toBe(dnaAssay.hgvsNt)
+    expect(coordinateFor(dnaAssay, 'genomic', 'submitted')).toBe(dnaAssay.hgvsNt)
+    expect(coordinateFor(genomicAssay, 'cdna', 'submitted')).toBe(genomicAssay.hgvsNt)
+    expect(coordinateFor(genomicAssay, 'genomic', 'submitted')).toBe(genomicAssay.hgvsNt)
   })
 
-  it('raw frame: protein reads hgvsPro', () => {
-    expect(coordinateFor(dnaAssay, 'protein', 'raw')).toBe(dnaAssay.hgvsPro)
-    expect(coordinateFor(proteinAssay, 'protein', 'raw')).toBe(proteinAssay.hgvsPro)
+  it('submitted frame: protein reads hgvsPro', () => {
+    expect(coordinateFor(dnaAssay, 'protein', 'submitted')).toBe(dnaAssay.hgvsPro)
+    expect(coordinateFor(proteinAssay, 'protein', 'submitted')).toBe(proteinAssay.hgvsPro)
   })
 
-  it('mapped frame: each level routes directly to its MappedTriple slot', () => {
-    expect(coordinateFor(dnaAssay, 'cdna', 'mapped')).toBe(dnaAssay.mapped!.cdna)
-    expect(coordinateFor(dnaAssay, 'genomic', 'mapped')).toBe(dnaAssay.mapped!.genomic)
-    expect(coordinateFor(dnaAssay, 'protein', 'mapped')).toBe(dnaAssay.mapped!.protein)
-    expect(coordinateFor(genomicAssay, 'genomic', 'mapped')).toBe(genomicAssay.mapped!.genomic)
-    expect(coordinateFor(genomicAssay, 'cdna', 'mapped')).toBe(genomicAssay.mapped!.cdna)
-    expect(coordinateFor(proteinAssay, 'protein', 'mapped')).toBe(proteinAssay.mapped!.protein)
+  it('reference frame: each level routes directly to its MappedTriple slot', () => {
+    expect(coordinateFor(dnaAssay, 'cdna', 'reference')).toBe(dnaAssay.mapped!.cdna)
+    expect(coordinateFor(dnaAssay, 'genomic', 'reference')).toBe(dnaAssay.mapped!.genomic)
+    expect(coordinateFor(dnaAssay, 'protein', 'reference')).toBe(dnaAssay.mapped!.protein)
+    expect(coordinateFor(genomicAssay, 'genomic', 'reference')).toBe(genomicAssay.mapped!.genomic)
+    expect(coordinateFor(genomicAssay, 'cdna', 'reference')).toBe(genomicAssay.mapped!.cdna)
+    expect(coordinateFor(proteinAssay, 'protein', 'reference')).toBe(proteinAssay.mapped!.protein)
   })
 
-  it('mapped cdna/genomic are null for a protein assay — never fabricates a coding coordinate (#784)', () => {
-    expect(coordinateFor(proteinAssay, 'cdna', 'mapped')).toBeNull()
-    expect(coordinateFor(proteinAssay, 'genomic', 'mapped')).toBeNull()
+  it('reference cdna/genomic are null for a protein assay — never fabricates a coding coordinate (#784)', () => {
+    expect(coordinateFor(proteinAssay, 'cdna', 'reference')).toBeNull()
+    expect(coordinateFor(proteinAssay, 'genomic', 'reference')).toBeNull()
   })
 
   it('returns null for an absent slot', () => {
-    expect(coordinateFor(proteinAssay, 'cdna', 'raw')).toBeNull()
-    expect(coordinateFor(variant({}), 'protein', 'raw')).toBeNull()
-    expect(coordinateFor(variant({}), 'cdna', 'mapped')).toBeNull()
+    expect(coordinateFor(proteinAssay, 'cdna', 'submitted')).toBeNull()
+    expect(coordinateFor(variant({}), 'protein', 'submitted')).toBeNull()
+    expect(coordinateFor(variant({}), 'cdna', 'reference')).toBeNull()
   })
 })
 
 describe('getHgvsNt / getHgvsPro — string convenience over coordinateFor', () => {
-  it('getHgvsNt returns hgvsNt directly in raw frame, coding-preferred in mapped frame', () => {
-    expect(getHgvsNt(dnaAssay, 'raw')).toBe('c.6C>T')
-    expect(getHgvsNt(genomicAssay, 'raw')).toBe('g.100C>T')
-    expect(getHgvsNt(dnaAssay, 'mapped')).toBe('NM_x:c.6C>T')
+  it('getHgvsNt returns hgvsNt directly in submitted frame, coding-preferred in reference frame', () => {
+    expect(getHgvsNt(dnaAssay, 'submitted')).toBe('c.6C>T')
+    expect(getHgvsNt(genomicAssay, 'submitted')).toBe('g.100C>T')
+    expect(getHgvsNt(dnaAssay, 'reference')).toBe('NM_x:c.6C>T')
     // Coding-preferred: a genomic-measured variant surfaces its NM_:c. coding key, not the NC_:g. one.
-    expect(getHgvsNt(genomicAssay, 'mapped')).toBe('NM_x:c.6C>T')
-    expect(getHgvsNt(proteinAssay, 'mapped')).toBeUndefined()
+    expect(getHgvsNt(genomicAssay, 'reference')).toBe('NM_x:c.6C>T')
+    expect(getHgvsNt(proteinAssay, 'reference')).toBeUndefined()
   })
 
   it('getHgvsNt falls back to genomic when a genomic assay has no coding projection', () => {
@@ -107,29 +107,29 @@ describe('getHgvsNt / getHgvsPro — string convenience over coordinateFor', ()
       assayLevel: 'genomic',
       mapped: {genomic: field('NC_x:g.100C>T', 100, 'C', 'T')}
     })
-    expect(getHgvsNt(genomicOnly, 'mapped')).toBe('NC_x:g.100C>T')
+    expect(getHgvsNt(genomicOnly, 'reference')).toBe('NC_x:g.100C>T')
   })
 
   it('getHgvsPro returns the resolved protein hgvs string or undefined', () => {
-    expect(getHgvsPro(proteinAssay, 'raw')).toBe('p.Leu6Gly')
-    expect(getHgvsPro(dnaAssay, 'mapped')).toBe('NP_x:p.Leu2Phe')
+    expect(getHgvsPro(proteinAssay, 'submitted')).toBe('p.Leu6Gly')
+    expect(getHgvsPro(dnaAssay, 'reference')).toBe('NP_x:p.Leu2Phe')
   })
 })
 
 describe('labelForVariant — frame coords → submitted HGVS → URN', () => {
   it('prefers protein, in the requested frame', () => {
-    expect(labelForVariant(dnaAssay, 'raw')).toBe('p.Leu2Phe')
-    expect(labelForVariant(dnaAssay, 'mapped')).toBe('NP_x:p.Leu2Phe')
+    expect(labelForVariant(dnaAssay, 'submitted')).toBe('p.Leu2Phe')
+    expect(labelForVariant(dnaAssay, 'reference')).toBe('NP_x:p.Leu2Phe')
   })
 
   it('falls back to nucleotide when protein is absent', () => {
     const ntOnly = variant({variantUrn: 'urn:nt', hgvsNt: field('c.9A>G', 9, 'A', 'G')})
-    expect(labelForVariant(ntOnly, 'raw')).toBe('c.9A>G')
+    expect(labelForVariant(ntOnly, 'submitted')).toBe('c.9A>G')
   })
 
-  it('in the mapped frame, an unmapped variant falls back to its submitted HGVS, not the URN', () => {
+  it('in the reference frame, an unmapped variant falls back to its submitted HGVS, not the URN', () => {
     const unmappedIntronic = variant({variantUrn: 'urn:intron', hgvsNt: field('c.122-6T>A')})
-    expect(labelForVariant(unmappedIntronic, 'mapped')).toBe('c.122-6T>A')
+    expect(labelForVariant(unmappedIntronic, 'reference')).toBe('c.122-6T>A')
   })
 
   it('prefers submitted protein over submitted nucleotide in the fallback', () => {
@@ -138,46 +138,46 @@ describe('labelForVariant — frame coords → submitted HGVS → URN', () => {
       hgvsNt: field('c.6C>T', 6, 'C', 'T'),
       hgvsPro: field('p.Leu2Phe', 2, 'Leu', 'Phe')
     })
-    expect(labelForVariant(unmapped, 'mapped')).toBe('p.Leu2Phe')
+    expect(labelForVariant(unmapped, 'reference')).toBe('p.Leu2Phe')
   })
 
   it('falls back to splice, then to the URN when no other HGVS exists', () => {
     const spliceOnly = variant({variantUrn: 'urn:sp', hgvsSplice: field('c.1-2A>G')})
-    expect(labelForVariant(spliceOnly, 'raw')).toBe('c.1-2A>G')
-    expect(labelForVariant(spliceOnly, 'mapped')).toBe('c.1-2A>G')
-    expect(labelForVariant(variant({variantUrn: 'urn:bare'}), 'raw')).toBe('urn:bare')
-    expect(labelForVariant(variant({variantUrn: 'urn:bare'}), 'mapped')).toBe('urn:bare')
+    expect(labelForVariant(spliceOnly, 'submitted')).toBe('c.1-2A>G')
+    expect(labelForVariant(spliceOnly, 'reference')).toBe('c.1-2A>G')
+    expect(labelForVariant(variant({variantUrn: 'urn:bare'}), 'submitted')).toBe('urn:bare')
+    expect(labelForVariant(variant({variantUrn: 'urn:bare'}), 'reference')).toBe('urn:bare')
   })
 })
 
 describe('levelAvailable / sequenceTypeOptions — availability per frame', () => {
-  it('in raw frame levelAvailable returns true for both cdna and genomic when hgvsNt is present', () => {
-    // cdna and genomic alias hgvsNt in raw frame — both are technically available.
+  it('in submitted frame levelAvailable returns true for both cdna and genomic when hgvsNt is present', () => {
+    // cdna and genomic alias hgvsNt in submitted frame — both are technically available.
     // sequenceTypeOptions collapses them into one option using assayLevel as a label hint.
-    expect(levelAvailable([dnaAssay], 'cdna', 'raw')).toBe(true)
-    expect(levelAvailable([dnaAssay], 'genomic', 'raw')).toBe(true)
-    expect(levelAvailable([genomicAssay], 'cdna', 'raw')).toBe(true)
-    expect(levelAvailable([genomicAssay], 'genomic', 'raw')).toBe(true)
+    expect(levelAvailable([dnaAssay], 'cdna', 'submitted')).toBe(true)
+    expect(levelAvailable([dnaAssay], 'genomic', 'submitted')).toBe(true)
+    expect(levelAvailable([genomicAssay], 'cdna', 'submitted')).toBe(true)
+    expect(levelAvailable([genomicAssay], 'genomic', 'submitted')).toBe(true)
   })
 
-  it('sequenceTypeOptions offers one NT option in raw frame labelled Nucleotide, value keyed by assayLevel', () => {
-    expect(sequenceTypeOptions([dnaAssay], 'raw')).toEqual([
+  it('sequenceTypeOptions offers one NT option in submitted frame labelled Nucleotide, value keyed by assayLevel', () => {
+    expect(sequenceTypeOptions([dnaAssay], 'submitted')).toEqual([
       {title: 'Nucleotide', value: 'cdna'},
       {title: 'Protein', value: 'protein'}
     ])
-    expect(sequenceTypeOptions([genomicAssay], 'raw')).toEqual([{title: 'Nucleotide', value: 'genomic'}])
+    expect(sequenceTypeOptions([genomicAssay], 'submitted')).toEqual([{title: 'Nucleotide', value: 'genomic'}])
   })
 
-  it('a cdna assay with all mapped slots offers cdna, genomic, protein in mapped frame', () => {
-    expect(sequenceTypeOptions([dnaAssay], 'mapped')).toEqual([
+  it('a cdna assay with all mapped slots offers cdna, genomic, protein in reference frame', () => {
+    expect(sequenceTypeOptions([dnaAssay], 'reference')).toEqual([
       {title: 'cDNA', value: 'cdna'},
       {title: 'Genomic', value: 'genomic'},
       {title: 'Protein', value: 'protein'}
     ])
   })
 
-  it('a genomic assay offers cdna, genomic, protein in mapped frame', () => {
-    expect(sequenceTypeOptions([genomicAssay], 'mapped')).toEqual([
+  it('a genomic assay offers cdna, genomic, protein in reference frame', () => {
+    expect(sequenceTypeOptions([genomicAssay], 'reference')).toEqual([
       {title: 'cDNA', value: 'cdna'},
       {title: 'Genomic', value: 'genomic'},
       {title: 'Protein', value: 'protein'}
@@ -185,14 +185,14 @@ describe('levelAvailable / sequenceTypeOptions — availability per frame', () =
   })
 
   it('a protein assay never offers cdna or genomic — in either frame (#784)', () => {
-    expect(sequenceTypeOptions([proteinAssay], 'raw')).toEqual([{title: 'Protein', value: 'protein'}])
-    expect(sequenceTypeOptions([proteinAssay], 'mapped')).toEqual([{title: 'Protein', value: 'protein'}])
-    expect(levelAvailable([proteinAssay], 'cdna', 'mapped')).toBe(false)
-    expect(levelAvailable([proteinAssay], 'genomic', 'mapped')).toBe(false)
+    expect(sequenceTypeOptions([proteinAssay], 'submitted')).toEqual([{title: 'Protein', value: 'protein'}])
+    expect(sequenceTypeOptions([proteinAssay], 'reference')).toEqual([{title: 'Protein', value: 'protein'}])
+    expect(levelAvailable([proteinAssay], 'cdna', 'reference')).toBe(false)
+    expect(levelAvailable([proteinAssay], 'genomic', 'reference')).toBe(false)
   })
 
   it('availability is a set-wide OR across variants', () => {
-    expect(sequenceTypeOptions([dnaAssay, proteinAssay], 'mapped')).toEqual([
+    expect(sequenceTypeOptions([dnaAssay, proteinAssay], 'reference')).toEqual([
       {title: 'cDNA', value: 'cdna'},
       {title: 'Genomic', value: 'genomic'},
       {title: 'Protein', value: 'protein'}
@@ -202,16 +202,16 @@ describe('levelAvailable / sequenceTypeOptions — availability per frame', () =
 
 describe('resolveLevel — explicit frame→level coupling', () => {
   it('keeps the desired level when available', () => {
-    expect(resolveLevel([dnaAssay], 'protein', 'mapped')).toBe('protein')
-    expect(resolveLevel([dnaAssay], 'cdna', 'mapped')).toBe('cdna')
-    expect(resolveLevel([dnaAssay], 'genomic', 'mapped')).toBe('genomic')
+    expect(resolveLevel([dnaAssay], 'protein', 'reference')).toBe('protein')
+    expect(resolveLevel([dnaAssay], 'cdna', 'reference')).toBe('cdna')
+    expect(resolveLevel([dnaAssay], 'genomic', 'reference')).toBe('genomic')
   })
 
   it('falls back deterministically when the desired level is stranded', () => {
-    expect(resolveLevel([proteinAssay], 'cdna', 'mapped')).toBe('protein')
+    expect(resolveLevel([proteinAssay], 'cdna', 'reference')).toBe('protein')
   })
 
   it('returns null when no level is available', () => {
-    expect(resolveLevel([variant({variantUrn: 'urn:bare'})], 'protein', 'raw')).toBeNull()
+    expect(resolveLevel([variant({variantUrn: 'urn:bare'})], 'protein', 'submitted')).toBeNull()
   })
 })
diff --git a/src/composables/use-variant-coordinates.ts b/src/composables/use-variant-coordinates.ts
index a08f4747..ebc4d8e1 100644
--- a/src/composables/use-variant-coordinates.ts
+++ b/src/composables/use-variant-coordinates.ts
@@ -1,18 +1,20 @@
+import type {components} from '@/schema/openapi'
 import type {HgvsField, LeanVariant} from '@/lib/variants'
 
-/** The sequence level a coordinate is expressed in, mirroring the backend's AnnotationLayer enum. */
-export type SequenceLevel = 'cdna' | 'genomic' | 'protein'
+/** The sequence level a coordinate is expressed in — the canonical alias of the backend enum. Also the
+ *  value space for a measurement's assay level (see `@/lib/measurement-types`). */
+export type SequenceLevel = components['schemas']['SequenceLevel']
 
-/** The coordinate frame: `raw` = submitted/target numbering, `mapped` = reference numbering. */
-export type CoordinateFrame = 'raw' | 'mapped'
+/** The coordinate frame: `submitted` = submitted/target numbering, `reference` = reference numbering. */
+export type CoordinateFrame = 'submitted' | 'reference'
 
 /**
  * Stateless resolution of a variant's HGVS coordinate across two orthogonal axes — sequence
- * **level** (cdna / genomic / protein) and **frame** (raw/submitted ↔ mapped/reference).
+ * **level** (cdna / genomic / protein) and **frame** (submitted ↔ reference).
  *
  * `coordinateFor` is the single source of truth: every downstream derivation (heatmap x/y,
  * axis availability, labels, tooltips) resolves through it, so the (level, frame) → coordinate
- * mapping lives in exactly one place. The frame axis is load-bearing — raw and mapped are
+ * mapping lives in exactly one place. The frame axis is load-bearing — submitted and reference are
  * genuinely different coordinate systems, not the same grid with different captions.
  *
  * Shared between ScoreSetView (search, labels, level options) and ScoreSetHeatmap (plotting).
@@ -22,27 +24,27 @@ export function useVariantCoordinates() {
    * Resolve the HGVS coordinate for a variant at a given level and frame, or `null` when that
    * cell does not exist for the variant.
    *
-   * In the **mapped** frame each level routes directly to its `MappedTriple` slot:
+   * In the **reference** frame each level routes directly to its `MappedTriple` slot:
    *
-   * | level   | mapped slot       |
+   * | level   | reference slot    |
    * | ------- | ----------------- |
    * | cdna    | `mapped.cdna`     |
    * | genomic | `mapped.genomic`  |
    * | protein | `mapped.protein`  |
    *
-   * In the **raw** frame `cdna` and `genomic` both alias `hgvsNt` — the depositor submitted one
+   * In the **submitted** frame `cdna` and `genomic` both alias `hgvsNt` — the depositor submitted one
    * nucleotide string and the schema has a single field for it. The cdna/genomic distinction is a
-   * post-mapping conclusion, since raw submitted HGVS strings only have meaning relative to the submitted
+   * post-mapping conclusion, since submitted HGVS strings only have meaning relative to the submitted
    * sequence. Both levels therefore return `hgvsNt` and `levelAvailable` will report both as true whenever
    * `hgvsNt` is present. `sequenceTypeOptions` handles the display concern of offering only one NT option
-   * in raw frame.
+   * in the submitted frame.
    */
   function coordinateFor(variant: LeanVariant, level: SequenceLevel, frame: CoordinateFrame): HgvsField | null {
-    if (frame === 'raw') {
+    if (frame === 'submitted') {
       if (level === 'protein') return variant.hgvsPro ?? null
       return variant.hgvsNt ?? null
     }
-    // mapped: direct slot lookup — no assayLevel indirection needed.
+    // reference: direct slot lookup — no assayLevel indirection needed.
     return variant.mapped?.[level] ?? null
   }
 
@@ -50,8 +52,8 @@ export function useVariantCoordinates() {
    * The canonical nucleotide HGVS string for a variant in the given frame, if any — the single
    * nucleotide coordinate a compact surface (label pair, tooltip note, search chip) should show.
    *
-   * In the raw frame reads `hgvsNt` directly — no level discrimination, since the submitted string is
-   * a single field. In the mapped frame the ordering is prescriptive: **coding (`cdna`) preferred,
+   * In the submitted frame reads `hgvsNt` directly — no level discrimination, since the submitted string
+   * is a single field. In the reference frame the ordering is prescriptive: **coding (`cdna`) preferred,
    * genomic fallback.** The coding `NM_:c.` string is the natural pair of the protein `NP_:p.` change
    * (same transcript, same frame, the conventional `c. (p.)` citation), so a genomic-*measured* variant
    * surfaces its coding coordinate here rather than the `NC_:g.` one. It becomes the string only when
@@ -60,10 +62,10 @@ export function useVariantCoordinates() {
    * The plotted-axis coordinate is a different concern: when a surface has a user-selected level (the
    * heatmap axis) it should read `coordinateFor(variant, level, frame)` directly, not this.
    *
-   * Returns `undefined` for protein assays or unmapped variants in the mapped frame.
+   * Returns `undefined` for protein assays or unmapped variants in the reference frame.
    */
   function getHgvsNt(variant: LeanVariant, frame: CoordinateFrame): string | undefined {
-    if (frame === 'raw') return variant.hgvsNt?.hgvs
+    if (frame === 'submitted') return variant.hgvsNt?.hgvs
     return (variant.mapped?.cdna ?? variant.mapped?.genomic)?.hgvs
   }
 
@@ -77,11 +79,11 @@ export function useVariantCoordinates() {
    * protein > coding > genomic (the last two via `getHgvsNt`), then submitted-string fallbacks:
    *   frame protein → frame nucleotide (coding-preferred) → submitted protein → submitted nucleotide → submitted splice → URN.
    *
-   * The mapped frame has no coordinate for an unmapped variant, so before giving up to the bare URN we
+   * The reference frame has no coordinate for an unmapped variant, so before giving up to the bare URN we
    * fall back to the variant's submitted (target-frame) HGVS: an unmapped intronic variant still carries
-   * its `c.122-6T>A`, which is far more informative than the URN. In the raw frame the first two slots
-   * already are the submitted strings, so the fallback is inert there. The URN surfaces only when the
-   * variant carries no HGVS at all.
+   * its `c.122-6T>A`, which is far more informative than the URN. In the submitted frame the first two
+   * slots already are the submitted strings, so the fallback is inert there. The URN surfaces only when
+   * the variant carries no HGVS at all.
    */
   function labelForVariant(variant: LeanVariant, frame: CoordinateFrame): string {
     return (
@@ -105,17 +107,17 @@ export function useVariantCoordinates() {
   /**
    * The level options to offer for the given frame, in display order.
    *
-   * In the **mapped** frame returns whichever of cDNA / Genomic / Protein have data (up to all three
-   * for a nucleotide assay). In the **raw** frame cdna and genomic both alias `hgvsNt`, so the
+   * In the **reference** frame returns whichever of cDNA / Genomic / Protein have data (up to all three
+   * for a nucleotide assay). In the **submitted** frame cdna and genomic both alias `hgvsNt`, so the
    * distinction is meaningless — the submitted string is target-relative and its level is only
    * determined after mapping. A single "Nucleotide" option is returned instead, with the `value`
-   * keyed to `assayLevel` so that a frame switch routes to the right mapped slot.
+   * keyed to `assayLevel` so that a frame switch routes to the right reference slot.
    */
   function sequenceTypeOptions(
     variants: LeanVariant[],
     frame: CoordinateFrame
   ): Array<{title: string; value: SequenceLevel}> {
-    if (frame === 'raw') {
+    if (frame === 'submitted') {
       const options: Array<{title: string; value: SequenceLevel}> = []
 
       if (variants.some((v) => v.hgvsNt != null)) {
@@ -153,11 +155,12 @@ export function useVariantCoordinates() {
 
   /**
    * Whether the mapping/annotation step produced no mapped allele for this variant — keyed on the
-   * authoritative allele digest, which is null exactly when nothing was mapped. In the mapped frame
-   * such a variant has no mapped coordinate, so its label falls back to the submitted (target-frame)
+   * authoritative allele digest, which is null exactly when nothing was mapped. In the reference frame
+   * such a variant has no reference coordinate, so its label falls back to the submitted (target-frame)
    * HGVS. That fallback string can look mapped (accession-based target) or plainly unmapped
    * (sequence-based target, bare `c.` coordinate), so callers gate a "could not be mapped" note on this
-   * being true and the frame being mapped. The submitted string is shown by intent in the raw frame.
+   * being true and the frame being reference. The submitted string is shown by intent in the submitted
+   * frame.
    */
   function isUnmapped(variant: LeanVariant): boolean {
     return variant.assayLevelDigest == null

From da75505f942d5f01f12d3763cf68cb16fe8942a9 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Mon, 13 Jul 2026 14:13:38 -0700
Subject: [PATCH 28/84] refactor(measurements): consolidate level typing,
 rename study to score set

- reuse SequenceLevel in measurement-types instead of a parallel
  AssayLevel alias; drop the "level" suffix from bucket labels and
  reword relationship labels to read relative to the user's variant
- rename the aggregation's "study" concept to "score set"
  (aggregateByStudy -> aggregateByScoreSet, StudyEvidence ->
  ScoreSetEvidence) and read preferredClassification
- coalesce grouped-allele annotations field-by-field (present-wins) so
  a missing field on one level is carried through rather than read as
  divergence; only a real present-vs-present conflict splits the block
---
 src/lib/allele-grouping.test.ts         | 25 ++++++++++++++++
 src/lib/allele-grouping.ts              | 40 +++++++++++++++++++++++--
 src/lib/measurement-aggregation.test.ts | 34 ++++++++++-----------
 src/lib/measurement-aggregation.ts      | 34 ++++++++++-----------
 src/lib/measurement-types.ts            | 28 +++++++++--------
 5 files changed, 111 insertions(+), 50 deletions(-)

diff --git a/src/lib/allele-grouping.test.ts b/src/lib/allele-grouping.test.ts
index e1e32aab..e4e89b9d 100644
--- a/src/lib/allele-grouping.test.ts
+++ b/src/lib/allele-grouping.test.ts
@@ -80,6 +80,31 @@ describe('groupAlleles — projection pairing + confidence', () => {
     expect(pair.annotationsMatch).toBe(true)
   })
 
+  it('coalesces missing-vs-present annotations (missingness is not a difference)', () => {
+    // Only the cdna member is annotated; the genomic member has nothing. This must NOT read as divergence.
+    const groups = run({
+      alleles: nucleotide,
+      annotations: {c: vep('missense_variant')}
+    })
+    const pair = groups.find((g) => g.members.length === 2)!
+    expect(pair.annotationsMatch).toBe(true)
+    expect(pair.coalescedAnnotations?.vep?.consequence).toBe('missense_variant')
+  })
+
+  it('coalesces disjoint fields across levels into one block', () => {
+    const groups = run({
+      alleles: nucleotide,
+      annotations: {
+        c: {vep: {consequence: 'missense_variant'}},
+        g: {gnomad: {alleleFrequency: 0.01}}
+      } as unknown as Record<string, AlleleAnnotations>
+    })
+    const pair = groups.find((g) => g.members.length === 2)!
+    expect(pair.annotationsMatch).toBe(true)
+    expect(pair.coalescedAnnotations?.vep?.consequence).toBe('missense_variant')
+    expect(pair.coalescedAnnotations?.gnomad?.alleleFrequency).toBe(0.01)
+  })
+
   it('leaves a projection-failed candidate (dangling projectionOf) as a one-member group', () => {
     const groups = run({
       alleles: {
diff --git a/src/lib/allele-grouping.ts b/src/lib/allele-grouping.ts
index 82e58274..15f6071a 100644
--- a/src/lib/allele-grouping.ts
+++ b/src/lib/allele-grouping.ts
@@ -33,8 +33,17 @@ export interface AlleleGroup {
   pageRoot: boolean
   /** Grouped confidence: the strongest derivation among the members. */
   derivation: Derivation | null
-  /** Members share one annotation block, so it renders once; otherwise render each level's separately. */
+  /**
+   * Whether the members' annotations can render as one block. Missingness is NOT a difference: a field
+   * present on one level and absent on the other coalesces to the present value. Only a genuine
+   * present-vs-present disagreement makes this false (→ render each level separately, with a note).
+   */
   annotationsMatch: boolean
+  /**
+   * The per-field union of the members' annotations (present-wins). Used to render the single block when
+   * `annotationsMatch` — so a coalesced group shows every field any member has, not just member[0]'s.
+   */
+  coalescedAnnotations: AlleleAnnotations | null
   /** Distinct linked CAIDs to surface, excluding the page anchor (which is this page). */
   clingenLinks: string[]
 }
@@ -46,6 +55,27 @@ export interface GroupAllelesInput {
   pageClingenAlleleId: string | null
 }
 
+/**
+ * Merge the members' annotations field-by-field, present-wins. Missingness is not divergence: a field on
+ * only one member is simply carried through. `conflict` is true only when two members both carry a field
+ * and disagree — the case worth flagging as "differs by level".
+ */
+function coalesceAnnotations(members: AlleleMember[]): {merged: AlleleAnnotations | null; conflict: boolean} {
+  const present = members.map((m) => m.annotations).filter((a): a is AlleleAnnotations => a != null)
+  if (present.length === 0) return {merged: null, conflict: false}
+  if (present.length === 1) return {merged: present[0], conflict: false}
+
+  const merged: Record<string, unknown> = {}
+  let conflict = false
+  for (const key of _.union(...present.map((a) => Object.keys(a)))) {
+    const values = present.map((a) => (a as Record<string, unknown>)[key]).filter((v) => v != null)
+    if (values.length === 0) continue
+    if (values.length > 1 && !values.every((v) => _.isEqual(v, values[0]))) conflict = true
+    merged[key] = values[0]
+  }
+  return {merged: merged as AlleleAnnotations, conflict}
+}
+
 function pickDerivation(members: AlleleMember[]): Derivation | null {
   let best: Derivation | null = null
   let bestRank = Infinity
@@ -115,14 +145,18 @@ export function groupAlleles(input: GroupAllelesInput): AlleleGroup[] {
     // Sort members genomic → cDNA → protein so the group reads consistently regardless of input order.
     members.sort((a, b) => (LEVEL_ORDER[a.level ?? ''] ?? 99) - (LEVEL_ORDER[b.level ?? ''] ?? 99))
 
+    // Coalesce annotations across levels (present-wins); only a real present-vs-present disagreement
+    // counts as divergence. Missing-on-one-level is not treated as different.
+    const {merged, conflict} = coalesceAnnotations(members)
+
     groups.push({
       key: members[0].digest,
       members,
       measured: members.some((m) => m.derivation === 'authoritative'),
       pageRoot: members.some((m) => m.pageRoot),
       derivation: pickDerivation(members),
-      // If both members carry identical annotations, the UI renders one shared block instead of two.
-      annotationsMatch: members.length < 2 || _.isEqual(members[0].annotations, members[1].annotations),
+      annotationsMatch: !conflict,
+      coalescedAnnotations: merged,
       clingenLinks: _.uniq(
         members.map((m) => m.clingenAlleleId).filter((id): id is string => id != null && id !== pageClingenAlleleId)
       )
diff --git a/src/lib/measurement-aggregation.test.ts b/src/lib/measurement-aggregation.test.ts
index 37f0142f..e55bbaa1 100644
--- a/src/lib/measurement-aggregation.test.ts
+++ b/src/lib/measurement-aggregation.test.ts
@@ -1,6 +1,6 @@
 import {describe, expect, it} from 'vitest'
 
-import {aggregateByStudy} from '@/lib/measurement-aggregation'
+import {aggregateByScoreSet} from '@/lib/measurement-aggregation'
 import type {components} from '@/schema/openapi'
 
 type AlleleMeasurement = components['schemas']['AlleleMeasurement']
@@ -11,21 +11,21 @@ function m(overrides: Partial<AlleleMeasurement>): AlleleMeasurement {
     relationship: 'nucleotide_encoding',
     assayLevel: 'cdna',
     scoreSetUrn: 'urn:mavedb:x',
-    scoreSetTitle: 'Study X',
+    scoreSetTitle: 'Score set X',
     ...overrides
   } as AlleleMeasurement
 }
 
-function classified(fc: string): AlleleMeasurement['primaryClassification'] {
-  return {functionalClassification: fc} as AlleleMeasurement['primaryClassification']
+function classified(fc: string): AlleleMeasurement['preferredClassification'] {
+  return {functionalClassification: fc} as AlleleMeasurement['preferredClassification']
 }
 
-describe('aggregateByStudy', () => {
-  it('collapses a study’s many nucleotide encodings into one entry with a score range', () => {
-    const result = aggregateByStudy([
-      m({scoreSetUrn: 'urn:s1', scoreSetTitle: 'Findlay', score: -2.0, primaryClassification: classified('abnormal')}),
-      m({scoreSetUrn: 'urn:s1', scoreSetTitle: 'Findlay', score: -1.7, primaryClassification: classified('abnormal')}),
-      m({scoreSetUrn: 'urn:s1', scoreSetTitle: 'Findlay', score: -1.9, primaryClassification: classified('abnormal')})
+describe('aggregateByScoreSet', () => {
+  it('collapses a score set’s many nucleotide encodings into one entry with a score range', () => {
+    const result = aggregateByScoreSet([
+      m({scoreSetUrn: 'urn:s1', scoreSetTitle: 'Findlay', score: -2.0, preferredClassification: classified('abnormal')}),
+      m({scoreSetUrn: 'urn:s1', scoreSetTitle: 'Findlay', score: -1.7, preferredClassification: classified('abnormal')}),
+      m({scoreSetUrn: 'urn:s1', scoreSetTitle: 'Findlay', score: -1.9, preferredClassification: classified('abnormal')})
     ])
     expect(result).toHaveLength(1)
     expect(result[0].measurements).toHaveLength(3)
@@ -34,8 +34,8 @@ describe('aggregateByStudy', () => {
     expect(result[0].scoreRange).toEqual({min: -2.0, max: -1.7})
   })
 
-  it('separates distinct studies and sorts the more-corroborated one first', () => {
-    const result = aggregateByStudy([
+  it('separates distinct score sets and sorts the more-corroborated one first', () => {
+    const result = aggregateByScoreSet([
       m({scoreSetUrn: 'urn:solo', scoreSetTitle: 'Giacomelli', assayLevel: 'protein', score: -2.1}),
       m({scoreSetUrn: 'urn:many', scoreSetTitle: 'Findlay', score: -2.0}),
       m({scoreSetUrn: 'urn:many', scoreSetTitle: 'Findlay', score: -1.8})
@@ -45,17 +45,17 @@ describe('aggregateByStudy', () => {
     expect(result[1].level).toBe('protein')
   })
 
-  it('flags a study that assayed both levels as mixed and surfaces internal disagreement', () => {
-    const result = aggregateByStudy([
-      m({scoreSetUrn: 'urn:s', assayLevel: 'protein', primaryClassification: classified('abnormal')}),
-      m({scoreSetUrn: 'urn:s', assayLevel: 'cdna', primaryClassification: classified('normal')})
+  it('flags a score set that assayed both levels as mixed and surfaces internal disagreement', () => {
+    const result = aggregateByScoreSet([
+      m({scoreSetUrn: 'urn:s', assayLevel: 'protein', preferredClassification: classified('abnormal')}),
+      m({scoreSetUrn: 'urn:s', assayLevel: 'cdna', preferredClassification: classified('normal')})
     ])
     expect(result[0].level).toBe('mixed')
     expect(new Set(result[0].classifications)).toEqual(new Set(['abnormal', 'normal']))
   })
 
   it('returns a null score range when no measurement carries a score', () => {
-    const result = aggregateByStudy([m({scoreSetUrn: 'urn:s', score: null})])
+    const result = aggregateByScoreSet([m({scoreSetUrn: 'urn:s', score: null})])
     expect(result[0].scoreRange).toBeNull()
   })
 })
diff --git a/src/lib/measurement-aggregation.ts b/src/lib/measurement-aggregation.ts
index 33cf8130..395878f2 100644
--- a/src/lib/measurement-aggregation.ts
+++ b/src/lib/measurement-aggregation.ts
@@ -2,20 +2,20 @@ import type {components} from '@/schema/openapi'
 
 type AlleleMeasurement = components['schemas']['AlleleMeasurement']
 type FunctionalClassification = NonNullable<
-  NonNullable<AlleleMeasurement['primaryClassification']>['functionalClassification']
+  NonNullable<AlleleMeasurement['preferredClassification']>['functionalClassification']
 >
 
 export type EvidenceLevel = 'protein' | 'nucleotide' | 'mixed'
 
-/** One study's evidence for a change, collapsed from however many equivalence-class representations it assayed. */
-export interface StudyEvidence {
+/** One score set's evidence for a change, collapsed from however many equivalence-class representations it assayed. */
+export interface ScoreSetEvidence {
   scoreSetUrn: string
   scoreSetTitle: string
   /** The underlying measurements, revealed on expand (a saturation screen may hold many). */
   measurements: AlleleMeasurement[]
-  /** The assay level(s) this study contributed: all-protein, all-nucleotide, or both. */
+  /** The assay level(s) this score set contributed: all-protein, all-nucleotide, or both. */
   level: EvidenceLevel
-  /** Distinct functional classifications present — one value = concordant, several = the study disagrees internally. */
+  /** Distinct functional classifications present — one value = concordant, several = the score set disagrees internally. */
   classifications: FunctionalClassification[]
   /** Span of functional scores, or null when none carry a score. `min === max` for a single value. */
   scoreRange: {min: number; max: number} | null
@@ -38,29 +38,29 @@ function levelOf(measurements: AlleleMeasurement[]): EvidenceLevel {
 
 /**
  * Collapse a closed equivalence set (a change's protein-consequence assays + its sibling nucleotide
- * encodings) into one entry per study. Reverse translation makes the individual members redundant — they
- * re-encode the same functional change — so search shows per-study evidence (level, call, score range)
- * rather than a row per representation. Studies with more corroborating measurements sort first.
+ * encodings) into one entry per score set. Reverse translation makes the individual members redundant —
+ * they re-encode the same functional change — so search shows per-score-set evidence (level, call, score
+ * range) rather than a row per representation. Score sets with more corroborating measurements sort first.
  */
-export function aggregateByStudy(measurements: AlleleMeasurement[]): StudyEvidence[] {
-  const byStudy = new Map<string, AlleleMeasurement[]>()
+export function aggregateByScoreSet(measurements: AlleleMeasurement[]): ScoreSetEvidence[] {
+  const byScoreSet = new Map<string, AlleleMeasurement[]>()
   for (const m of measurements) {
-    const existing = byStudy.get(m.scoreSetUrn)
+    const existing = byScoreSet.get(m.scoreSetUrn)
     if (existing) existing.push(m)
-    else byStudy.set(m.scoreSetUrn, [m])
+    else byScoreSet.set(m.scoreSetUrn, [m])
   }
 
-  const studies: StudyEvidence[] = []
-  for (const [scoreSetUrn, list] of byStudy) {
+  const scoreSets: ScoreSetEvidence[] = []
+  for (const [scoreSetUrn, list] of byScoreSet) {
     const scores = list.map((m) => m.score).filter((s): s is number => s != null)
     const classifications = [
       ...new Set(
         list
-          .map((m) => m.primaryClassification?.functionalClassification)
+          .map((m) => m.preferredClassification?.functionalClassification)
           .filter((c): c is FunctionalClassification => c != null)
       )
     ]
-    studies.push({
+    scoreSets.push({
       scoreSetUrn,
       scoreSetTitle: list[0].scoreSetTitle,
       measurements: list,
@@ -70,7 +70,7 @@ export function aggregateByStudy(measurements: AlleleMeasurement[]): StudyEviden
     })
   }
 
-  return studies.sort(
+  return scoreSets.sort(
     (a, b) => b.measurements.length - a.measurements.length || a.scoreSetTitle.localeCompare(b.scoreSetTitle)
   )
 }
diff --git a/src/lib/measurement-types.ts b/src/lib/measurement-types.ts
index a271b6c7..c7a5d636 100644
--- a/src/lib/measurement-types.ts
+++ b/src/lib/measurement-types.ts
@@ -1,8 +1,9 @@
 import type {components} from '@/schema/openapi'
+import type {SequenceLevel} from '@/composables/use-variant-coordinates'
 
-// The assayed level of a measurement (from the mapping record). The two nucleotide levels share one
-// visual bucket; protein is its own.
-export type AssayLevel = components['schemas']['AnnotationLayer'] // 'protein' | 'cdna' | 'genomic'
+// A measurement is assayed at one of the three sequence levels ('protein' | 'cdna' | 'genomic'). The two
+// nucleotide levels share one visual bucket; protein is its own. "Assay level" is the concept; the value
+// space is just `SequenceLevel`, so we reuse that type rather than mint a parallel one.
 export type MeasurementRelationship = components['schemas']['MeasurementRelationship']
 export type LevelBucket = 'nucleotide' | 'protein'
 
@@ -11,7 +12,7 @@ export function assayLevelBucket(level: string | null | undefined): LevelBucket
 }
 
 // Per-level display labels for the three assay levels (distinct from the two-way bucket labels above).
-export const ASSAY_LEVEL_LABELS: Record<AssayLevel, string> = {
+export const ASSAY_LEVEL_LABELS: Record<SequenceLevel, string> = {
   genomic: 'Genomic',
   cdna: 'Coding',
   protein: 'Protein'
@@ -19,12 +20,12 @@ export const ASSAY_LEVEL_LABELS: Record<AssayLevel, string> = {
 
 // A score set's variants are all assayed at one level, but some may be unmapped (null). Return the most
 // common non-null level, or null when nothing is mapped.
-export function dominantAssayLevel(levels: Array<AssayLevel | null | undefined>): AssayLevel | null {
-  const counts = new Map<AssayLevel, number>()
+export function dominantAssayLevel(levels: Array<SequenceLevel | null | undefined>): SequenceLevel | null {
+  const counts = new Map<SequenceLevel, number>()
   for (const level of levels) {
     if (level) counts.set(level, (counts.get(level) ?? 0) + 1)
   }
-  let best: AssayLevel | null = null
+  let best: SequenceLevel | null = null
   let bestCount = 0
   for (const [level, count] of counts) {
     if (count > bestCount) {
@@ -36,8 +37,8 @@ export function dominantAssayLevel(levels: Array<AssayLevel | null | undefined>)
 }
 
 export const LEVEL_BUCKET_LABELS: Record<LevelBucket, {full: string; short: string}> = {
-  nucleotide: {full: 'Nucleotide level', short: 'Nucleotide'},
-  protein: {full: 'Protein level', short: 'Protein'}
+  nucleotide: {full: 'Nucleotide', short: 'Nucleotide'},
+  protein: {full: 'Protein', short: 'Protein'}
 }
 
 export const LEVEL_BUCKET_CLASSES: Record<LevelBucket, string> = {
@@ -45,9 +46,10 @@ export const LEVEL_BUCKET_CLASSES: Record<LevelBucket, string> = {
   protein: 'bg-protein-light text-protein'
 }
 
-// How a measurement relates to the queried ClinGen allele — the RT asymmetry.
+// How a measurement relates to the queried ClinGen allele — the RT asymmetry. Phrased relative to the
+// user's variant, so the labels self-explain under the "relative to your variant" anchor heading.
 export const RELATIONSHIP_LABELS: Record<MeasurementRelationship, string> = {
-  direct: 'Direct measurement',
-  protein_consequence: 'Protein consequence',
-  nucleotide_encoding: 'Nucleotide encoding'
+  direct: 'Your variant',
+  protein_consequence: 'Its protein consequence',
+  nucleotide_encoding: 'Encodes the protein consequence'
 }

From 1c38f90f91f028e67ce2f5fbfbfb99bfb8f062c3 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Mon, 13 Jul 2026 14:45:11 -0700
Subject: [PATCH 29/84] feat(clinvar-controls): add placement reducer,
 notables, and store

Rename clinical-controls to clinvar-controls and build out the ClinVar
control data layer the variant page and histogram consume.

- add reduceControlPlacement (the D78 divergence fold) producing a
  representative call plus winning-set classifications and directional
  flags, exposed as ClinvarControlPlacement
- add notables helpers: per-class clinical extremes, consequence
  exemplars, score extremes, and median/MAD deviation
- add the useClinvarControls store composable
- alias control types to the generated schema instead of hand-mirroring
  them, and add isClassifiedSignificance to reject ClinVar's "-"
  placeholder significances
- move formatClinvarVersion in from lib/formats and point
  ClinvarControlVariant at ClinvarControlPlacement
- add tooltipFootnote and tooltipEmptyLine helpers
---
 src/composables/use-clinvar-controls.test.ts  |  86 +++++++
 src/composables/use-clinvar-controls.ts       | 217 +++++++++++++++++
 src/lib/clinvar-control-placement.test.ts     | 226 ++++++++++++++++++
 src/lib/clinvar-control-placement.ts          | 127 ++++++++++
 ...inical-controls.ts => clinvar-controls.ts} |  66 +++--
 src/lib/formats.ts                            |   7 -
 src/lib/notables.test.ts                      | 162 +++++++++++++
 src/lib/notables.ts                           | 140 +++++++++++
 src/lib/tooltips.ts                           |   8 +
 src/lib/variants.ts                           |  17 +-
 10 files changed, 1024 insertions(+), 32 deletions(-)
 create mode 100644 src/composables/use-clinvar-controls.test.ts
 create mode 100644 src/composables/use-clinvar-controls.ts
 create mode 100644 src/lib/clinvar-control-placement.test.ts
 create mode 100644 src/lib/clinvar-control-placement.ts
 rename src/lib/{clinical-controls.ts => clinvar-controls.ts} (69%)
 create mode 100644 src/lib/notables.test.ts
 create mode 100644 src/lib/notables.ts

diff --git a/src/composables/use-clinvar-controls.test.ts b/src/composables/use-clinvar-controls.test.ts
new file mode 100644
index 00000000..75022790
--- /dev/null
+++ b/src/composables/use-clinvar-controls.test.ts
@@ -0,0 +1,86 @@
+import {effectScope, nextTick, ref} from 'vue'
+import {afterEach, beforeEach, describe, expect, test, vi} from 'vitest'
+
+import axios from 'axios'
+
+import {useClinvarControls} from '@/composables/use-clinvar-controls'
+import type {DisplayVariant} from '@/lib/variants'
+
+vi.mock('axios')
+
+const OPTIONS = [{dbName: 'ClinVar', availableVersions: ['clinvar_2025']}]
+const CONTROLS = [
+  {
+    dbName: 'ClinVar',
+    dbVersion: 'clinvar_2025',
+    dbIdentifier: '12345',
+    clinicalSignificance: 'Pathogenic',
+    clinicalReviewStatus: 'criteria provided, single submitter',
+    clinvarLinks: [{variantUrn: 'urn:mavedb:1#1'}]
+  }
+]
+
+function mockAxios() {
+  ;(axios.get as unknown as ReturnType<typeof vi.fn>).mockImplementation((url: string) => {
+    if (url.endsWith('/clinical-controls/options')) return Promise.resolve({status: 200, data: OPTIONS})
+    if (url.includes('/clinical-controls')) return Promise.resolve({status: 200, data: CONTROLS})
+    return Promise.reject(new Error(`unexpected url ${url}`))
+  })
+}
+
+async function settle(ticks = 6) {
+  for (let i = 0; i < ticks; i++) {
+    await nextTick()
+    await Promise.resolve()
+  }
+}
+
+describe('useClinvarControls', () => {
+  beforeEach(() => {
+    vi.clearAllMocks()
+    mockAxios()
+  })
+  afterEach(() => {
+    vi.restoreAllMocks()
+    mockAxios()
+  })
+
+  test('variants present before controls: associates and flips someVariants', async () => {
+    const variants = ref<DisplayVariant[] | null>([
+      {variantUrn: 'urn:mavedb:1#1', score: -2} as unknown as DisplayVariant,
+      {variantUrn: 'urn:mavedb:1#2', score: 0.1} as unknown as DisplayVariant
+    ])
+    const scope = effectScope()
+    let store!: ReturnType<typeof useClinvarControls>
+    scope.run(() => {
+      store = useClinvarControls(ref('urn:mavedb:1'), variants)
+    })
+    await settle()
+
+    expect(store.refreshed).toBe(true)
+    expect(store.controls.length).toBe(1)
+    expect(store.someVariantsHaveClinicalSignificance).toBe(true)
+    expect((variants.value![0] as {control?: unknown}).control).toBeTruthy()
+    expect((variants.value![1] as {control?: unknown}).control ?? null).toBeNull()
+    scope.stop()
+  })
+
+  test('variants arrive AFTER controls: re-associates when variants populate', async () => {
+    const variants = ref<DisplayVariant[] | null>(null)
+    const scope = effectScope()
+    let store!: ReturnType<typeof useClinvarControls>
+    scope.run(() => {
+      store = useClinvarControls(ref('urn:mavedb:1'), variants)
+    })
+    await settle()
+    // Controls loaded, but no variants yet to associate.
+    expect(store.controls.length).toBe(1)
+    expect(store.someVariantsHaveClinicalSignificance).toBe(false)
+
+    variants.value = [{variantUrn: 'urn:mavedb:1#1', score: -2} as unknown as DisplayVariant]
+    await settle()
+    expect(store.someVariantsHaveClinicalSignificance).toBe(true)
+    expect((variants.value[0] as {control?: unknown}).control).toBeTruthy()
+    scope.stop()
+  })
+})
diff --git a/src/composables/use-clinvar-controls.ts b/src/composables/use-clinvar-controls.ts
new file mode 100644
index 00000000..adf46505
--- /dev/null
+++ b/src/composables/use-clinvar-controls.ts
@@ -0,0 +1,217 @@
+import axios from 'axios'
+import {reactive, watch, watchEffect, type Ref} from 'vue'
+
+import config from '@/config'
+import {reduceControlPlacement, type ControlLink} from '@/lib/clinvar-control-placement'
+import {DEFAULT_CLINVAR_CONTROL_DB, DEFAULT_CLNREVSTAT_FIELD, DEFAULT_CLNSIG_FIELD} from '@/lib/clinvar-controls'
+import type {ClinvarControl, ClinvarControlOption} from '@/lib/clinvar-controls'
+import type {DisplayVariant} from '@/lib/variants'
+
+/**
+ * Shared clinical-control state for a single score set. This was previously owned privately by
+ * `ScoreSetHistogram.vue`. The fetch is keyed purely by (db, version) — the interactive minimum-star
+ * filter stays a per-consumer display concern and is NOT part of this store.
+ *
+ * The store owns db/version selection, the controls fetch (cached per db+version), and mutation of
+ * `variant.control` onto the passed-in variants. It self-drives via watchers on `urn` and `variants`;
+ * consumers only read state and (for the histogram's selectors) two-way bind `controlDb`/`controlVersion`.
+ */
+export interface ClinvarControlsStore {
+  /** Available (db, versions) pairs for this score set. */
+  options: ClinvarControlOption[]
+  /** Controls for the currently selected (db, version). */
+  controls: ClinvarControl[]
+  /** Selected control database. Two-way bound by the histogram's DB selector. */
+  controlDb: ClinvarControlOption | null
+  /** Selected control version. Two-way bound by the histogram's version selector. */
+  controlVersion: string | null
+  /** True once an options+controls fetch cycle has settled (drives loading spinners / gating). */
+  refreshed: boolean
+  /** True once controls have been associated onto the variants (or a load failed). */
+  associated: boolean
+  /** True when at least one variant carries a matched clinvar control. */
+  someVariantsHaveClinicalSignificance: boolean
+  /** Derived: whether a DB/version selector is worth showing (more than one choice exists). Read-only in practice. */
+  showOptions: boolean
+}
+
+export function useClinvarControls(
+  urn: Ref<string | null | undefined>,
+  variants: Ref<DisplayVariant[] | null>
+): ClinvarControlsStore {
+  const state: ClinvarControlsStore = reactive({
+    options: [] as ClinvarControlOption[],
+    controls: [] as ClinvarControl[],
+    controlDb: null as ClinvarControlOption | null,
+    controlVersion: null as string | null,
+    refreshed: false,
+    associated: false,
+    someVariantsHaveClinicalSignificance: false,
+    showOptions: false
+  })
+
+  // A DB/version selector is only worth showing when there's more than one choice.
+  watchEffect(() => {
+    const hasMultipleDbs = state.options.length > 1
+    const hasSingleDbWithMultipleVersions = state.options.length === 1 && state.options[0].availableVersions.length > 1
+    state.showOptions = hasMultipleDbs || hasSingleDbWithMultipleVersions
+  })
+
+  // Non-reactive controls cache, keyed [dbName][version]. Rebuilt whenever the options change.
+  let cache: Record<string, Record<string, ClinvarControl[]>> = {}
+
+  async function loadOptions() {
+    const scoreSetUrn = urn.value
+    if (!scoreSetUrn) {
+      return
+    }
+    try {
+      const response = await axios.get(`${config.apiBaseUrl}/score-sets/${scoreSetUrn}/clinical-controls/options`)
+      if (response.status === 200) {
+        state.options = response.data
+      }
+    } catch {
+      // Still settle the flags so loading spinners clear and dependent views fall into an empty state.
+      state.refreshed = true
+      state.associated = true
+    }
+  }
+
+  async function loadControls() {
+    if (state.controlDb && state.controlVersion && cache[state.controlDb.dbName]?.[state.controlVersion].length > 0) {
+      state.controls = cache[state.controlDb.dbName][state.controlVersion]
+      state.refreshed = true
+      return
+    }
+
+    state.refreshed = false
+    let queryString = ''
+    if (state.controlDb) {
+      queryString += `?db=${encodeURIComponent(state.controlDb.dbName)}`
+    }
+    if (state.controlVersion) {
+      queryString += queryString
+        ? `&version=${encodeURIComponent(state.controlVersion)}`
+        : `?version=${encodeURIComponent(state.controlVersion)}`
+    }
+
+    const scoreSetUrn = urn.value
+    if (scoreSetUrn) {
+      try {
+        const response = await axios.get(
+          `${config.apiBaseUrl}/score-sets/${scoreSetUrn}/clinical-controls${queryString}`
+        )
+        if (response.data) {
+          state.controls = response.data
+          if (state.controlDb && state.controlVersion) {
+            cache[state.controlDb.dbName][state.controlVersion] = response.data
+          }
+        }
+      } catch {
+        state.associated = true
+      }
+    }
+    state.refreshed = true
+  }
+
+  function disassociate() {
+    state.associated = false
+    state.someVariantsHaveClinicalSignificance = false
+    for (const variant of variants.value ?? []) {
+      variant.control = null
+    }
+  }
+
+  function associate() {
+    const list = variants.value ?? []
+
+    // Gather every control reaching each variant, tagged with the digest of the allele it annotates, then
+    // reduce based on precedence + hard/soft discordance. A protein-change variant whose DNA siblings
+    // disagree can be reached by several controls; the fold — not last-write-wins — decides its placement.
+    const linksByUrn = new Map<string, ControlLink[]>()
+    for (const control of state.controls) {
+      for (const clinvarLink of control.clinvarLinks) {
+        if (!clinvarLink.variantUrn) {
+          continue
+        }
+        const links = linksByUrn.get(clinvarLink.variantUrn) ?? []
+        links.push({
+          significance: control[DEFAULT_CLNSIG_FIELD],
+          reviewStatus: control[DEFAULT_CLNREVSTAT_FIELD],
+          alleleDigest: clinvarLink.alleleDigest,
+          dbIdentifier: control.dbIdentifier
+        })
+        linksByUrn.set(clinvarLink.variantUrn, links)
+      }
+    }
+
+    let usableAny = false
+    for (const variant of list) {
+      const links = linksByUrn.get(variant.variantUrn)
+      const placement = links ? reduceControlPlacement(links, variant.assayLevelDigest) : null
+      variant.control = placement
+      // "Has clinical significance" gates the clinical view — a hard-discordant variant carries ClinVar
+      // data but is not a usable control, so it doesn't count toward showing the view.
+      if (placement && !placement.excluded) {
+        usableAny = true
+      }
+    }
+    state.associated = true
+    state.someVariantsHaveClinicalSignificance = usableAny
+  }
+
+  // A new score set resets everything and refetches the available options.
+  watch(
+    urn,
+    () => {
+      state.options = []
+      state.controls = []
+      state.controlDb = null
+      state.controlVersion = null
+      state.refreshed = false
+      state.associated = false
+      state.someVariantsHaveClinicalSignificance = false
+      cache = {}
+      loadOptions()
+    },
+    {immediate: true}
+  )
+
+  // Fresh options pick a default db+version (preferring ClinVar) and rebuild the cache skeleton.
+  watch(
+    () => state.options,
+    () => {
+      if (!state.controlDb) {
+        const defaultDb = state.options.find((option) => option.dbName === DEFAULT_CLINVAR_CONTROL_DB)
+        state.controlDb = defaultDb ? defaultDb : (state.options[0] ?? null)
+      }
+      if (!state.controlVersion) {
+        state.controlVersion = state.controlDb?.availableVersions[0] ?? null
+      }
+      const next: Record<string, Record<string, ClinvarControl[]>> = {}
+      for (const dbOption of state.options) {
+        next[dbOption.dbName] = {}
+        for (const version of dbOption.availableVersions) {
+          next[dbOption.dbName][version] = []
+        }
+      }
+      cache = next
+    }
+  )
+
+  // Any change to the selected (db, version) reloads controls.
+  watch(
+    () => `${state.controlDb?.dbName}|${state.controlVersion}`,
+    () => {
+      loadControls()
+    }
+  )
+
+  // New controls (or a new variant set arriving) re-associates onto the variants.
+  watch([() => state.controls, variants], () => {
+    disassociate()
+    associate()
+  })
+
+  return state
+}
diff --git a/src/lib/clinvar-control-placement.test.ts b/src/lib/clinvar-control-placement.test.ts
new file mode 100644
index 00000000..01b16335
--- /dev/null
+++ b/src/lib/clinvar-control-placement.test.ts
@@ -0,0 +1,226 @@
+import {describe, expect, test} from 'vitest'
+
+import {reduceControlPlacement, type ClinvarControlPlacement, type ControlLink} from '@/lib/clinvar-control-placement'
+
+// Review statuses and their star ratings (mirrors CLINVAR_REVIEW_STATUS_STARS), so the representative-pick
+// and per-classification-status tests are explicit about stars.
+const NO_CRITERIA = 'no assertion criteria provided' // 0★
+const ONE_STAR = 'criteria provided, single submitter' // 1★
+const TWO_STAR = 'criteria provided, multiple submitters, no conflicts' // 2★
+const THREE_STAR = 'reviewed by expert panel' // 3★
+
+const ASSAY = 'assayed-level-digest'
+const SIB = 'sibling-digest'
+const SIB2 = 'sibling-digest-2'
+
+// Significances (exact strings the P/LP and B/LB membership lists key on).
+const P = 'Pathogenic'
+const LP = 'Likely pathogenic'
+const PLP = 'Pathogenic/Likely pathogenic'
+const B = 'Benign'
+const LB = 'Likely benign'
+const BLB = 'Benign/Likely benign'
+const VUS = 'Uncertain significance'
+const CONFLICTING = 'Conflicting classifications of pathogenicity'
+
+function link(significance: string, alleleDigest?: string, reviewStatus: string = ONE_STAR): ControlLink {
+  return {significance, reviewStatus, alleleDigest, dbIdentifier: `${significance}@${alleleDigest ?? '?'}`}
+}
+
+/** The set of distinct significances in a placement (order-independent assertions). */
+const sigs = (p: ClinvarControlPlacement) => p.classifications.map((c) => c.significance).sort()
+
+describe('reduceControlPlacement — divergence fold', () => {
+  test('no controls reach the variant → null', () => {
+    expect(reduceControlPlacement([], ASSAY)).toBeNull()
+  })
+
+  describe('single direct call at the assayed level (projected = false)', () => {
+    test.each([
+      [P, {directional: true, excluded: false}],
+      [LP, {directional: true, excluded: false}],
+      [PLP, {directional: true, excluded: false}],
+      [B, {directional: true, excluded: false}],
+      [LB, {directional: true, excluded: false}],
+      [BLB, {directional: true, excluded: false}],
+      [VUS, {directional: false, excluded: false}],
+      // ClinVar's own aggregate "conflicting" value is neither pathogenic- nor benign-side, so it is not
+      // directional and does not by itself trigger hard-discordance exclusion.
+      [CONFLICTING, {directional: false, excluded: false}]
+    ])('%s → directional/excluded flags, not projected', (significance, expected) => {
+      const p = reduceControlPlacement([link(significance, ASSAY)], ASSAY)!
+      expect(p.directional).toBe(expected.directional)
+      expect(p.excluded).toBe(expected.excluded)
+      expect(p.projected).toBe(false)
+      expect(sigs(p)).toEqual([significance])
+      expect(p.clinicalSignificance).toBe(significance)
+    })
+  })
+
+  describe('precedence — the assayed level wins; siblings are ignored', () => {
+    test('a lone assayed VUS blocks a sibling LP (any assayed call stops the fall-through)', () => {
+      const p = reduceControlPlacement([link(VUS, ASSAY), link(LP, SIB)], ASSAY)!
+      expect(sigs(p)).toEqual([VUS])
+      expect(p.directional).toBe(false)
+      expect(p.projected).toBe(false)
+    })
+
+    test('an assayed directional call is not overridden into hard discordance by a discordant sibling', () => {
+      const p = reduceControlPlacement([link(P, ASSAY), link(B, SIB)], ASSAY)!
+      expect(sigs(p)).toEqual([P])
+      expect(p.excluded).toBe(false)
+      expect(p.projected).toBe(false)
+    })
+
+    test('multiple assayed-level calls are all consulted (assayed-level discordance is still real)', () => {
+      // Two ClinVar submissions on the *same* assayed allele that disagree on direction → excluded.
+      const p = reduceControlPlacement([link(P, ASSAY), link(B, ASSAY), link(LP, SIB)], ASSAY)!
+      expect(p.excluded).toBe(true)
+      expect(p.projected).toBe(false)
+      // The sibling LP is not consulted — only the two assayed-level calls.
+      expect(sigs(p)).toEqual([B, P])
+    })
+  })
+
+  describe('fall-through to projection siblings (measured allele unannotated → projected = true)', () => {
+    test('single sibling call → placed on its side, flagged projected', () => {
+      const p = reduceControlPlacement([link(LB, SIB)], ASSAY)!
+      expect(sigs(p)).toEqual([LB])
+      expect(p.directional).toBe(true)
+      expect(p.projected).toBe(true)
+    })
+
+    describe('hard discordance (both directions present) → excluded', () => {
+      test.each([
+        ['P + B', [P, B]],
+        ['P + LB', [P, LB]],
+        ['LP + B', [LP, B]],
+        ['LP + LB', [LP, LB]],
+        ['PLP + BLB', [PLP, BLB]],
+        ['P + B + VUS (VUS does not rescue)', [P, B, VUS]]
+      ])('%s → excluded', (_label, significances) => {
+        const links = significances.map((s, i) => link(s, i === 0 ? SIB : SIB2))
+        const p = reduceControlPlacement(links, ASSAY)!
+        expect(p.excluded).toBe(true)
+        expect(p.projected).toBe(true)
+      })
+    })
+
+    describe('soft discordance (one direction, ± VUS) → included, multi-membership', () => {
+      test('same-side {P, LP} → both calls carried, pathogenic, not excluded', () => {
+        const p = reduceControlPlacement([link(P, SIB), link(LP, SIB2)], ASSAY)!
+        expect(p.excluded).toBe(false)
+        expect(p.directional).toBe(true)
+        expect(sigs(p)).toEqual([LP, P])
+      })
+
+      test('same-side {B, LB} → benign', () => {
+        const p = reduceControlPlacement([link(B, SIB), link(LB, SIB2)], ASSAY)!
+        expect(p.excluded).toBe(false)
+        expect(sigs(p)).toEqual([B, LB])
+      })
+
+      test('directional + VUS {LP, VUS} → directional (VUS suppressed downstream)', () => {
+        const p = reduceControlPlacement([link(LP, SIB), link(VUS, SIB2)], ASSAY)!
+        expect(p.directional).toBe(true)
+        expect(p.excluded).toBe(false)
+        expect(sigs(p)).toEqual([LP, VUS])
+      })
+
+      test('benign + VUS {B, VUS} → directional benign', () => {
+        const p = reduceControlPlacement([link(B, SIB), link(VUS, SIB2)], ASSAY)!
+        expect(p.directional).toBe(true)
+        expect(sigs(p)).toEqual([B, VUS])
+      })
+    })
+
+    test('VUS-only siblings → not directional (lands in the VUS series)', () => {
+      const p = reduceControlPlacement([link(VUS, SIB), link(VUS, SIB2)], ASSAY)!
+      expect(p.directional).toBe(false)
+      expect(p.excluded).toBe(false)
+      // Duplicate significances collapse to one classification.
+      expect(sigs(p)).toEqual([VUS])
+    })
+  })
+
+  describe('classifications set — distinct, order-preserving, status-carrying', () => {
+    test('duplicate significances across siblings collapse to one classification', () => {
+      const p = reduceControlPlacement([link(P, SIB), link(P, SIB2)], ASSAY)!
+      expect(p.classifications).toHaveLength(1)
+      expect(p.classifications[0].significance).toBe(P)
+    })
+
+    test('each classification keeps its own review status (for the downstream ≥minStar gate)', () => {
+      const p = reduceControlPlacement([link(P, SIB, TWO_STAR), link(LP, SIB2, NO_CRITERIA)], ASSAY)!
+      const byName = Object.fromEntries(p.classifications.map((c) => [c.significance, c.reviewStatus]))
+      expect(byName[P]).toBe(TWO_STAR)
+      expect(byName[LP]).toBe(NO_CRITERIA)
+    })
+
+    test('first-seen order is preserved', () => {
+      const p = reduceControlPlacement([link(LP, SIB), link(P, SIB2)], ASSAY)!
+      expect(p.classifications.map((c) => c.significance)).toEqual([LP, P])
+    })
+  })
+
+  describe('representative pick (for one-label surfaces: search dot, notables, tooltip)', () => {
+    test('a directional call is preferred over a higher-star VUS', () => {
+      const p = reduceControlPlacement([link(LP, SIB, ONE_STAR), link(VUS, SIB2, THREE_STAR)], ASSAY)!
+      expect(p.clinicalSignificance).toBe(LP)
+    })
+
+    test('among directional calls, the highest-star one represents', () => {
+      const p = reduceControlPlacement([link(LP, SIB, ONE_STAR), link(P, SIB2, TWO_STAR)], ASSAY)!
+      expect(p.clinicalSignificance).toBe(P)
+      expect(p.clinicalReviewStatus).toBe(TWO_STAR)
+    })
+
+    test('VUS-only → the VUS represents', () => {
+      const p = reduceControlPlacement([link(VUS, SIB, TWO_STAR)], ASSAY)!
+      expect(p.clinicalSignificance).toBe(VUS)
+    })
+  })
+
+  describe('representative allele digest (for resolving the winning call on a per-variant surface)', () => {
+    test('carries the digest of the representative call', () => {
+      const p = reduceControlPlacement([link(LP, 's1', ONE_STAR), link(P, 's2', TWO_STAR)], 'assay')!
+      // Representative is the highest-star directional (P on s2), so its digest surfaces.
+      expect(p.alleleDigest).toBe('s2')
+    })
+
+    test('a direct assayed-level call surfaces the assayed digest', () => {
+      const p = reduceControlPlacement([link(P, ASSAY), link(LP, SIB)], ASSAY)!
+      expect(p.alleleDigest).toBe(ASSAY)
+      expect(p.projected).toBe(false)
+    })
+  })
+
+  describe('unclassified ClinVar values ("-"/empty) are not treated as calls', () => {
+    test('a dash-only set → null (not a control, not a call)', () => {
+      expect(reduceControlPlacement([link('-', ASSAY), link('-', SIB)], ASSAY)).toBeNull()
+    })
+
+    test('a dash on the assayed allele does NOT block fall-through to a real sibling', () => {
+      // The `-` (no germline classification) is filtered, so the assayed allele reads as unannotated and
+      // the real sibling LP wins — the fall-through fires, projected.
+      const p = reduceControlPlacement([link('-', ASSAY), link(LP, SIB)], ASSAY)!
+      expect(sigs(p)).toEqual([LP])
+      expect(p.projected).toBe(true)
+    })
+
+    test('empty/whitespace/multi-dash significances are ignored', () => {
+      const p = reduceControlPlacement([link('', SIB), link('--', SIB2), link(P, SIB2)], ASSAY)!
+      expect(sigs(p)).toEqual([P])
+    })
+  })
+
+  describe('unknown assayed-level digest — provenance not claimed', () => {
+    test.each([[null], [undefined]])('digest = %s → all links win, projected = false', (digest) => {
+      const p = reduceControlPlacement([link(P, SIB), link(LP, SIB2)], digest)!
+      // With no assayed digest we cannot say a call is "on the measured allele", so we do NOT flag it as
+      // projected (which would wrongly imply we know it is about a *different* level).
+      expect(p.projected).toBe(false)
+      expect(sigs(p)).toEqual([LP, P])
+    })
+  })
+})
diff --git a/src/lib/clinvar-control-placement.ts b/src/lib/clinvar-control-placement.ts
new file mode 100644
index 00000000..9e257042
--- /dev/null
+++ b/src/lib/clinvar-control-placement.ts
@@ -0,0 +1,127 @@
+import {
+  BENIGN_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS,
+  CLINVAR_REVIEW_STATUS_STARS,
+  DEFAULT_CLNREVSTAT_FIELD,
+  DEFAULT_CLNSIG_FIELD,
+  isClassifiedSignificance,
+  PATHOGENIC_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS
+} from '@/lib/clinvar-controls'
+
+/**
+ * The ClinVar clinical-control divergence fold.
+ *
+ * For an AA-resolution score set one measured protein change is encoded by several DNA variants, whose
+ * ClinVar classifications can disagree. This module reduces the set of controls that reach a single
+ * variant to one placement the histogram can bin off — applying source precedence (the assayed-level
+ * allele's own call wins; projection siblings are only a fallback) and the hard/soft discordance rule.
+ */
+
+/** A distinct ClinVar call in a variant's winning set. */
+export interface ControlClassification {
+  significance: string
+  reviewStatus: string
+}
+
+/** One ClinVar control reaching a variant, tagged with the digest of the allele it annotates. */
+export interface ControlLink extends ControlClassification {
+  /** VRS digest of the allele the control annotates; compared to the variant's `assayLevelDigest`. */
+  alleleDigest?: string | null
+  dbIdentifier?: string
+}
+
+/** The reduced result for one variant — what the histogram and per-variant surfaces read. */
+export interface ClinvarControlPlacement {
+  /** Representative single call (directional-preferred, then highest-star) for one-label surfaces. */
+  [DEFAULT_CLNSIG_FIELD]: string
+  [DEFAULT_CLNREVSTAT_FIELD]: string
+  dbIdentifier?: string
+  /** The winning set's distinct calls (assayed-level controls if any, else the projection siblings). */
+  classifications: ControlClassification[]
+  /** Hard discordance — the winning set holds both a P/LP and a B/LB call; not a usable control. */
+  excluded: boolean
+  /** Whether any confident directional (P/LP or B/LB) call is present — directional dominates VUS. */
+  directional: boolean
+  /**
+   * VRS digest of the representative call's allele — lets a per-variant surface resolve that allele's
+   * level/HGVS (to name a projected sibling) and its ClinVar link-out. Undefined only when the winning
+   * links carried no digest.
+   */
+  alleleDigest?: string | null
+  /**
+   * True when the winning set came from **projection siblings** — the measured allele itself had no
+   * ClinVar record, so this classification is about a *related* variant at a different level, not the
+   * entity we assayed. Drives the "related variant" tooltip note that reconciles a control series
+   * membership with an empty measured-level ClinVar. Only asserted when the assayed-level digest is
+   * known (so a genuinely-direct call is never mislabeled when the digest is merely absent).
+   */
+  projected: boolean
+}
+
+const isPathogenic = (significance: string) => PATHOGENIC_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS.includes(significance)
+const isBenign = (significance: string) => BENIGN_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS.includes(significance)
+const isDirectional = (significance: string) => isPathogenic(significance) || isBenign(significance)
+const starsOf = (reviewStatus: string) => CLINVAR_REVIEW_STATUS_STARS[reviewStatus] ?? -1
+
+/**
+ * Reduce the ClinVar controls reaching one variant to a single {@link ClinvarControlPlacement}.
+ *
+ * **Precedence:** if any control annotates the variant's own assayed-level allele
+ * (`alleleDigest === assayLevelDigest`), those controls are the winning set and the projection siblings
+ * are ignored — a direct call on the assayed entity is not diluted by the fan-out. Otherwise the
+ * siblings are the winning set. Over the winning set:
+ *   - **hard discordance** (both a P/LP and a B/LB call) → `excluded` (not a usable control);
+ *   - otherwise the distinct calls flow through as `classifications`, and `directional` records whether
+ *     any confident P/LP or B/LB call is present, so the histogram can drop VUS when a directional call
+ *     dominates.
+ *
+ * Returns `null` when no *classified* control reaches the variant.
+ */
+export function reduceControlPlacement(
+  links: ControlLink[],
+  assayLevelDigest: string | null | undefined
+): ClinvarControlPlacement | null {
+  // Drop ClinVar "no classification" placeholders (a literal `-`/empty) up front, so they neither become a
+  // call nor — as a `-` on the assayed allele — block fall-through to a real projection sibling.
+  const classified = links.filter((link) => isClassifiedSignificance(link.significance))
+  if (classified.length === 0) {
+    return null
+  }
+
+  const assayedLevel = assayLevelDigest ? classified.filter((link) => link.alleleDigest === assayLevelDigest) : []
+  const winning = assayedLevel.length > 0 ? assayedLevel : classified
+  // Fell through to siblings — but only *claim* projection when the assayed digest is known; an absent
+  // digest means unknown provenance, which we don't surface as "related variant" (avoids mislabeling).
+  const projected = Boolean(assayLevelDigest) && assayedLevel.length === 0
+
+  // Distinct calls, preserving first-seen order.
+  const seen = new Set<string>()
+  const classifications: ControlClassification[] = []
+  for (const link of winning) {
+    if (!seen.has(link.significance)) {
+      seen.add(link.significance)
+      classifications.push({significance: link.significance, reviewStatus: link.reviewStatus})
+    }
+  }
+
+  const pathogenicPresent = classifications.some((c) => isPathogenic(c.significance))
+  const benignPresent = classifications.some((c) => isBenign(c.significance))
+  const directional = pathogenicPresent || benignPresent
+
+  // Representative for one-label surfaces (search dot, notables, tooltip): a directional call is more
+  // informative than a co-occurring VUS, so prefer directional calls when present, then highest star.
+  const candidates = directional ? winning.filter((link) => isDirectional(link.significance)) : winning
+  const representative = candidates.reduce((best, link) =>
+    starsOf(link.reviewStatus) > starsOf(best.reviewStatus) ? link : best
+  )
+
+  return {
+    [DEFAULT_CLNSIG_FIELD]: representative.significance,
+    [DEFAULT_CLNREVSTAT_FIELD]: representative.reviewStatus,
+    dbIdentifier: representative.dbIdentifier,
+    classifications,
+    excluded: pathogenicPresent && benignPresent,
+    directional,
+    alleleDigest: representative.alleleDigest,
+    projected
+  }
+}
diff --git a/src/lib/clinical-controls.ts b/src/lib/clinvar-controls.ts
similarity index 69%
rename from src/lib/clinical-controls.ts
rename to src/lib/clinvar-controls.ts
index 7d565456..3ff924a3 100644
--- a/src/lib/clinical-controls.ts
+++ b/src/lib/clinvar-controls.ts
@@ -1,3 +1,12 @@
+import type {components} from '@/schema/openapi'
+
+export type ClinvarControlOption = components['schemas']['ClinicalControlOptions']
+export type ClinvarVariantLink = components['schemas']['ClinvarVariantLink']
+export type ClinvarControl = components['schemas']['ClinicalControlWithClinvarLinks']
+
+type AlleleAnnotations = components['schemas']['AlleleAnnotations']
+type ClinvarAnnotation = components['schemas']['ClinvarAnnotation']
+
 /**
  * List of ClinVar clinical significance classifications.
  *
@@ -28,7 +37,7 @@ export const CLINVAR_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS = [
   {
     name: 'Pathogenic/Likely pathogenic',
     description: 'Pathogenic/Likely pathogenic variant (in different submissions)',
-    shortDescription: 'Path/LP (both)'
+    shortDescription: 'Pathogenic / Likely pathogenic'
   },
   {
     name: 'Benign',
@@ -43,7 +52,7 @@ export const CLINVAR_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS = [
   {
     name: 'Benign/Likely benign',
     description: 'Benign/Likely benign variant (in different submissions)',
-    shortDescription: 'B/LB (both)'
+    shortDescription: 'Benign / Likely benign'
   },
   {
     name: 'Uncertain significance',
@@ -71,7 +80,8 @@ export const CLINVAR_REVIEW_STATUS_STARS: {[status: string]: number} = {
   'criteria provided, conflicting classifications': 1,
   'criteria provided, single submitter': 1,
   'criteria provided, multiple submitters, no conflicts': 2,
-  'reviewed by expert panel': 3
+  'reviewed by expert panel': 3,
+  'practice guideline': 4
 }
 
 export const DEFAULT_CLNSIG_FIELD = 'clinicalSignificance'
@@ -87,23 +97,45 @@ export const DEFAULT_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS = [
 ]
 export const DEFAULT_MIN_STAR_RATING = 1
 
-export const DEFAULT_CLINICAL_CONTROL_DB = 'ClinVar'
+export const DEFAULT_CLINVAR_CONTROL_DB = 'ClinVar'
 
-export interface ClinicalControlOption {
-  dbName: string
-  availableVersions: string[]
+/** Turn a ClinVar `dbVersion` like `03_2024` into "March 2024"; pass through anything unrecognized. */
+export function formatClinvarVersion(dbVersion: string): string {
+  const match = dbVersion.match(/^(\d{2})_(\d{4})$/)
+  if (!match) return dbVersion
+  const [, month, year] = match
+  return new Date(Number(year), Number(month) - 1).toLocaleString('en-US', {month: 'long', year: 'numeric'})
 }
 
-export interface ClinicalControl {
-  dbName: string
-  dbVersion: string
-  dbIdentifier: string
-  clnsigField: string
-  clnrevstatField: string
-  geneSymbol: string
-  modificationDate: Date
-  creationDate: Date
-  mappedVariants: Array<object>
+/** Deep link to a ClinVar allele record, or null when the allele id is missing. */
+export function clinvarAlleleUrl(alleleId: string | null | undefined): string | null {
+  if (!alleleId) return null
+  return `https://www.ncbi.nlm.nih.gov/clinvar/allele/${encodeURIComponent(alleleId)}/`
+}
+
+/** Deep link to a ClinVar variation record, or null when the variation id is missing. */
+export function clinvarVariationUrl(variationId: string | null | undefined): string | null {
+  if (!variationId) return null
+  return `https://www.ncbi.nlm.nih.gov/clinvar/variation/${encodeURIComponent(variationId)}/`
+}
+
+/** The most recent ClinVar annotation (by `dbVersion`), or null when there are none. */
+export function latestClinvar(annotations: AlleleAnnotations | null): ClinvarAnnotation | null {
+  const clinvar = annotations?.clinvar
+  if (!clinvar?.length) return null
+  return clinvar.reduce((best, c) => (c.dbVersion > best.dbVersion ? c : best))
+}
+
+/**
+ * Whether a ClinVar `clinicalSignificance` is an actual classification. ClinVar's split germline/somatic
+ * model emits a literal `-` (occasionally empty) on an axis with no submission — e.g. a record carrying
+ * somatic/oncogenicity data but no germline classification. Such a value is not a usable classification:
+ * it must not become a clinvar control, render as a call, or (as a `-` on the *assayed* allele) block
+ * fall-through to a sibling allele. Filter significances through this before treating them as calls.
+ */
+export function isClassifiedSignificance(significance: string | null | undefined): boolean {
+  const s = significance?.trim()
+  return !!s && !/^-+$/.test(s)
 }
 
 /**
diff --git a/src/lib/formats.ts b/src/lib/formats.ts
index 09e1b41d..f8446199 100644
--- a/src/lib/formats.ts
+++ b/src/lib/formats.ts
@@ -2,13 +2,6 @@ import moment from 'moment'
 import {Opts} from 'linkifyjs'
 import linkifyHtml from 'linkify-html'
 
-export function formatClinvarVersion(dbVersion: string): string {
-  const match = dbVersion.match(/^(\d{2})_(\d{4})$/)
-  if (!match) return dbVersion
-  const [, month, year] = match
-  return new Date(Number(year), Number(month) - 1).toLocaleString('en-US', {month: 'long', year: 'numeric'})
-}
-
 export function formatDate(x: string) {
   return moment(x).format('MMM DD, YYYY')
 }
diff --git a/src/lib/notables.test.ts b/src/lib/notables.test.ts
new file mode 100644
index 00000000..de669172
--- /dev/null
+++ b/src/lib/notables.test.ts
@@ -0,0 +1,162 @@
+import {describe, expect, it} from 'vitest'
+
+import {
+  clinicalExtremesPerClass,
+  consequenceExemplars,
+  deviationsFromMedian,
+  medianAndMad,
+  scoreExtremes
+} from '@/lib/notables'
+import type {DisplayVariant} from '@/lib/variants'
+
+// Minimal variant factory — only the fields the notable samplers read.
+function v(
+  urn: string,
+  score: number | null,
+  extras: {consequence?: string | null; clnsig?: string; stars?: keyof typeof STARS} = {}
+): DisplayVariant {
+  const variant = {variantUrn: urn, score, consequence: extras.consequence ?? null} as DisplayVariant
+  if (extras.clnsig) {
+    variant.control = {
+      clinicalSignificance: extras.clnsig,
+      clinicalReviewStatus: extras.stars ?? '1-star'
+    } as DisplayVariant['control']
+  }
+  return variant
+}
+
+// Review-status strings that map to the star ratings we care about (see CLINVAR_REVIEW_STATUS_STARS).
+const STARS = {
+  '0-star': 'no assertion criteria provided',
+  '1-star': 'criteria provided, single submitter',
+  '2-star': 'criteria provided, multiple submitters, no conflicts'
+} as const
+
+// Rewrite the factory's star shorthand into the real review-status strings.
+function withStars(variant: DisplayVariant): DisplayVariant {
+  const shorthand = variant.control?.clinicalReviewStatus as keyof typeof STARS | undefined
+  if (shorthand && STARS[shorthand]) {
+    ;(variant.control as {clinicalReviewStatus: string}).clinicalReviewStatus = STARS[shorthand]
+  }
+  return variant
+}
+
+describe('clinicalExtremesPerClass', () => {
+  it('returns one exemplar per class, separated along the learned damaging direction', () => {
+    // Pathogenic scores low, benign high → damaging direction is negative. Expect the lowest P and
+    // highest B, not the middling members.
+    const variants = [
+      v('p-mid', -1, {clnsig: 'Pathogenic'}),
+      v('p-extreme', -3, {clnsig: 'Likely pathogenic'}),
+      v('b-mid', 1, {clnsig: 'Benign'}),
+      v('b-extreme', 3, {clnsig: 'Likely benign'})
+    ].map(withStars)
+    const result = clinicalExtremesPerClass(variants)
+    expect(result.map((r) => r.variantUrn)).toEqual(['p-extreme', 'b-extreme'])
+  })
+
+  it('learns the opposite polarity too (pathogenic high, benign low)', () => {
+    const variants = [
+      v('p-extreme', 5, {clnsig: 'Pathogenic'}),
+      v('p-mid', 2, {clnsig: 'Pathogenic'}),
+      v('b-extreme', -4, {clnsig: 'Benign'}),
+      v('b-mid', -1, {clnsig: 'Benign'})
+    ].map(withStars)
+    expect(clinicalExtremesPerClass(variants).map((r) => r.variantUrn)).toEqual(['p-extreme', 'b-extreme'])
+  })
+
+  it('falls back to furthest-from-median when only one class is present', () => {
+    const variants = [
+      v('p-near', 0.1, {clnsig: 'Pathogenic'}),
+      v('p-far', 4, {clnsig: 'Pathogenic'}),
+      v('unclassified-a', -2, {}),
+      v('unclassified-b', 0, {})
+    ].map(withStars)
+    const result = clinicalExtremesPerClass(variants)
+    // Set median is ~0.05; p-far (4) is furthest.
+    expect(result.map((r) => r.variantUrn)).toEqual(['p-far'])
+  })
+
+  it('excludes controls below the star threshold and VUS/unclassified', () => {
+    const variants = [
+      v('p-lowstar', -3, {clnsig: 'Pathogenic', stars: '0-star'}),
+      v('vus', -2, {clnsig: 'Uncertain significance', stars: '2-star'}),
+      v('b-ok', 3, {clnsig: 'Benign', stars: '1-star'})
+    ].map(withStars)
+    const result = clinicalExtremesPerClass(variants, 1)
+    // Only the benign passes → single-class fallback, benign returned.
+    expect(result.map((r) => r.variantUrn)).toEqual(['b-ok'])
+  })
+
+  it('returns nothing when no definitive controls clear the star gate', () => {
+    const variants = [v('vus', 1, {clnsig: 'Uncertain significance', stars: '2-star'}), v('plain', 2)].map(withStars)
+    expect(clinicalExtremesPerClass(variants)).toEqual([])
+  })
+})
+
+describe('consequenceExemplars', () => {
+  it('returns one representative per present bucket in canonical order, skipping No consequence', () => {
+    const variants = [
+      v('syn-1', 1, {consequence: 'synonymous_variant'}),
+      v('mis-1', 2, {consequence: 'missense_variant'}),
+      v('mis-2', 3, {consequence: 'missense_variant'}),
+      v('non-1', 4, {consequence: 'stop_gained'}),
+      v('none-1', 5, {consequence: null})
+    ]
+    const result = consequenceExemplars(variants)
+    // Canonical order is Missense, Synonymous, Nonsense, … → first-seen rep of each, No consequence dropped.
+    expect(result.map((r) => r.variantUrn)).toEqual(['mis-1', 'syn-1', 'non-1'])
+  })
+
+  it('is empty when every variant lacks a consequence (truly-unmapped set)', () => {
+    const variants = [v('a', 1, {consequence: null}), v('b', 2, {consequence: 'NA'})]
+    expect(consequenceExemplars(variants)).toEqual([])
+  })
+
+  it('ignores unscored variants', () => {
+    const variants = [v('unscored', null, {consequence: 'missense_variant'}), v('scored', 1, {consequence: 'stop_gained'})]
+    expect(consequenceExemplars(variants).map((r) => r.variantUrn)).toEqual(['scored'])
+  })
+})
+
+describe('scoreExtremes', () => {
+  it('returns the n variants furthest from the median, both tails', () => {
+    const variants = [v('a', 0), v('b', 1), v('c', 2), v('d', 10), v('e', -8)]
+    // Median 1; distances: e=9, d=9, a=1, c=1, b=0. Top 2 are the two tails.
+    expect(scoreExtremes(variants, 2).map((r) => r.variantUrn).sort()).toEqual(['d', 'e'])
+  })
+
+  it('caps at the requested count and ignores unscored variants', () => {
+    const variants = [v('a', 0), v('b', 5), v('unscored', null)]
+    const result = scoreExtremes(variants, 5)
+    expect(result).toHaveLength(2)
+    expect(result.every((r) => typeof r.score === 'number')).toBe(true)
+  })
+
+  it('is empty on a set with no scored variants', () => {
+    expect(scoreExtremes([v('a', null)], 3)).toEqual([])
+  })
+})
+
+describe('medianAndMad / deviationsFromMedian', () => {
+  it('computes median and MAD', () => {
+    // Values 1,2,4,6,8: median 4; abs devs 3,2,0,2,4 → MAD 2.
+    expect(medianAndMad([1, 2, 4, 6, 8])).toEqual({median: 4, mad: 2})
+  })
+
+  it('reports signed deviations in MAD units', () => {
+    const spread = {median: 4, mad: 2}
+    expect(deviationsFromMedian(10, spread)).toBe(3)
+    expect(deviationsFromMedian(0, spread)).toBe(-2)
+  })
+
+  it('returns null deviations when the scale is degenerate (MAD 0)', () => {
+    const spread = medianAndMad([5, 5, 5, 5, 9])
+    expect(spread.mad).toBe(0)
+    expect(deviationsFromMedian(9, spread)).toBeNull()
+  })
+
+  it('handles an even-length array', () => {
+    expect(medianAndMad([1, 3]).median).toBe(2)
+  })
+})
diff --git a/src/lib/notables.ts b/src/lib/notables.ts
new file mode 100644
index 00000000..d83d9829
--- /dev/null
+++ b/src/lib/notables.ts
@@ -0,0 +1,140 @@
+/**
+ * Notable-variant samplers for the score-set variant search's empty state.
+ *
+ * When the search box is empty the dropdown offers a few "interesting" variants to jump to instead of a
+ * blank list. Interest is graded by signal-richness, and each sampler here is one rung: clinical controls
+ * (richest, needs a fetch), consequence exemplars (intrinsic, mapping-derived), and score extremes (the
+ * universal floor — every score set has some variants with a score). A score set shows whichever rungs have data.
+ *
+ * These are PURE functions over the variant list so they stay trivially testable; the component groups
+ * their output into the AutoComplete and renders the captions.
+ */
+
+import {
+  BENIGN_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS,
+  CLINVAR_REVIEW_STATUS_STARS,
+  DEFAULT_CLNREVSTAT_FIELD,
+  DEFAULT_CLNSIG_FIELD,
+  DEFAULT_MIN_STAR_RATING,
+  PATHOGENIC_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS
+} from '@/lib/clinvar-controls'
+import {consequenceBucket, EFFECT_BUCKETS} from '@/lib/consequences'
+import type {DisplayVariant} from '@/lib/variants'
+
+/** Variants carrying a numeric score — the only ones with a point to jump to. */
+function scored(variants: DisplayVariant[]): DisplayVariant[] {
+  return variants.filter((v) => typeof v.score === 'number')
+}
+
+/** Star rating of a control's review status; -1 when the status is absent/unknown (never passes a ≥ gate). */
+function controlStars(variant: DisplayVariant): number {
+  const status = variant.control?.[DEFAULT_CLNREVSTAT_FIELD]
+  return status != null ? (CLINVAR_REVIEW_STATUS_STARS[status] ?? -1) : -1
+}
+
+/**
+ * Clinical-control exemplars: one variant per definitive ClinVar class (P/LP, B/LB) at ≥ `minStar`,
+ * picked to show the assay separating the classes. When both classes are present the "damaging"
+ * direction is learned from the data (sign of the difference between the two class medians), and each
+ * class's exemplar is the variant furthest into its own end — the most functionally-extreme pathogenic
+ * and the most wild-type-like benign. When only one class is present there is no axis to separate, so
+ * that class's exemplar is simply the variant furthest from the whole set's median. Returns ≤2 rows, in
+ * pathogenic-then-benign order; empty when no definitive controls clear the star gate.
+ */
+export function clinicalExtremesPerClass(
+  variants: DisplayVariant[],
+  minStar: number = DEFAULT_MIN_STAR_RATING
+): DisplayVariant[] {
+  const definitive = (classes: string[]) =>
+    scored(variants).filter(
+      (v) =>
+        // Skip hard-discordant variants: they carry ClinVar data but aren't usable controls.
+        !v.control?.excluded && classes.includes(v.control?.[DEFAULT_CLNSIG_FIELD] ?? '') && controlStars(v) >= minStar
+    )
+  const pathogenic = definitive(PATHOGENIC_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS)
+  const benign = definitive(BENIGN_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS)
+  if (!pathogenic.length && !benign.length) return []
+
+  // A direct call on the assayed allele is a stronger headliner than one projected from a sibling allele,
+  // so pick the exemplar from the direct members when a class has any; fall back to the whole (projected)
+  // group only when the class is present solely via siblings.
+  const preferDirect = (group: DisplayVariant[]) => {
+    const direct = group.filter((v) => !v.control?.projected)
+    return direct.length ? direct : group
+  }
+
+  const scoreOf = (v: DisplayVariant) => v.score as number
+  const furthestFrom = (group: DisplayVariant[], anchor: number) =>
+    group.reduce((best, v) => (Math.abs(scoreOf(v) - anchor) > Math.abs(scoreOf(best) - anchor) ? v : best))
+
+  // Both classes present: separate along the learned damaging direction. Only one: fall back to the
+  // variant furthest from the set's median (still a headline extreme, just without a contrast class).
+  if (pathogenic.length && benign.length) {
+    const pathMedian = median(pathogenic.map(scoreOf))
+    const benignMedian = median(benign.map(scoreOf))
+    const damagingWard = Math.sign(pathMedian - benignMedian) || 1
+    const mostWard = (group: DisplayVariant[], ward: number) =>
+      group.reduce((best, v) => (scoreOf(v) * ward > scoreOf(best) * ward ? v : best))
+    return [mostWard(preferDirect(pathogenic), damagingWard), mostWard(preferDirect(benign), -damagingWard)]
+  }
+  const anchor = median(scored(variants).map(scoreOf))
+  const group = pathogenic.length ? pathogenic : benign
+  return [furthestFrom(preferDirect(group), anchor)]
+}
+
+/**
+ * Consequence exemplars: one representative per VEP effect bucket present, in canonical bucket order — a
+ * quick sampler of the data's shape (a missense, a synonymous, a nonsense, …). 'No consequence' is
+ * skipped (the unmapped/unannotated pile is not a headline). Empty on truly-unmapped sets, where VEP
+ * consequence is absent for every variant.
+ */
+export function consequenceExemplars(variants: DisplayVariant[]): DisplayVariant[] {
+  const pool = scored(variants)
+  if (!pool.length) return []
+  const exemplars: DisplayVariant[] = []
+  for (const bucket of EFFECT_BUCKETS) {
+    if (bucket.name === 'No consequence') continue
+    const match = pool.find((v) => consequenceBucket(v.consequence) === bucket.name)
+    if (match) exemplars.push(match)
+  }
+  return exemplars
+}
+
+/**
+ * The `n` most extreme-scoring variants, ranked by distance from the median in robust (MAD) units.
+ * MAD-from-median is used instead of standard deviation because MAVE score distributions are typically
+ * bimodal — squaring residuals would let one far tail dominate the scale. Ranking by absolute deviation
+ * naturally surfaces both tails. The universal fallback rung: every scored variant qualifies.
+ */
+export function scoreExtremes(variants: DisplayVariant[], n: number): DisplayVariant[] {
+  const pool = scored(variants)
+  if (!pool.length) return []
+  const {median: med} = medianAndMad(pool.map((v) => v.score as number))
+  return [...pool].sort((a, b) => Math.abs((b.score as number) - med) - Math.abs((a.score as number) - med)).slice(0, n)
+}
+
+/** Median of a non-empty numeric array. Assumes at least one element. */
+function median(values: number[]): number {
+  const sorted = [...values].sort((a, b) => a - b)
+  const mid = Math.floor(sorted.length / 2)
+  return sorted.length % 2 ? sorted[mid] : (sorted[mid - 1] + sorted[mid]) / 2
+}
+
+/**
+ * Median and median absolute deviation of a score set — the robust center/scale pair the score-extremes
+ * caption reports against. `mad` is 0 when more than half the scores are identical (a degenerate scale);
+ * callers should treat that as "deviations not reportable".
+ */
+export function medianAndMad(scores: number[]): {median: number; mad: number} {
+  if (!scores.length) return {median: 0, mad: 0}
+  const med = median(scores)
+  return {median: med, mad: median(scores.map((s) => Math.abs(s - med)))}
+}
+
+/**
+ * Signed distance of a score from the median in MAD units ("N deviations from median"), for the
+ * score-extremes row caption. Null when the scale is degenerate (`mad` 0), where the count is meaningless.
+ */
+export function deviationsFromMedian(score: number, spread: {median: number; mad: number}): number | null {
+  return spread.mad === 0 ? null : (score - spread.median) / spread.mad
+}
diff --git a/src/lib/tooltips.ts b/src/lib/tooltips.ts
index d9748e92..ca1cc961 100644
--- a/src/lib/tooltips.ts
+++ b/src/lib/tooltips.ts
@@ -39,10 +39,18 @@ export function tooltipNote(text: string): string {
   return `<div class="italic opacity-[.75]">${text}</div>`
 }
 
+export function tooltipFootnote(text: string): string {
+  return `<div class="text-[11px] opacity-[.65] italic mt-1">*${text}</div>`
+}
+
 export function tooltipText(text: string): string {
   return `<div>${text}</div>`
 }
 
+export function tooltipEmptyLine(): string {
+  return `<div class="h-1"></div>`
+}
+
 export function tooltipKeyValue(label: string, value: string | number | null | undefined): string {
   return `<div><span class="opacity-60">${label}:</span> ${value ?? ''}</div>`
 }
diff --git a/src/lib/variants.ts b/src/lib/variants.ts
index 5d057501..a544663e 100644
--- a/src/lib/variants.ts
+++ b/src/lib/variants.ts
@@ -1,7 +1,7 @@
 import _ from 'lodash'
 
 import {AMINO_ACIDS_WITH_TER, singleLetterAminoAcidOrHgvsCode} from '@/lib/amino-acids'
-import {DEFAULT_CLNREVSTAT_FIELD, DEFAULT_CLNSIG_FIELD} from '@/lib/clinical-controls'
+import type {ClinvarControlPlacement} from '@/lib/clinvar-control-placement'
 import geneticCodes from '@/lib/genetic-codes'
 import {parseSimpleNtVariant, parseSimpleProVariant} from '@/lib/mave-hgvs'
 import {parseScoresOrCounts} from '@/lib/scores'
@@ -22,7 +22,7 @@ export type LeanVariant = components['schemas']['LeanVariant']
  * visualizations and search consume this shape.
  */
 export type DisplayVariant = LeanVariant & {
-  control?: ClinicalControlVariant | null
+  control?: ClinvarControlVariant | null
 }
 
 export type HgvsReferenceSequenceType = 'c' | 'p' // | 'n'
@@ -32,11 +32,12 @@ export interface SequenceRange {
   length: number
 }
 
-export interface ClinicalControlVariant {
-  [DEFAULT_CLNSIG_FIELD]: string
-  [DEFAULT_CLNREVSTAT_FIELD]: string
-  dbIdentifier?: string
-}
+/**
+ * The clinical-control facet merged onto a variant: the divergence fold's placement
+ * ({@link ClinvarControlPlacement}) — representative call for one-label surfaces, plus the winning-set
+ * classifications and the excluded/directional flags the histogram bins off.
+ */
+export type ClinvarControlVariant = ClinvarControlPlacement
 
 type ParsedSimpleDnaVariation = SimpleDnaVariation & {
   residueType?: 'nt'
@@ -73,7 +74,7 @@ export interface RawVariant {
     clingen_allele_id?: string
   }
 
-  control?: ClinicalControlVariant
+  control?: ClinvarControlVariant
   mavedb_label?: string
 }
 

From 1931d70b1e21314a731e1443b31ca50bacc0af56 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Mon, 13 Jul 2026 14:57:32 -0700
Subject: [PATCH 30/84] feat(key-drawer): add vocabulary Key drawer and
 v-key-term directive

Build the disclosure-ladder infrastructure: a single Key drawer that
any badge can deep-link into, so jargon is explained in one shared
place rather than scattered tooltips.

- add useKeyDrawer, a module-level singleton store driving one drawer
  mounted at the variant-page root, opened via open(term) from any
  subtree
- add the v-key-term directive that turns a badge into a keyboard- and
  screen-reader-accessible deep link into the drawer, centralizing the
  handlers, ARIA, and hover affordance
- add MvKeyDrawer and the variant key-section content definitions
- register the directive and brand the PrimeVue tooltip (sage
  background, body font) as the ladder's first rung
---
 src/assets/app.css                            |  13 ++
 src/components/common/MvKeyDrawer.vue         | 179 ++++++++++++++++
 .../variant/variant-key-sections.ts           | 192 ++++++++++++++++++
 src/composables/use-key-drawer.ts             |  45 ++++
 src/directives/key-term.ts                    |  60 ++++++
 src/main.js                                   |  23 ++-
 6 files changed, 511 insertions(+), 1 deletion(-)
 create mode 100644 src/components/common/MvKeyDrawer.vue
 create mode 100644 src/components/variant/variant-key-sections.ts
 create mode 100644 src/composables/use-key-drawer.ts
 create mode 100644 src/directives/key-term.ts

diff --git a/src/assets/app.css b/src/assets/app.css
index 197e89ad..4dd65f26 100644
--- a/src/assets/app.css
+++ b/src/assets/app.css
@@ -171,6 +171,19 @@
   --nav-height: 58px;
 }
 
+/* Badges/tags wired to the vocabulary Key via `v-key-term`. The hover ring (inset box-shadow) follows
+   the element's own border-radius and text color, matching the ad-hoc affordance the inline badges used. */
+.key-term {
+  cursor: help;
+}
+.key-term:hover {
+  box-shadow: inset 0 0 0 1px currentColor;
+}
+.key-term:focus-visible {
+  outline: 2px solid var(--color-sage);
+  outline-offset: 1px;
+}
+
 /* ── Base Styles ───────────────────────────────────────────────── */
 
 /* All headings use the Exo 2 display font */
diff --git a/src/components/common/MvKeyDrawer.vue b/src/components/common/MvKeyDrawer.vue
new file mode 100644
index 00000000..911b9911
--- /dev/null
+++ b/src/components/common/MvKeyDrawer.vue
@@ -0,0 +1,179 @@
+<template>
+  <Transition name="key-drawer">
+    <!-- Non-modal: this drawer is intentionally non-modal so the page stays fully interactive while the Key is open.
+         Closes on ✕ or Esc only (never on outside click) so a reader can keep it open while scanning. -->
+    <!-- Sits below the sticky global nav (var(--nav-height), z-100) so its close button isn't obscured and
+         the nav stays usable. Mobile: a floating pop-out card under the nav (base classes). Tablet+: a
+         full-height side drawer anchored right (tablet: overrides). -->
+    <aside
+      v-if="drawer.isOpen.value"
+      :aria-label="`${title}: what these terms mean`"
+      class="fixed inset-x-4 top-[var(--nav-height)] z-40 mt-3 flex max-h-[75vh] flex-col overflow-hidden rounded-lg border border-border bg-surface shadow-[0_12px_32px_-8px_rgba(0,0,0,0.3)] tablet:inset-x-auto tablet:bottom-0 tablet:left-auto tablet:right-0 tablet:mt-0 tablet:max-h-none tablet:w-[360px] tablet:max-w-[90vw] tablet:rounded-none tablet:border-y-0 tablet:border-r-0 tablet:shadow-[-8px_0_24px_-12px_rgba(0,0,0,0.25)]"
+      role="complementary"
+    >
+      <!-- Header -->
+      <div
+        class="mave-gradient-bar relative flex items-center gap-2 overflow-hidden border-b border-border px-5 py-3.5"
+      >
+        <i class="pi pi-key text-sm text-sage" />
+        <span class="text-sm font-bold uppercase tracking-[0.5px] text-text-primary">{{ title }}</span>
+        <button
+          :aria-label="`Close ${title.toLowerCase()}`"
+          class="ml-auto flex cursor-pointer items-center justify-center rounded-full border-none bg-transparent p-1 text-text-muted hover:bg-border-light hover:text-text-primary"
+          type="button"
+          @click="drawer.close()"
+        >
+          <i class="pi pi-times text-sm" />
+        </button>
+      </div>
+
+      <!-- Definitions -->
+      <div ref="scroller" class="flex-1 overflow-y-auto px-5 py-4">
+        <section
+          v-for="section in sections"
+          :id="`key-${section.id}`"
+          :key="section.id"
+          class="scroll-mt-4 border-b border-border-light py-3 first:pt-0 last:border-b-0"
+          :class="{'key-flash': highlighted === section.id}"
+        >
+          <h3 class="mb-1 text-xs-minus font-bold uppercase tracking-[0.5px] text-black">{{ section.title }}</h3>
+          <p v-if="section.gloss" class="mb-2 text-xs-plus leading-snug text-text-secondary">{{ section.gloss }}</p>
+          <dl class="flex flex-col gap-1.5">
+            <div v-for="term in section.terms" :key="term.label" class="flex flex-col gap-0.5">
+              <dt>
+                <span
+                  class="inline-block rounded-sm px-1.5 py-0.5 text-[10px] font-semibold uppercase tracking-[0.3px]"
+                  :class="term.class ?? 'bg-border-light text-text-muted'"
+                  >{{ term.label }}</span
+                >
+              </dt>
+              <dd class="text-xs-plus leading-snug text-text-secondary">{{ term.definition }}</dd>
+            </div>
+          </dl>
+          <a
+            v-if="section.docsUrl ?? docsUrl"
+            class="mt-2 inline-flex items-center gap-1 cursor-pointer text-xs font-semibold text-link hover:underline"
+            :href="section.docsUrl ?? docsUrl"
+            rel="noopener noreferrer"
+            target="_blank"
+            >more <i class="pi pi-arrow-right"
+          /></a>
+        </section>
+      </div>
+    </aside>
+  </Transition>
+</template>
+
+<script lang="ts">
+import {defineComponent, nextTick, type PropType} from 'vue'
+
+import {useKeyDrawer, type KeySection} from '@/composables/use-key-drawer'
+
+/**
+ * Generic vocabulary "Key" — a non-modal, right-side (mobile: pop-out card) definitions drawer. Content
+ * is injected via `sections`, so this component carries no page-specific text; a page supplies its own
+ * sections (see e.g. the variant page's `variant-key-sections`). Mounted once per page; opened from a
+ * trigger or deep-linked from a badge via the shared {@link useKeyDrawer} singleton (or the `v-key-term`
+ * directive). On a deep link it scrolls the target section into view and flashes it. Closes only on ✕ or
+ * Esc, so it can stay open while the reader scans the page beneath it.
+ */
+export default defineComponent({
+  name: 'MvKeyDrawer',
+
+  props: {
+    /** The definition sections to render, in display order. */
+    sections: {type: Array as PropType<KeySection[]>, required: true},
+    /** Header label (and the noun in the close button's aria-label). */
+    title: {type: String, default: 'Key'},
+    /** Default "more →" docs link for every section; a section may override via its own `docsUrl`. */
+    docsUrl: {type: String as PropType<string | undefined>, default: undefined}
+  },
+
+  setup() {
+    return {drawer: useKeyDrawer()}
+  },
+
+  data() {
+    return {highlighted: null as string | null, flashTimer: undefined as ReturnType<typeof setTimeout> | undefined}
+  },
+
+  watch: {
+    'drawer.isOpen.value'(open: boolean) {
+      if (open) {
+        window.addEventListener('keydown', this.onKeydown)
+        void this.scrollToActiveTerm()
+      } else {
+        window.removeEventListener('keydown', this.onKeydown)
+      }
+    }
+  },
+
+  beforeUnmount() {
+    window.removeEventListener('keydown', this.onKeydown)
+    if (this.flashTimer) clearTimeout(this.flashTimer)
+  },
+
+  methods: {
+    onKeydown(event: KeyboardEvent) {
+      if (event.key === 'Escape') this.drawer.close()
+    },
+    async scrollToActiveTerm() {
+      const term = this.drawer.activeTerm.value
+      await nextTick()
+      const scroller = this.$refs.scroller as HTMLElement | undefined
+      if (!term || !scroller) {
+        if (scroller) scroller.scrollTop = 0
+        return
+      }
+      const el = scroller.querySelector<HTMLElement>(`#key-${term}`)
+      if (!el) return
+      el.scrollIntoView({block: 'start', behavior: 'smooth'})
+      this.highlighted = term
+      if (this.flashTimer) clearTimeout(this.flashTimer)
+      this.flashTimer = setTimeout(() => (this.highlighted = null), 1600)
+    }
+  }
+})
+</script>
+
+<style scoped>
+/* Mobile: pop-out card (fade + slight rise). */
+.key-drawer-enter-active,
+.key-drawer-leave-active {
+  transition:
+    transform 0.2s ease,
+    opacity 0.2s ease;
+}
+.key-drawer-enter-from,
+.key-drawer-leave-to {
+  opacity: 0;
+  transform: translateY(-8px) scale(0.98);
+}
+
+/* Tablet+: slide-in drawer from the right (breakpoint matches --breakpoint-tablet). */
+@media (min-width: 56rem) {
+  .key-drawer-enter-active,
+  .key-drawer-leave-active {
+    transition: transform 0.2s ease;
+  }
+  .key-drawer-enter-from,
+  .key-drawer-leave-to {
+    opacity: 1;
+    transform: translateX(100%);
+  }
+}
+
+/* Transient highlight when a badge deep-links to a section. */
+.key-flash {
+  animation: key-flash 1.6s ease;
+}
+@keyframes key-flash {
+  0%,
+  40% {
+    background: var(--color-sage-light, rgba(122, 158, 126, 0.18));
+  }
+  100% {
+    background: transparent;
+  }
+}
+</style>
diff --git a/src/components/variant/variant-key-sections.ts b/src/components/variant/variant-key-sections.ts
new file mode 100644
index 00000000..bbcb5883
--- /dev/null
+++ b/src/components/variant/variant-key-sections.ts
@@ -0,0 +1,192 @@
+import config from '@/config'
+import type {KeySection} from '@/composables/use-key-drawer'
+
+/**
+ * Variant-page content for the generic {@link MvKeyDrawer}. These are the tier-2 vocabulary glosses; the
+ * section `id`s are the deep-link anchors that badges pass to the Key drawer (via `v-key-term`).
+ */
+
+// TODO- Interim target: the general key-concepts page. Repoint to the dedicated mapping/annotation docs
+// section once it exists (see the mapping-docs plan).
+export const VARIANT_KEY_DOCS_URL = `${config.appBaseUrl}/docs/mavedb/getting-started/key-concepts.html`
+
+export const VARIANT_KEY_SECTIONS: KeySection[] = [
+  {
+    id: 'relationship',
+    title: 'Relationship to your variant',
+    gloss: 'How each result relates to the allele you searched.',
+    terms: [
+      {
+        label: 'Your variant',
+        definition: 'The result assayed exactly the allele you searched.',
+        class: 'bg-sage/15 text-sage'
+      },
+      {
+        label: 'Its protein consequence',
+        definition: 'The result assayed the protein change your variant produces.'
+      },
+      {
+        label: 'Encodes the protein consequence',
+        definition: 'The result assayed a nucleotide allele that encodes the same protein change as your variant.'
+      }
+    ]
+  },
+  {
+    id: 'assay-level',
+    title: 'Assay level',
+    gloss: 'The level at which a result measured the change.',
+    terms: [
+      {
+        label: 'Nucleotide',
+        definition: 'Assayed as a DNA/RNA change (coding or genomic).',
+        class: 'bg-nucleotide-light text-nucleotide'
+      },
+      {label: 'Protein', definition: 'Assayed as an amino-acid change.', class: 'bg-protein-light text-protein'}
+    ]
+  },
+  {
+    id: 'confidence',
+    title: 'How a coordinate was established',
+    terms: [
+      {label: 'Measured', definition: 'Directly assayed in this score set.', class: 'bg-sage/15 text-sage'},
+      {
+        label: 'Resolved',
+        definition:
+          'Derived from the measured allele by reverse translation — the same change expressed at another level.',
+        class: 'bg-nucleotide-light text-nucleotide'
+      },
+      {
+        label: 'Candidate',
+        definition:
+          'A change that encodes the same protein change as your variant, but is a distinct nucleotide change.',
+        class: 'bg-amber-100 text-amber-700'
+      }
+    ]
+  },
+  {
+    id: 'selected-allele',
+    title: 'Selected allele',
+    terms: [
+      {
+        label: 'Selected allele',
+        definition: 'The allele this page is anchored on — the ClinGen allele you navigated to.',
+        class: 'bg-link/10 text-link'
+      }
+    ]
+  },
+  {
+    id: 'frame',
+    title: 'Coordinate frame',
+    terms: [
+      {
+        label: 'Submitted',
+        definition: 'Coordinates exactly as the depositor submitted them, relative to the target sequence.'
+      },
+      {
+        label: 'Reference',
+        definition: "Coordinates re-expressed against a standard reference sequence by MaveDB's mapping pipeline."
+      }
+    ]
+  },
+  {
+    id: 'consequence',
+    title: 'Consequence vs impact',
+    terms: [
+      {
+        label: 'Molecular consequence',
+        definition: 'The predicted effect on the transcript or protein (e.g. missense), from VEP.'
+      },
+      {label: 'Functional impact', definition: "The assay's verdict on whether the variant alters function."},
+      {
+        label: 'Functionally Abnormal',
+        definition: 'The assay scored the variant as altering function.',
+        class: 'mave-classification-abnormal'
+      },
+      {
+        label: 'Functionally Normal',
+        definition: 'The assay scored the variant as retaining function.',
+        class: 'mave-classification-normal'
+      }
+    ]
+  },
+  {
+    id: 'acmg',
+    title: 'ACMG functional evidence',
+    gloss: 'How the functional result maps onto clinical-classification evidence.',
+    terms: [
+      {label: 'PS3', definition: 'Functional evidence supporting a pathogenic classification.'},
+      {label: 'BS3', definition: 'Functional evidence supporting a benign classification.'},
+      {
+        label: 'Evidence strength',
+        definition: 'How much weight the evidence carries: supporting → moderate → strong → very strong.'
+      },
+      {label: 'OddsPath', definition: 'The odds of pathogenicity implied by the score; sets the evidence strength.'}
+    ]
+  },
+  {
+    id: 'population',
+    title: 'Population frequency (gnomAD)',
+    gloss: 'How often the allele is seen in reference populations — high frequency argues against pathogenicity.',
+    terms: [
+      {
+        label: 'Allele frequency (AF)',
+        definition:
+          'The fraction of sampled reference-population chromosomes carrying this allele in gnomAD (allele count ÷ allele number).'
+      },
+      {
+        label: 'AC / AN',
+        definition:
+          'Allele count and allele number: the observed carriers and the total chromosomes sampled that the frequency is computed from.'
+      },
+      {
+        label: 'FAF95',
+        definition:
+          "Filtering allele frequency at 95% confidence: a sampling-adjusted, conservative estimate of the population frequency. When it exceeds a disease's maximum credible allele frequency, the variant is too common to be pathogenic (ACMG BA1/BS1)."
+      }
+    ]
+  },
+  {
+    id: 'clinical',
+    title: 'Clinical significance (ClinVar)',
+    gloss: 'Germline classifications, shown with their ClinVar review-star rating.',
+    terms: [
+      {label: 'Pathogenic / Likely pathogenic', definition: 'Classified as disease-causing, or likely to be.'},
+      {label: 'Benign / Likely benign', definition: 'Classified as not disease-causing, or likely not to be.'},
+      {label: 'VUS', definition: 'Variant of uncertain significance — not enough evidence to classify.'},
+      {label: 'Conflicting', definition: 'Submitters disagree on the classification.'}
+    ]
+  },
+  {
+    id: 'passthrough',
+    title: 'Sibling-allele controls',
+    terms: [
+      {
+        label: 'From a sibling allele',
+        definition:
+          'A ClinVar call carried over from a sibling allele that shares the protein consequence, shown when the assayed variant itself has no ClinVar record. Marked with *.'
+      }
+    ]
+  },
+  {
+    id: 'as-of',
+    title: 'As of',
+    terms: [
+      {
+        label: 'As of MaveDB …',
+        definition: 'MaveDB reconstructs its molecular and annotation layer as of the chosen date; scores never change.'
+      },
+      {label: 'As of ClinVar …', definition: 'The ClinVar release a clinical call was drawn from.'}
+    ]
+  },
+  {
+    id: 'superseded',
+    title: 'Superseded',
+    terms: [
+      {
+        label: 'Superseded',
+        definition:
+          'The measurement comes from an older version of its score set. A newer version exists but may not contain a corresponding variant.'
+      }
+    ]
+  }
+]
diff --git a/src/composables/use-key-drawer.ts b/src/composables/use-key-drawer.ts
new file mode 100644
index 00000000..5bc6b20d
--- /dev/null
+++ b/src/composables/use-key-drawer.ts
@@ -0,0 +1,45 @@
+import {ref} from 'vue'
+
+/** One defined term shown in the Key drawer. `class` styles the term chip (e.g. to match its badge). */
+export interface KeyTerm {
+  label: string
+  definition: string
+  class?: string
+}
+
+/**
+ * A titled group of related terms. `id` is the deep-link anchor: a badge opens the drawer with
+ * `open(id)` and the drawer scrolls to `#key-<id>` and flashes it. `docsUrl` optionally overrides the
+ * drawer-level docs link for this section's "more →".
+ */
+export interface KeySection {
+  id: string
+  title: string
+  gloss?: string
+  terms: KeyTerm[]
+  docsUrl?: string
+}
+
+/**
+ * Module-level singleton driving the vocabulary "Key" drawer. Any component can call `open(term)` to
+ * surface a definition without threading props/events through the page — the drawer itself is mounted
+ * once at the variant-page root and reads this shared state. `activeTerm` is the anchor id the drawer
+ * scrolls to and briefly highlights on open; passing nothing opens it at the top.
+ *
+ * Deliberately global rather than provide/inject: the trigger (control header) and the deep-linking
+ * badges (measurement cards, per-level annotations) live in unrelated subtrees, and there is only ever
+ * one Key drawer on screen.
+ */
+const isOpen = ref(false)
+const activeTerm = ref<string | null>(null)
+
+export function useKeyDrawer() {
+  function open(term?: string) {
+    activeTerm.value = term ?? null
+    isOpen.value = true
+  }
+  function close() {
+    isOpen.value = false
+  }
+  return {isOpen, activeTerm, open, close}
+}
diff --git a/src/directives/key-term.ts b/src/directives/key-term.ts
new file mode 100644
index 00000000..7bbcc68c
--- /dev/null
+++ b/src/directives/key-term.ts
@@ -0,0 +1,60 @@
+import type {Directive, DirectiveBinding} from 'vue'
+
+import {useKeyDrawer} from '@/composables/use-key-drawer'
+
+const TITLE = 'What does this mean? — opens the Key'
+
+interface KeyTermEl extends HTMLElement {
+  __keyTerm?: {onClick: (e: Event) => void; onKeydown: (e: KeyboardEvent) => void}
+}
+
+/**
+ * `v-key-term="'assay-level'"` — turns any badge/tag into a deep link into the vocabulary Key drawer.
+ * Adds the click + keyboard handlers, ARIA/affordance attributes, and the `.key-term` hover style, so
+ * the deep-link behaviour lives in one place rather than being copy-pasted onto every badge. Applies to
+ * the root element (works on plain elements and single-root components like MvEvidenceTag).
+ *
+ * `stopPropagation` keeps a badge click from also triggering an enclosing clickable card.
+ */
+function bind(el: KeyTermEl, binding: DirectiveBinding<string>) {
+  const {open} = useKeyDrawer()
+  const term = binding.value
+
+  const onClick = (e: Event) => {
+    e.stopPropagation()
+    open(term)
+  }
+  const onKeydown = (e: KeyboardEvent) => {
+    if (e.key === 'Enter' || e.key === ' ') {
+      e.preventDefault()
+      e.stopPropagation()
+      open(term)
+    }
+  }
+
+  el.addEventListener('click', onClick)
+  el.addEventListener('keydown', onKeydown)
+  el.classList.add('key-term')
+  el.setAttribute('role', 'button')
+  el.setAttribute('tabindex', '0')
+  if (!el.getAttribute('title')) el.setAttribute('title', TITLE)
+  el.__keyTerm = {onClick, onKeydown}
+}
+
+function unbind(el: KeyTermEl) {
+  if (!el.__keyTerm) return
+  el.removeEventListener('click', el.__keyTerm.onClick)
+  el.removeEventListener('keydown', el.__keyTerm.onKeydown)
+  delete el.__keyTerm
+}
+
+export const vKeyTerm: Directive<KeyTermEl, string> = {
+  mounted: bind,
+  updated(el, binding) {
+    if (binding.value !== binding.oldValue) {
+      unbind(el)
+      bind(el, binding)
+    }
+  },
+  unmounted: unbind
+}
diff --git a/src/main.js b/src/main.js
index d22af0d1..a66eee7a 100644
--- a/src/main.js
+++ b/src/main.js
@@ -16,6 +16,7 @@ import {installAxiosAuthHeaderInterceptor, installAxiosUnauthorizedResponseInter
 import {initializeAuthentication as initializeOrcidAuthentication} from '@/lib/orcid'
 import router from '@/router'
 import store from '@/store'
+import {vKeyTerm} from '@/directives/key-term'
 
 import 'primeicons/primeicons.css'
 
@@ -224,7 +225,26 @@ const MaveDbTheme = definePreset(Aura, {
               }
             },
           },
-        }
+        },
+        tooltip: {
+          root: {
+            borderRadius: '6px',
+            padding: '0.5rem 0.75rem',
+            maxWidth: '18rem',
+          },
+          colorScheme: {
+            // Solid brand sage (--color-sage-dark), white text, matching sage
+            // arrow (it follows the background token). Same in light and dark.
+            light: {root: {background: '#5a9375', color: '#ffffff'}},
+            dark: {root: {background: '#5a9375', color: '#ffffff'}},
+          },
+          // font-family isn't a token, so the brand body font rides along here.
+          css: () => `
+            .p-tooltip-text {
+              font-family: var(--font-body);
+            }
+          `,
+        },
     },
 })
 
@@ -246,6 +266,7 @@ createApp(App)
   .use(ConfirmationService)
   .use(ToastService)
   .directive('tooltip', Tooltip)
+  .directive('key-term', vKeyTerm)
   .mount('#app')
 
 // Add the FontAwesome icons to the library so that they can be used in components.

From 8b450be17d4ed89fdfc8dabd802956a8fb0f9087 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Tue, 14 Jul 2026 11:50:30 -0700
Subject: [PATCH 31/84] feat(clinvar-controls): add unified variant deep link
 and significance color

- add clinvarVariantUrl, a structural helper that prefers the ClinVar
  variation page and falls back to the allele page, accepting either a
  ClinvarAnnotation or a clinical-control record
- add clinicalSignificanceColor mapping pathogenic/benign significances
  (including the aggregate P/LP and B/LB labels) to a badge color, and
  returning undefined for VUS, conflicting, and placeholder values
- correct the allele deep link to the alleleid term-search form and make
  clinvarAlleleUrl/clinvarVariationUrl private behind clinvarVariantUrl
---
 src/lib/clinvar-controls.test.ts | 36 ++++++++++++++++++++++++++++++++
 src/lib/clinvar-controls.ts      | 36 +++++++++++++++++++++++++++++---
 2 files changed, 69 insertions(+), 3 deletions(-)
 create mode 100644 src/lib/clinvar-controls.test.ts

diff --git a/src/lib/clinvar-controls.test.ts b/src/lib/clinvar-controls.test.ts
new file mode 100644
index 00000000..592422e4
--- /dev/null
+++ b/src/lib/clinvar-controls.test.ts
@@ -0,0 +1,36 @@
+import {describe, expect, test} from 'vitest'
+
+import {clinicalSignificanceColor} from '@/lib/clinvar-controls'
+
+const PATHOGENIC = 'var(--color-badge-pathogenic)'
+const BENIGN = 'var(--color-badge-benign)'
+
+describe('clinicalSignificanceColor', () => {
+  test.each([
+    ['Pathogenic', PATHOGENIC],
+    ['Likely pathogenic', PATHOGENIC],
+    ['Pathogenic/Likely pathogenic', PATHOGENIC],
+    ['Benign', BENIGN],
+    ['Likely benign', BENIGN],
+    ['Benign/Likely benign', BENIGN]
+  ])('%s → directional color', (significance, color) => {
+    expect(clinicalSignificanceColor(significance)).toBe(color)
+  })
+
+  test.each([
+    'Uncertain significance',
+    'Conflicting classifications of pathogenicity',
+    'Conflicting interpretations of pathogenicity',
+    '-',
+    '',
+    null,
+    undefined
+  ])('%s → undefined (caller keeps its default color)', (significance) => {
+    expect(clinicalSignificanceColor(significance)).toBeUndefined()
+  })
+
+  test('case-insensitive', () => {
+    expect(clinicalSignificanceColor('PATHOGENIC')).toBe(PATHOGENIC)
+    expect(clinicalSignificanceColor('likely benign')).toBe(BENIGN)
+  })
+})
diff --git a/src/lib/clinvar-controls.ts b/src/lib/clinvar-controls.ts
index 3ff924a3..a8b11938 100644
--- a/src/lib/clinvar-controls.ts
+++ b/src/lib/clinvar-controls.ts
@@ -108,17 +108,47 @@ export function formatClinvarVersion(dbVersion: string): string {
 }
 
 /** Deep link to a ClinVar allele record, or null when the allele id is missing. */
-export function clinvarAlleleUrl(alleleId: string | null | undefined): string | null {
+function clinvarAlleleUrl(alleleId: string | null | undefined): string | null {
   if (!alleleId) return null
-  return `https://www.ncbi.nlm.nih.gov/clinvar/allele/${encodeURIComponent(alleleId)}/`
+  return `http://www.ncbi.nlm.nih.gov/clinvar/?term=${encodeURIComponent(alleleId)}[alleleid]`
 }
 
 /** Deep link to a ClinVar variation record, or null when the variation id is missing. */
-export function clinvarVariationUrl(variationId: string | null | undefined): string | null {
+function clinvarVariationUrl(variationId: string | null | undefined): string | null {
   if (!variationId) return null
   return `https://www.ncbi.nlm.nih.gov/clinvar/variation/${encodeURIComponent(variationId)}/`
 }
 
+/**
+ * Deep link to a ClinVar record — prefers the variation page, falls back to the allele page. Structural:
+ * accepts any object carrying the id fields, whichever format it arrives in — a `ClinvarAnnotation`
+ * (`clinvarVariationId`/`clinvarAlleleId`) or a clinical control (`dbIdentifier`, an allele id).
+ */
+export function clinvarVariantUrl(record: {
+  clinvarVariationId?: string | null
+  clinvarAlleleId?: string | null
+  dbIdentifier?: string | null
+}): string | null {
+  return (
+    clinvarVariationUrl(record.clinvarVariationId) ??
+    clinvarAlleleUrl(record.clinvarAlleleId ?? record.dbIdentifier) ??
+    null
+  )
+}
+
+/**
+ * The badge color for a ClinVar clinical significance — pathogenic red, benign green, and `undefined` for
+ * everything else (VUS, conflicting, a `-`), so callers fall back to their own default text color.
+ * Substring match so the P/LP and B/LB aggregate labels all resolve to the directional color.
+ */
+export function clinicalSignificanceColor(significance: string | null | undefined): string | undefined {
+  const s = significance?.toLowerCase() ?? ''
+  if (s.includes('conflicting')) return undefined
+  if (s.includes('pathogenic')) return 'var(--color-badge-pathogenic)'
+  if (s.includes('benign')) return 'var(--color-badge-benign)'
+  return undefined
+}
+
 /** The most recent ClinVar annotation (by `dbVersion`), or null when there are none. */
 export function latestClinvar(annotations: AlleleAnnotations | null): ClinvarAnnotation | null {
   const clinvar = annotations?.clinvar

From 0765269845588a6fde08616a52312d53490da10d Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Tue, 14 Jul 2026 11:51:32 -0700
Subject: [PATCH 32/84] fix(key-drawer): treat an empty v-key-term binding as a
 no-op

Widen the directive's value type to string | null | undefined and skip
binding entirely when the term is falsy, so a badge bound to a dynamic
term that resolves to null gets no handlers or affordance instead of
opening the drawer at the top.
---
 src/directives/key-term.ts | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/src/directives/key-term.ts b/src/directives/key-term.ts
index 7bbcc68c..44138c97 100644
--- a/src/directives/key-term.ts
+++ b/src/directives/key-term.ts
@@ -16,9 +16,11 @@ interface KeyTermEl extends HTMLElement {
  *
  * `stopPropagation` keeps a badge click from also triggering an enclosing clickable card.
  */
-function bind(el: KeyTermEl, binding: DirectiveBinding<string>) {
-  const {open} = useKeyDrawer()
+function bind(el: KeyTermEl, binding: DirectiveBinding<string | null | undefined>) {
   const term = binding.value
+  if (!term) return
+
+  const {open} = useKeyDrawer()
 
   const onClick = (e: Event) => {
     e.stopPropagation()
@@ -48,7 +50,7 @@ function unbind(el: KeyTermEl) {
   delete el.__keyTerm
 }
 
-export const vKeyTerm: Directive<KeyTermEl, string> = {
+export const vKeyTerm: Directive<KeyTermEl, string | null | undefined> = {
   mounted: bind,
   updated(el, binding) {
     if (binding.value !== binding.oldValue) {

From b32de41888a9e2f50e85f62732a0c10c39480cd9 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 16 Jul 2026 14:43:30 -0700
Subject: [PATCH 33/84] chore(ui): add vite-env.d.ts

---
 src/vite-env.d.ts | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 src/vite-env.d.ts

diff --git a/src/vite-env.d.ts b/src/vite-env.d.ts
new file mode 100644
index 00000000..11f02fe2
--- /dev/null
+++ b/src/vite-env.d.ts
@@ -0,0 +1 @@
+/// <reference types="vite/client" />

From 0713a5dab26c6a29acbf3bfbd8069f74858ed21b Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 16 Jul 2026 14:44:44 -0700
Subject: [PATCH 34/84] feat(formats): add formatConsequence and hgvsLabelRank

---
 src/lib/formats.ts | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/src/lib/formats.ts b/src/lib/formats.ts
index f8446199..39313bd1 100644
--- a/src/lib/formats.ts
+++ b/src/lib/formats.ts
@@ -2,6 +2,23 @@ import moment from 'moment'
 import {Opts} from 'linkifyjs'
 import linkifyHtml from 'linkify-html'
 
+/** Humanize a `snake_case` enum token → "Title Case", e.g. `missense_variant` → "Missense Variant". */
+export function formatConsequence(value: string | null | undefined): string {
+  if (!value) return '—'
+  return value.replace(/_/g, ' ').replace(/\b\w/g, (ch) => ch.toUpperCase())
+}
+
+/**
+ * Rank an HGVS label for use as a human display label when several alleles collapse to one annotation:
+ * prefer a coding `c.` (reads more naturally), then genomic `g.`, then anything, then nothing.
+ */
+export function hgvsLabelRank(hgvs: string | null): number {
+  if (!hgvs) return 0
+  if (/(^|:)c\./.test(hgvs)) return 3
+  if (/(^|:)g\./.test(hgvs)) return 2
+  return 1
+}
+
 export function formatDate(x: string) {
   return moment(x).format('MMM DD, YYYY')
 }

From 615bbbccdcca2c029895b6dac83b8664a477aa48 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 16 Jul 2026 14:47:51 -0700
Subject: [PATCH 35/84] refactor(calibrations): extract type aliases, add
 chooseDefaultCalibration - Add ScoreCalibration and
 ScoreCalibrationFunctionalClassification   aliases and use them in place of
 inline components['schemas'][...]   references throughout for readability -
 Add chooseDefaultCalibration to resolve the default calibration from   the
 score set's list alone (primary, investigator-provided,  
 non-research-use-only, any with classifications, then first), so it   can
 resolve without variant scores on the fast path

---
 src/lib/calibrations.ts | 56 ++++++++++++++++++++++++++++-------------
 1 file changed, 38 insertions(+), 18 deletions(-)

diff --git a/src/lib/calibrations.ts b/src/lib/calibrations.ts
index d015c657..e65107ff 100644
--- a/src/lib/calibrations.ts
+++ b/src/lib/calibrations.ts
@@ -1,9 +1,17 @@
+/**
+ * @fileoverview
+ * Calibration utilities for score interpretation and histogram visualization.
+ */
+
 import axios from 'axios'
 
 import {createScoreCalibration, updateScoreCalibration} from '@/api/mavedb'
 import {HistogramBin, HistogramShader} from '@/lib/histogram'
 import {components} from '@/schema/openapi'
 
+export type ScoreCalibration = components['schemas']['ScoreCalibration']
+export type ScoreCalibrationFunctionalClassification =
+  components['schemas']['mavedb__view_models__score_calibration__FunctionalClassification']
 export type FunctionalClassificationVariants = components['schemas']['FunctionalClassificationVariants']
 export type FunctionalClassificationVariant = components['schemas']['VariantEffectMeasurement']
 
@@ -79,9 +87,7 @@ export const EVIDENCE_STRENGTHS_REVERSED = Object.fromEntries(
  * - This function assumes that variant scores are numeric and filters out any non-numeric or NaN values.
  * - The color derivation logic is centralized in `getRangeColor` to maintain consistency across the application.
  */
-export function prepareCalibrationsForHistogram(
-  scoreCalibrations: components['schemas']['ScoreCalibration']
-): HistogramShader[] {
+export function prepareCalibrationsForHistogram(scoreCalibrations: ScoreCalibration): HistogramShader[] {
   const preparedCalibrations: HistogramShader[] = []
 
   if (!scoreCalibrations.functionalClassifications || scoreCalibrations.functionalClassifications.length === 0) {
@@ -129,9 +135,7 @@ export function prepareCalibrationsForHistogram(
  * const color = getRangeColor({ classification: 'normal' }); // e.g. '#3BAA5C'
  * @remarks If new classifications are introduced, extend this function to handle them explicitly.
  */
-export function getClassificationColor(
-  range: components['schemas']['mavedb__view_models__score_calibration__FunctionalClassification']
-): string {
+export function getClassificationColor(range: ScoreCalibrationFunctionalClassification): string {
   if (range.functionalClassification === 'normal') {
     return NORMAL_RANGE_DEFAULT_COLOR
   } else if (range.functionalClassification === 'abnormal') {
@@ -201,7 +205,7 @@ export function shaderOverlapsBin(range: HistogramShader, bin: HistogramBin): bo
  * - Upper bound check uses <= if inclusive, < if exclusive
  */
 export function functionalClassificationContainsVariant(
-  functionalClassification: components['schemas']['mavedb__view_models__score_calibration__FunctionalClassification'],
+  functionalClassification: ScoreCalibrationFunctionalClassification,
   variantScore: number | null
 ): boolean {
   if (variantScore === null) {
@@ -230,7 +234,7 @@ export function functionalClassificationContainsVariant(
  * @returns True if any calibration has at least one functional classification with an evidence strength
  */
 export function hasPathogenicityCalibrations(
-  scoreSet: {scoreCalibrations?: components['schemas']['ScoreCalibration'][] | null} | null | undefined,
+  scoreSet: {scoreCalibrations?: ScoreCalibration[] | null} | null | undefined,
   {excludeResearchUseOnly = true}: {excludeResearchUseOnly?: boolean} = {}
 ): boolean {
   const scoreCalibrations = scoreSet?.scoreCalibrations
@@ -255,7 +259,7 @@ export function hasPathogenicityCalibrations(
  * @returns True if any calibration has at least one functional classification
  */
 export function hasFunctionalCalibrations(
-  scoreSet: {scoreCalibrations?: components['schemas']['ScoreCalibration'][] | null} | null | undefined,
+  scoreSet: {scoreCalibrations?: ScoreCalibration[] | null} | null | undefined,
   {excludeResearchUseOnly = true}: {excludeResearchUseOnly?: boolean} = {}
 ): boolean {
   const scoreCalibrations = scoreSet?.scoreCalibrations
@@ -277,21 +281,40 @@ export function hasFunctionalCalibrations(
  * failing that, the one marked `investigatorProvided`. Returns null if neither exists.
  */
 export function getPrimaryCalibration(
-  scoreSet: {scoreCalibrations?: components['schemas']['ScoreCalibration'][] | null} | null | undefined
-): components['schemas']['ScoreCalibration'] | null {
+  scoreSet: {scoreCalibrations?: ScoreCalibration[] | null} | null | undefined
+): ScoreCalibration | null {
   const calibrations = scoreSet?.scoreCalibrations
   if (!calibrations || calibrations.length === 0) return null
   return calibrations.find((c) => c.primary) || calibrations.find((c) => c.investigatorProvided) || null
 }
 
+/**
+ * Picks the calibration to show by default: primary, else investigator-provided, else the first
+ * non-research-use-only, else any with functional classifications, else the first. Depends only on the
+ * score set's calibrations (not on variant scores), so it can resolve on the fast path.
+ */
+export function chooseDefaultCalibration(
+  scoreCalibrations: ScoreCalibration[] | null | undefined
+): ScoreCalibration | null {
+  if (!scoreCalibrations || scoreCalibrations.length === 0) return null
+  return (
+    scoreCalibrations.find((c) => c.primary === true) ||
+    scoreCalibrations.find((c) => c.investigatorProvided === true) ||
+    scoreCalibrations.find((c) => c.researchUseOnly !== true) ||
+    scoreCalibrations.find((c) => (c.functionalClassifications?.length ?? 0) > 0) ||
+    scoreCalibrations[0] ||
+    null
+  )
+}
+
 /**
  * Finds a functional classification by type (e.g. 'normal', 'abnormal') from a calibration's
  * classifications list. Returns null if not found.
  */
 export function findClassificationByType(
-  calibration: components['schemas']['ScoreCalibration'] | null | undefined,
+  calibration: ScoreCalibration | null | undefined,
   type: string
-): components['schemas']['mavedb__view_models__score_calibration__FunctionalClassification'] | null {
+): ScoreCalibrationFunctionalClassification | null {
   return calibration?.functionalClassifications?.find((r) => r.functionalClassification === type) || null
 }
 
@@ -300,7 +323,7 @@ export function findClassificationByType(
  * or null if not available. Uses the specified precision (default 2).
  */
 export function getClassificationOddsPath(
-  calibration: components['schemas']['ScoreCalibration'] | null | undefined,
+  calibration: ScoreCalibration | null | undefined,
   type: string,
   precision: number = 2
 ): string | null {
@@ -316,10 +339,7 @@ export function getClassificationOddsPath(
  * @returns A formatted code like "PS3_STRONG", or an empty string if evidence data is missing.
  */
 export function formatEvidenceCode(
-  classification:
-    | components['schemas']['mavedb__view_models__score_calibration__FunctionalClassification']
-    | null
-    | undefined
+  classification: ScoreCalibrationFunctionalClassification | null | undefined
 ): string {
   if (!classification?.acmgClassification?.evidenceStrength) return ''
   const criterion = classification.acmgClassification.criterion

From 5e64525d2f62b72e0b2651b68118a190c6df4ea2 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 16 Jul 2026 14:49:18 -0700
Subject: [PATCH 36/84] refactor(measurements): split score loading and track
 in-flight state

- Separate loadScores from loadDetail in the measurement cache so the
  heavier lean score distribution loads independently of the detail
  envelope, letting most of a selection render before visualizations
- Track pending details and scores, exposing isDetailLoading and
  isScoresLoading, and surface selectedLoading on the selection
- Default the selected calibration from the score set via
  chooseDefaultCalibration once it loads, resetting the pick when the
  score set changes while retaining any manual choice
- Source the selected variant score from the measurement rather than
  the lean score row, and prioritize loading the display variant's
  detail before background prefetch
---
 src/composables/use-measurement-cache.ts     | 49 ++++++++++++++++----
 src/composables/use-measurement-selection.ts | 33 ++++++++++++-
 src/composables/use-variant-lookup.ts        |  6 +++
 3 files changed, 77 insertions(+), 11 deletions(-)

diff --git a/src/composables/use-measurement-cache.ts b/src/composables/use-measurement-cache.ts
index b9b76ba0..c35288c7 100644
--- a/src/composables/use-measurement-cache.ts
+++ b/src/composables/use-measurement-cache.ts
@@ -16,17 +16,21 @@ export interface UseMeasurementCacheReturn {
   scoreSets: Ref<Record<string, ScoreSet>>
   scores: Ref<Record<string, DisplayVariant[]>>
   loadDetail: (variantUrn: string) => Promise<void>
+  loadScores: (scoreSetUrn: string) => Promise<void>
+  // In-flight flags for loading affordances.
+  isDetailLoading: (variantUrn: string) => boolean
+  isScoresLoading: (scoreSetUrn: string) => boolean
   clear: () => void
 }
 
 /**
  * Per-URN cache for a measurement's detail envelope, its score set, and its lean score distribution.
  *
- * `loadDetail` resolves all three for a variant URN — the score set (calibrations, target, experiment)
- * and scores are keyed by the URN's score-set prefix and shared across measurements from the same assay.
- * Request dedup + reads are memoized in the api layer (@/api/cache); these Records are just the reactive
- * projection the template renders. `clear()` drops everything for a new query epoch (a changed `as_of`
- * must re-resolve the molecular/annotation layer).
+ * `loadDetail` resolves the envelope + its score set for a variant URN; `loadScores` fetches the heavier
+ * lean score distribution separately. Score set + scores are keyed by the URN's score-set prefix and
+ * shared across measurements from the same assay. Request dedup + reads are memoized in the api layer
+ * (@/api/cache); these Records are just the reactive projection the template renders. `clear()` drops
+ * everything for a new query epoch (a changed `as_of` must re-resolve the molecular/annotation layer).
  *
  * Used by: useVariantLookup, useMeasurementSelection
  */
@@ -35,6 +39,18 @@ export function useMeasurementCache(asOf: Ref<string | null>): UseMeasurementCac
   const scoreSets = shallowRef<Record<string, ScoreSet>>({})
   const scores = shallowRef<Record<string, DisplayVariant[]>>({})
 
+  // In-flight keys, tracked so consumers can show a per-selection loading affordance. Reassigned (not
+  // mutated) so the shallowRefs stay reactive.
+  const pendingDetails = shallowRef<Set<string>>(new Set())
+  const pendingScores = shallowRef<Set<string>>(new Set())
+  function setPending(pending: Ref<Set<string>>, key: string, active: boolean) {
+    if (pending.value.has(key) === active) return
+    const next = new Set(pending.value)
+    if (active) next.add(key)
+    else next.delete(key)
+    pending.value = next
+  }
+
   async function loadScoreSet(scoreSetUrn: string) {
     if (scoreSets.value[scoreSetUrn]) return
     try {
@@ -51,6 +67,7 @@ export function useMeasurementCache(asOf: Ref<string | null>): UseMeasurementCac
 
   async function loadScores(scoreSetUrn: string) {
     if (scores.value[scoreSetUrn]) return
+    setPending(pendingScores, scoreSetUrn, true)
     try {
       // Await into a local before spreading — see loadScoreSet for why an inline `await` in the spread
       // literal races and drops keys under concurrent loads.
@@ -58,21 +75,24 @@ export function useMeasurementCache(asOf: Ref<string | null>): UseMeasurementCac
       scores.value = {...scores.value, [scoreSetUrn]: leanVariants}
     } catch (error) {
       console.error(`Error fetching scores for score set "${scoreSetUrn}"`, error)
+    } finally {
+      setPending(pendingScores, scoreSetUrn, false)
     }
   }
 
   async function loadDetail(variantUrn: string) {
     const scoreSetUrn = scoreSetUrnOf(variantUrn)
-    // The score set and lean scores are needed regardless of whether the envelope is cached, so kick
-    // those off first.
+    // The score set backs certain metadata displayed alongside variant detail.
     loadScoreSet(scoreSetUrn)
-    loadScores(scoreSetUrn)
     if (variantDetails.value[variantUrn]) return
+    setPending(pendingDetails, variantUrn, true)
     try {
       const detail = await getVariantDetail(variantUrn, {asOf: asOf.value ?? undefined})
       variantDetails.value = {...variantDetails.value, [variantUrn]: detail}
     } catch (error) {
       console.error(`Error fetching variant detail for "${variantUrn}"`, error)
+    } finally {
+      setPending(pendingDetails, variantUrn, false)
     }
   }
 
@@ -80,7 +100,18 @@ export function useMeasurementCache(asOf: Ref<string | null>): UseMeasurementCac
     variantDetails.value = {}
     scoreSets.value = {}
     scores.value = {}
+    pendingDetails.value = new Set()
+    pendingScores.value = new Set()
   }
 
-  return {variantDetails, scoreSets, scores, loadDetail, clear}
+  return {
+    variantDetails,
+    scoreSets,
+    scores,
+    loadDetail,
+    loadScores,
+    isDetailLoading: (variantUrn: string) => pendingDetails.value.has(variantUrn),
+    isScoresLoading: (scoreSetUrn: string) => pendingScores.value.has(scoreSetUrn),
+    clear
+  }
 }
diff --git a/src/composables/use-measurement-selection.ts b/src/composables/use-measurement-selection.ts
index c8e00a86..a0d2a8f2 100644
--- a/src/composables/use-measurement-selection.ts
+++ b/src/composables/use-measurement-selection.ts
@@ -2,6 +2,7 @@ import {computed, ref, watch, type ComputedRef, type Ref} from 'vue'
 
 import {useCalibrationResolution, type UseCalibrationResolutionReturn} from '@/composables/use-calibration-resolution'
 import {scoreSetUrnOf, type UseMeasurementCacheReturn} from '@/composables/use-measurement-cache'
+import {chooseDefaultCalibration} from '@/lib/calibrations'
 import type {DisplayVariant} from '@/lib/variants'
 import type {components} from '@/schema/openapi'
 
@@ -25,6 +26,8 @@ export interface UseMeasurementSelectionReturn {
   selectedCalibration: Ref<string | null>
   selectedCalibrationObject: ComputedRef<ScoreCalibration | null>
   calibrationResolution: UseCalibrationResolutionReturn
+  // True while the selected measurement's detail or lean scores are still in flight.
+  selectedLoading: ComputedRef<boolean>
 }
 
 /**
@@ -48,6 +51,11 @@ export function useMeasurementSelection(
   const selectedCalibration = ref<string | null>(null)
 
   const selectedVariant = computed(() => variants.value.find((m) => m.variantUrn === selectedVariantUrn.value))
+  const selectedLoading = computed(() => {
+    const urn = selectedVariantUrn.value
+    if (!urn) return false
+    return cache.isDetailLoading(urn) || cache.isScoresLoading(scoreSetUrnOf(urn))
+  })
   const selectedVariantDetail = computed<VariantDetail | null>(() => {
     if (!selectedVariantUrn.value) return null
     return cache.variantDetails.value[selectedVariantUrn.value] || null
@@ -72,7 +80,7 @@ export function useMeasurementSelection(
     return cache.scores.value[selectedScoreSetUrn.value] || null
   })
   const variantScoreRow = computed(() => (scores.value || []).find((s) => s.variantUrn === selectedVariantUrn.value))
-  const selectedVariantScore = computed(() => variantScoreRow.value?.score ?? null)
+  const selectedVariantScore = computed(() => selectedVariant.value?.score ?? null)
 
   const selectedCalibrationObject = computed<ScoreCalibration | null>(() => {
     if (!selectedCalibration.value || !selectedScoreSet.value?.scoreCalibrations) return null
@@ -107,14 +115,35 @@ export function useMeasurementSelection(
   })
 
   watch(selectedVariantUrn, async (newUrn) => {
+    if (!newUrn) return
+    // Load the display essentials (detail + score set) first, then the heavier lean score distribution.
+    // This allows the majority of data to render while we wait for any visualizations to load.
+    await cache.loadDetail(newUrn)
+    cache.loadScores(scoreSetUrnOf(newUrn))
+  })
+
+  // A new score set invalidates any manual calibration pick (a stale URN wouldn't match the new set).
+  watch(selectedScoreSetUrn, () => {
     selectedCalibration.value = null
-    if (newUrn) await cache.loadDetail(newUrn)
   })
 
+  // Default the calibration from the score set as soon as it loads. Only fills an empty selection,
+  // so a user's manual pick via the histogram dropdown is always retained.
+  watch(
+    selectedScoreSet,
+    (scoreSet) => {
+      if (!selectedCalibration.value) {
+        selectedCalibration.value = chooseDefaultCalibration(scoreSet?.scoreCalibrations)?.urn ?? null
+      }
+    },
+    {immediate: true}
+  )
+
   return {
     selectedVariantUrn,
     selectVariant,
     selectedVariant,
+    selectedLoading,
     selectedVariantDetail,
     selectedVariantName,
     selectedClingenAlleleId,
diff --git a/src/composables/use-variant-lookup.ts b/src/composables/use-variant-lookup.ts
index 77f1d42d..ee15694d 100644
--- a/src/composables/use-variant-lookup.ts
+++ b/src/composables/use-variant-lookup.ts
@@ -185,6 +185,12 @@ export function useVariantLookup(
       const selected = highlighted ? highlightUrn.value! : variants.value[0].variantUrn
       selection.selectedVariantUrn.value = selected
 
+      // Prioritize the display variant: load its detail + score set (both quick, and enough to explore —
+      // score, classification, identity, assay facts) before fanning out. The selection watcher loads the
+      // heavier lean score distribution (histogram only), which rides behind this and the prefetch below.
+      await cache.loadDetail(selected)
+      if (epoch !== queryEpoch) return
+
       // Background-fetch the rest (details + their score sets, which back the cards' assay facts), capped so
       // a large equivalence class doesn't fire a request storm. Skip if a newer query epoch has started.
       for (const m of variants.value) {

From c3c4b0c0c24f382359f6267d7c0317795ee09247 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 16 Jul 2026 14:52:31 -0700
Subject: [PATCH 37/84] feat(clinvar-controls): grade discordance and resolve
 single series membership

Replace the binary excluded flag with a four-level discordance grade
(none, concordant, soft, hard) and make ClinvarControlPlacement a
discriminated union so hard-discordant placements withhold the
representative fields no surface should read.

- Redefine soft as a directional lean co-occurring with an uncertain or
  Conflicting record; place it as its directional lean but flag it
- Add clinvar-control-series with resolveControlSeries, mapping a
  placement to exactly one of pathogenic/benign/uncertain/conflicting
  under a soft-conflicts toggle so controls are never double-counted
- Add a record-resolution layer (resolveClinvarRecords,
  enumerateUnderlyingClinvar, resolveClinvarHeadline) plus selectClinvar,
  clinvarVersionKey, isUncertainSignificance, and formatClinicalSignificance
- Restrict notables to definitive (none/concordant) controls
- Update use-clinvar-controls to gate usability on discordance !== hard
---
 src/composables/use-clinvar-controls.ts   |   2 +-
 src/lib/clinvar-control-placement.test.ts | 241 ++++++++++++++++++----
 src/lib/clinvar-control-placement.ts      | 197 +++++++++++++++---
 src/lib/clinvar-control-series.test.ts    | 117 +++++++++++
 src/lib/clinvar-control-series.ts         |  88 ++++++++
 src/lib/clinvar-controls.test.ts          | 195 ++++++++++++++++-
 src/lib/clinvar-controls.ts               | 136 +++++++++++-
 src/lib/notables.test.ts                  |  32 ++-
 src/lib/notables.ts                       |  23 ++-
 9 files changed, 942 insertions(+), 89 deletions(-)
 create mode 100644 src/lib/clinvar-control-series.test.ts
 create mode 100644 src/lib/clinvar-control-series.ts

diff --git a/src/composables/use-clinvar-controls.ts b/src/composables/use-clinvar-controls.ts
index adf46505..8b868e02 100644
--- a/src/composables/use-clinvar-controls.ts
+++ b/src/composables/use-clinvar-controls.ts
@@ -152,7 +152,7 @@ export function useClinvarControls(
       variant.control = placement
       // "Has clinical significance" gates the clinical view — a hard-discordant variant carries ClinVar
       // data but is not a usable control, so it doesn't count toward showing the view.
-      if (placement && !placement.excluded) {
+      if (placement && placement.discordance !== 'hard') {
         usableAny = true
       }
     }
diff --git a/src/lib/clinvar-control-placement.test.ts b/src/lib/clinvar-control-placement.test.ts
index 01b16335..7b665974 100644
--- a/src/lib/clinvar-control-placement.test.ts
+++ b/src/lib/clinvar-control-placement.test.ts
@@ -1,6 +1,13 @@
 import {describe, expect, test} from 'vitest'
 
-import {reduceControlPlacement, type ClinvarControlPlacement, type ControlLink} from '@/lib/clinvar-control-placement'
+import {
+  reduceControlPlacement,
+  resolveClinvarHeadline,
+  type ClinvarControlPlacement,
+  type ControlLink,
+  type UsableControlPlacement
+} from '@/lib/clinvar-control-placement'
+import type {MeasurementClinvarRecord} from '@/lib/clinvar-controls'
 
 // Review statuses and their star ratings (mirrors CLINVAR_REVIEW_STATUS_STARS), so the representative-pick
 // and per-classification-status tests are explicit about stars.
@@ -30,6 +37,12 @@ function link(significance: string, alleleDigest?: string, reviewStatus: string
 /** The set of distinct significances in a placement (order-independent assertions). */
 const sigs = (p: ClinvarControlPlacement) => p.classifications.map((c) => c.significance).sort()
 
+/** Narrow to a usable placement — hard discordance has no representative, so asserting one there is a bug. */
+function usable(p: ClinvarControlPlacement): UsableControlPlacement {
+  if (p.discordance === 'hard') throw new Error('expected a usable placement, got hard discordance')
+  return p
+}
+
 describe('reduceControlPlacement — divergence fold', () => {
   test('no controls reach the variant → null', () => {
     expect(reduceControlPlacement([], ASSAY)).toBeNull()
@@ -37,23 +50,23 @@ describe('reduceControlPlacement — divergence fold', () => {
 
   describe('single direct call at the assayed level (projected = false)', () => {
     test.each([
-      [P, {directional: true, excluded: false}],
-      [LP, {directional: true, excluded: false}],
-      [PLP, {directional: true, excluded: false}],
-      [B, {directional: true, excluded: false}],
-      [LB, {directional: true, excluded: false}],
-      [BLB, {directional: true, excluded: false}],
-      [VUS, {directional: false, excluded: false}],
+      [P, {directional: true}],
+      [LP, {directional: true}],
+      [PLP, {directional: true}],
+      [B, {directional: true}],
+      [LB, {directional: true}],
+      [BLB, {directional: true}],
+      [VUS, {directional: false}],
       // ClinVar's own aggregate "conflicting" value is neither pathogenic- nor benign-side, so it is not
-      // directional and does not by itself trigger hard-discordance exclusion.
-      [CONFLICTING, {directional: false, excluded: false}]
-    ])('%s → directional/excluded flags, not projected', (significance, expected) => {
+      // directional and does not by itself trigger any discordance.
+      [CONFLICTING, {directional: false}]
+    ])('%s → directional flag, no discordance, not projected', (significance, expected) => {
       const p = reduceControlPlacement([link(significance, ASSAY)], ASSAY)!
-      expect(p.directional).toBe(expected.directional)
-      expect(p.excluded).toBe(expected.excluded)
+      expect(usable(p).directional).toBe(expected.directional)
+      expect(p.discordance).toBe('none')
       expect(p.projected).toBe(false)
       expect(sigs(p)).toEqual([significance])
-      expect(p.clinicalSignificance).toBe(significance)
+      expect(usable(p).clinicalSignificance).toBe(significance)
     })
   })
 
@@ -61,21 +74,21 @@ describe('reduceControlPlacement — divergence fold', () => {
     test('a lone assayed VUS blocks a sibling LP (any assayed call stops the fall-through)', () => {
       const p = reduceControlPlacement([link(VUS, ASSAY), link(LP, SIB)], ASSAY)!
       expect(sigs(p)).toEqual([VUS])
-      expect(p.directional).toBe(false)
+      expect(usable(p).directional).toBe(false)
       expect(p.projected).toBe(false)
     })
 
     test('an assayed directional call is not overridden into hard discordance by a discordant sibling', () => {
       const p = reduceControlPlacement([link(P, ASSAY), link(B, SIB)], ASSAY)!
       expect(sigs(p)).toEqual([P])
-      expect(p.excluded).toBe(false)
+      expect(p.discordance).toBe('none')
       expect(p.projected).toBe(false)
     })
 
     test('multiple assayed-level calls are all consulted (assayed-level discordance is still real)', () => {
-      // Two ClinVar submissions on the *same* assayed allele that disagree on direction → excluded.
+      // Two ClinVar submissions on the *same* assayed allele that disagree on direction → hard.
       const p = reduceControlPlacement([link(P, ASSAY), link(B, ASSAY), link(LP, SIB)], ASSAY)!
-      expect(p.excluded).toBe(true)
+      expect(p.discordance).toBe('hard')
       expect(p.projected).toBe(false)
       // The sibling LP is not consulted — only the two assayed-level calls.
       expect(sigs(p)).toEqual([B, P])
@@ -86,11 +99,12 @@ describe('reduceControlPlacement — divergence fold', () => {
     test('single sibling call → placed on its side, flagged projected', () => {
       const p = reduceControlPlacement([link(LB, SIB)], ASSAY)!
       expect(sigs(p)).toEqual([LB])
-      expect(p.directional).toBe(true)
+      expect(usable(p).directional).toBe(true)
+      expect(p.discordance).toBe('none')
       expect(p.projected).toBe(true)
     })
 
-    describe('hard discordance (both directions present) → excluded', () => {
+    describe('hard discordance (both directions present) → discordance = hard', () => {
       test.each([
         ['P + B', [P, B]],
         ['P + LB', [P, LB]],
@@ -98,46 +112,81 @@ describe('reduceControlPlacement — divergence fold', () => {
         ['LP + LB', [LP, LB]],
         ['PLP + BLB', [PLP, BLB]],
         ['P + B + VUS (VUS does not rescue)', [P, B, VUS]]
-      ])('%s → excluded', (_label, significances) => {
+      ])('%s → hard', (_label, significances) => {
         const links = significances.map((s, i) => link(s, i === 0 ? SIB : SIB2))
         const p = reduceControlPlacement(links, ASSAY)!
-        expect(p.excluded).toBe(true)
+        expect(p.discordance).toBe('hard')
         expect(p.projected).toBe(true)
       })
+
+      test('carries the full set to reconstruct, but no representative — no fake single winner', () => {
+        const p = reduceControlPlacement([link(P, SIB, ONE_STAR), link(B, SIB2, TWO_STAR)], ASSAY)!
+        expect(p.discordance).toBe('hard')
+        // The conflicting calls are still enumerable by any surface.
+        expect(sigs(p)).toEqual([B, P])
+        // But there is physically no winner: the representative fields are absent from the value (and type).
+        expect('clinicalSignificance' in p).toBe(false)
+        expect('alleleDigest' in p).toBe(false)
+        expect('directional' in p).toBe(false)
+      })
     })
 
-    describe('soft discordance (one direction, ± VUS) → included, multi-membership', () => {
-      test('same-side {P, LP} → both calls carried, pathogenic, not excluded', () => {
+    describe('concordant (≥2 distinct calls in one direction, no uncertain record) → discordance = concordant', () => {
+      test('same-side {P, LP} → both calls carried, pathogenic, concordant', () => {
         const p = reduceControlPlacement([link(P, SIB), link(LP, SIB2)], ASSAY)!
-        expect(p.excluded).toBe(false)
-        expect(p.directional).toBe(true)
+        expect(p.discordance).toBe('concordant')
+        expect(usable(p).directional).toBe(true)
         expect(sigs(p)).toEqual([LP, P])
       })
 
-      test('same-side {B, LB} → benign', () => {
+      test('same-side {B, LB} → benign, concordant', () => {
         const p = reduceControlPlacement([link(B, SIB), link(LB, SIB2)], ASSAY)!
-        expect(p.excluded).toBe(false)
+        expect(p.discordance).toBe('concordant')
         expect(sigs(p)).toEqual([B, LB])
       })
+    })
 
-      test('directional + VUS {LP, VUS} → directional (VUS suppressed downstream)', () => {
+    describe('soft conflict (a directional lean + an uncertain record) → discordance = soft', () => {
+      // The VUS widening: a directional lean beside a VUS is now a *soft conflict* (was previously `none`).
+      // The lean still represents and `directional` stays true; the histogram folds it into the directional
+      // series only while its soft-conflicts toggle is on.
+      test('directional + VUS {LP, VUS} → soft, lean represents', () => {
         const p = reduceControlPlacement([link(LP, SIB), link(VUS, SIB2)], ASSAY)!
-        expect(p.directional).toBe(true)
-        expect(p.excluded).toBe(false)
+        expect(p.discordance).toBe('soft')
+        expect(usable(p).directional).toBe(true)
+        expect(usable(p).clinicalSignificance).toBe(LP)
         expect(sigs(p)).toEqual([LP, VUS])
       })
 
-      test('benign + VUS {B, VUS} → directional benign', () => {
+      test('benign + VUS {B, VUS} → soft, benign lean represents', () => {
         const p = reduceControlPlacement([link(B, SIB), link(VUS, SIB2)], ASSAY)!
-        expect(p.directional).toBe(true)
+        expect(p.discordance).toBe('soft')
+        expect(usable(p).directional).toBe(true)
+        expect(usable(p).clinicalSignificance).toBe(B)
         expect(sigs(p)).toEqual([B, VUS])
       })
+
+      // A directional lean beside a ClinVar-*Conflicting* record is the same soft conflict (folds in what was
+      // the retired `contested` value).
+      test('directional + Conflicting {P, CONFLICTING} → soft, directional lean represents', () => {
+        const p = reduceControlPlacement([link(P, SIB), link(CONFLICTING, SIB2)], ASSAY)!
+        expect(p.discordance).toBe('soft')
+        expect(usable(p).directional).toBe(true)
+        expect(usable(p).clinicalSignificance).toBe(P)
+        expect(sigs(p)).toEqual([CONFLICTING, P].sort())
+      })
+
+      test('same-direction multiplicity + an uncertain record → soft outranks concordant', () => {
+        const p = reduceControlPlacement([link(P, SIB), link(LP, SIB2), link(CONFLICTING, SIB)], ASSAY)!
+        expect(p.discordance).toBe('soft')
+        expect(usable(p).directional).toBe(true)
+      })
     })
 
     test('VUS-only siblings → not directional (lands in the VUS series)', () => {
       const p = reduceControlPlacement([link(VUS, SIB), link(VUS, SIB2)], ASSAY)!
-      expect(p.directional).toBe(false)
-      expect(p.excluded).toBe(false)
+      expect(usable(p).directional).toBe(false)
+      expect(p.discordance).toBe('none')
       // Duplicate significances collapse to one classification.
       expect(sigs(p)).toEqual([VUS])
     })
@@ -166,18 +215,18 @@ describe('reduceControlPlacement — divergence fold', () => {
   describe('representative pick (for one-label surfaces: search dot, notables, tooltip)', () => {
     test('a directional call is preferred over a higher-star VUS', () => {
       const p = reduceControlPlacement([link(LP, SIB, ONE_STAR), link(VUS, SIB2, THREE_STAR)], ASSAY)!
-      expect(p.clinicalSignificance).toBe(LP)
+      expect(usable(p).clinicalSignificance).toBe(LP)
     })
 
     test('among directional calls, the highest-star one represents', () => {
-      const p = reduceControlPlacement([link(LP, SIB, ONE_STAR), link(P, SIB2, TWO_STAR)], ASSAY)!
+      const p = usable(reduceControlPlacement([link(LP, SIB, ONE_STAR), link(P, SIB2, TWO_STAR)], ASSAY)!)
       expect(p.clinicalSignificance).toBe(P)
       expect(p.clinicalReviewStatus).toBe(TWO_STAR)
     })
 
     test('VUS-only → the VUS represents', () => {
       const p = reduceControlPlacement([link(VUS, SIB, TWO_STAR)], ASSAY)!
-      expect(p.clinicalSignificance).toBe(VUS)
+      expect(usable(p).clinicalSignificance).toBe(VUS)
     })
   })
 
@@ -185,16 +234,37 @@ describe('reduceControlPlacement — divergence fold', () => {
     test('carries the digest of the representative call', () => {
       const p = reduceControlPlacement([link(LP, 's1', ONE_STAR), link(P, 's2', TWO_STAR)], 'assay')!
       // Representative is the highest-star directional (P on s2), so its digest surfaces.
-      expect(p.alleleDigest).toBe('s2')
+      expect(usable(p).alleleDigest).toBe('s2')
     })
 
     test('a direct assayed-level call surfaces the assayed digest', () => {
       const p = reduceControlPlacement([link(P, ASSAY), link(LP, SIB)], ASSAY)!
-      expect(p.alleleDigest).toBe(ASSAY)
+      expect(usable(p).alleleDigest).toBe(ASSAY)
       expect(p.projected).toBe(false)
     })
   })
 
+  describe('none (a single call, or uncertain-only records) → discordance = none', () => {
+    test('a lone Conflicting record (no directional lean) is not a soft conflict', () => {
+      const p = reduceControlPlacement([link(CONFLICTING, SIB)], ASSAY)!
+      expect(p.discordance).toBe('none')
+      expect(usable(p).directional).toBe(false)
+      expect(usable(p).clinicalSignificance).toBe(CONFLICTING)
+    })
+
+    test('uncertain-only {VUS, Conflicting} → none (no directional lean to conflict with)', () => {
+      const p = reduceControlPlacement([link(VUS, SIB), link(CONFLICTING, SIB2)], ASSAY)!
+      expect(p.discordance).toBe('none')
+      expect(usable(p).directional).toBe(false)
+      expect(sigs(p)).toEqual([CONFLICTING, VUS].sort())
+    })
+
+    test('opposite directions outrank an uncertain record → hard, not soft', () => {
+      const p = reduceControlPlacement([link(P, SIB), link(B, SIB2), link(CONFLICTING, SIB2)], ASSAY)!
+      expect(p.discordance).toBe('hard')
+    })
+  })
+
   describe('unclassified ClinVar values ("-"/empty) are not treated as calls', () => {
     test('a dash-only set → null (not a control, not a call)', () => {
       expect(reduceControlPlacement([link('-', ASSAY), link('-', SIB)], ASSAY)).toBeNull()
@@ -224,3 +294,94 @@ describe('reduceControlPlacement — divergence fold', () => {
     })
   })
 })
+
+/** A resolved record for one allele — the walk's output that the headline projects from. */
+function rec(significance: string, digest: string, reviewStatus: string = ONE_STAR): MeasurementClinvarRecord {
+  return {
+    digest,
+    onAssayed: digest === ASSAY,
+    hgvs: null,
+    classified: !!significance.trim() && !/^-+$/.test(significance.trim()),
+    clinvar: {
+      clinicalSignificance: significance,
+      clinicalReviewStatus: reviewStatus,
+      clinvarVariationId: null,
+      clinvarAlleleId: `${significance}@${digest}`,
+      dbVersion: '03_2024'
+    }
+  }
+}
+
+describe('resolveClinvarHeadline — the display decision', () => {
+  test('no records → none', () => {
+    expect(resolveClinvarHeadline([], ASSAY)).toEqual({kind: 'none'})
+  })
+
+  test('a usable call → kind "call", carrying the representative record and placement', () => {
+    const headline = resolveClinvarHeadline([rec(P, ASSAY), rec(VUS, SIB)], ASSAY)
+    expect(headline.kind).toBe('call')
+    if (headline.kind !== 'call') throw new Error('expected a call')
+    expect(headline.clinvar.clinicalSignificance).toBe(P)
+    expect(headline.placement.discordance).not.toBe('hard')
+  })
+
+  test('opposite-direction calls in the winning set → kind "conflicting"', () => {
+    const headline = resolveClinvarHeadline([rec(P, ASSAY), rec(B, ASSAY)], ASSAY)
+    expect(headline.kind).toBe('conflicting')
+  })
+
+  test('a directional lean + a Conflicting sibling → kind "call", note "soft-conflicting"', () => {
+    const headline = resolveClinvarHeadline([rec(P, SIB), rec(CONFLICTING, SIB2)], ASSAY)
+    expect(headline.kind).toBe('call')
+    if (headline.kind !== 'call') throw new Error('expected a call')
+    // The lean shows, and the note flags ClinVar's own conflict verdict for the surface to render.
+    expect(headline.clinvar.clinicalSignificance).toBe(P)
+    expect(headline.placement.discordance).toBe('soft')
+    expect(headline.note).toBe('soft-conflicting')
+  })
+
+  test('a directional lean + a VUS sibling → kind "call", note "soft-vus"', () => {
+    const headline = resolveClinvarHeadline([rec(LP, SIB), rec(VUS, SIB2)], ASSAY)
+    expect(headline.kind).toBe('call')
+    if (headline.kind !== 'call') throw new Error('expected a call')
+    expect(headline.clinvar.clinicalSignificance).toBe(LP)
+    expect(headline.placement.discordance).toBe('soft')
+    expect(headline.note).toBe('soft-vus')
+  })
+
+  test('≥2 agreeing same-direction records → kind "call", note "concordant"', () => {
+    const headline = resolveClinvarHeadline([rec(P, SIB), rec(LP, SIB2)], ASSAY)
+    expect(headline.kind).toBe('call')
+    if (headline.kind !== 'call') throw new Error('expected a call')
+    expect(headline.placement.discordance).toBe('concordant')
+    expect(headline.note).toBe('concordant')
+  })
+
+  test('a lone unambiguous call → kind "call", note "none"', () => {
+    const headline = resolveClinvarHeadline([rec(P, ASSAY)], ASSAY)
+    expect(headline.kind).toBe('call')
+    if (headline.kind !== 'call') throw new Error('expected a call')
+    expect(headline.note).toBe('none')
+  })
+
+  test('only a `-` record → kind "presence" (not dropped; precedence, not the fold)', () => {
+    const headline = resolveClinvarHeadline([rec('-', ASSAY)], ASSAY)
+    expect(headline.kind).toBe('presence')
+    if (headline.kind !== 'presence') throw new Error('expected presence')
+    expect(headline.record.digest).toBe(ASSAY)
+  })
+
+  test('a real call outranks a co-occurring `-` — presence never shadows a classification', () => {
+    const headline = resolveClinvarHeadline([rec('-', ASSAY), rec(LP, SIB)], ASSAY)
+    expect(headline.kind).toBe('call')
+    if (headline.kind !== 'call') throw new Error('expected a call')
+    expect(headline.clinvar.clinicalSignificance).toBe(LP)
+  })
+
+  test('presence prefers the measured allele`s own `-` record over a sibling`s', () => {
+    const headline = resolveClinvarHeadline([rec('-', SIB), rec('-', ASSAY)], ASSAY)
+    expect(headline.kind).toBe('presence')
+    if (headline.kind !== 'presence') throw new Error('expected presence')
+    expect(headline.record.onAssayed).toBe(true)
+  })
+})
diff --git a/src/lib/clinvar-control-placement.ts b/src/lib/clinvar-control-placement.ts
index 9e257042..6e0cffc6 100644
--- a/src/lib/clinvar-control-placement.ts
+++ b/src/lib/clinvar-control-placement.ts
@@ -1,20 +1,41 @@
+/**
+ * @fileoverview
+ * The ClinVar clinical-control divergence fold.
+ *
+ * For an AA-resolution score set one measured protein change is encoded by several DNA variants, whose
+ * ClinVar classifications can disagree. This module reduces the set of controls that reach a single
+ * variant to one placement the histogram can bin off — applying source precedence (the assayed-level
+ * allele's own call wins; projection siblings are only a fallback) and grading how the winning calls
+ * disagree ({@link Discordance}). Directional-over-uncertain is precedence, not discordance.
+ */
+
 import {
   BENIGN_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS,
+  clinvarVariantUrl,
   CLINVAR_REVIEW_STATUS_STARS,
+  CONFLICTING_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS,
   DEFAULT_CLNREVSTAT_FIELD,
   DEFAULT_CLNSIG_FIELD,
   isClassifiedSignificance,
+  type MeasurementClinvarRecord,
   PATHOGENIC_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS
 } from '@/lib/clinvar-controls'
+import type {components} from '@/schema/openapi'
+
+type ClinvarAnnotation = components['schemas']['ClinvarAnnotation']
 
 /**
- * The ClinVar clinical-control divergence fold.
- *
- * For an AA-resolution score set one measured protein change is encoded by several DNA variants, whose
- * ClinVar classifications can disagree. This module reduces the set of controls that reach a single
- * variant to one placement the histogram can bin off — applying source precedence (the assayed-level
- * allele's own call wins; projection siblings are only a fallback) and the hard/soft discordance rule.
+ * How the ClinVar calls reaching a measurement disagree, ordered by placement difficulty.
+ * - `none` — a single call, or uncertain-only records (a lone VUS, VUS + Conflicting). Nothing to reconcile.
+ * - `concordant` — ≥2 distinct calls in a *single* direction (e.g. Likely benign + Benign); usable, and we
+ *   picked a representative via star tiebreak. Purely informational: the direction is not in doubt.
+ * - `soft` — a *soft conflict*: one directional lean co-occurs with an uncertain record (a VUS or a
+ *   ClinVar-*Conflicting* call). Usable (the directional call is the representative) but flagged because the
+ *   uncertain record hints the direction may not be settled. Places as its directional lean.
+ * - `hard` — opposing directional *assertions* (P/LP and B/LB); the projection premise is broken, so there is
+ *   no usable representative. Categorical — confidence within a direction never changes this.
  */
+export type Discordance = 'none' | 'concordant' | 'soft' | 'hard'
 
 /** A distinct ClinVar call in a variant's winning set. */
 export interface ControlClassification {
@@ -24,42 +45,56 @@ export interface ControlClassification {
 
 /** One ClinVar control reaching a variant, tagged with the digest of the allele it annotates. */
 export interface ControlLink extends ControlClassification {
-  /** VRS digest of the allele the control annotates; compared to the variant's `assayLevelDigest`. */
   alleleDigest?: string | null
   dbIdentifier?: string
 }
 
-/** The reduced result for one variant — what the histogram and per-variant surfaces read. */
-export interface ClinvarControlPlacement {
+/** Fields present on every placement, usable or not — enough to reconstruct the winning set behind the fold. */
+interface BaseControlPlacement {
+  /** The winning set's distinct calls (assayed-level controls if any, else the projection siblings). */
+  classifications: ControlClassification[]
+  /**
+   * True when the winning set came from **projection siblings**. The measured allele itself had no
+   * ClinVar record, so this classification is about a *related* variant at a different level, not the
+   * entity we assayed.
+   */
+  projected: boolean
+}
+
+/**
+ * A hard-discordant placement: the winning set holds both a P/LP and a B/LB call, so there is *physically*
+ * no representative — no single call can stand for a contradiction. Carries only the set (so a surface can
+ * still list the conflicting calls); the representative fields are absent from the type to avoid accidental
+ * misuse.
+ */
+export interface HardDiscordantPlacement extends BaseControlPlacement {
+  discordance: 'hard'
+}
+
+/** A usable placement (`none`/`concordant`/`soft`): a single representative call the one-label surfaces read. */
+export interface UsableControlPlacement extends BaseControlPlacement {
+  discordance: 'none' | 'concordant' | 'soft'
   /** Representative single call (directional-preferred, then highest-star) for one-label surfaces. */
   [DEFAULT_CLNSIG_FIELD]: string
   [DEFAULT_CLNREVSTAT_FIELD]: string
   dbIdentifier?: string
-  /** The winning set's distinct calls (assayed-level controls if any, else the projection siblings). */
-  classifications: ControlClassification[]
-  /** Hard discordance — the winning set holds both a P/LP and a B/LB call; not a usable control. */
-  excluded: boolean
   /** Whether any confident directional (P/LP or B/LB) call is present — directional dominates VUS. */
   directional: boolean
-  /**
-   * VRS digest of the representative call's allele — lets a per-variant surface resolve that allele's
-   * level/HGVS (to name a projected sibling) and its ClinVar link-out. Undefined only when the winning
-   * links carried no digest.
-   */
+  /** VRS digest of the representative call's allele. Undefined only when the winning links carried no digest. */
   alleleDigest?: string | null
-  /**
-   * True when the winning set came from **projection siblings** — the measured allele itself had no
-   * ClinVar record, so this classification is about a *related* variant at a different level, not the
-   * entity we assayed. Drives the "related variant" tooltip note that reconciles a control series
-   * membership with an empty measured-level ClinVar. Only asserted when the assayed-level digest is
-   * known (so a genuinely-direct call is never mislabeled when the digest is merely absent).
-   */
-  projected: boolean
 }
 
+/**
+ * The reduced result for one variant — what the histogram and per-variant surfaces read. A discriminated
+ * union on `discordance`: narrow to a {@link UsableControlPlacement} (or check `discordance !== 'hard'`)
+ * before reading the representative call.
+ */
+export type ClinvarControlPlacement = HardDiscordantPlacement | UsableControlPlacement
+
 const isPathogenic = (significance: string) => PATHOGENIC_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS.includes(significance)
 const isBenign = (significance: string) => BENIGN_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS.includes(significance)
 const isDirectional = (significance: string) => isPathogenic(significance) || isBenign(significance)
+const isConflicting = (significance: string) => CONFLICTING_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS.includes(significance)
 const starsOf = (reviewStatus: string) => CLINVAR_REVIEW_STATUS_STARS[reviewStatus] ?? -1
 
 /**
@@ -69,10 +104,13 @@ const starsOf = (reviewStatus: string) => CLINVAR_REVIEW_STATUS_STARS[reviewStat
  * (`alleleDigest === assayLevelDigest`), those controls are the winning set and the projection siblings
  * are ignored — a direct call on the assayed entity is not diluted by the fan-out. Otherwise the
  * siblings are the winning set. Over the winning set:
- *   - **hard discordance** (both a P/LP and a B/LB call) → `excluded` (not a usable control);
- *   - otherwise the distinct calls flow through as `classifications`, and `directional` records whether
- *     any confident P/LP or B/LB call is present, so the histogram can drop VUS when a directional call
- *     dominates.
+ *   - **hard** (both a P/LP and a B/LB call) → `discordance: 'hard'`, not a usable control;
+ *   - **soft** (a directional lean + an uncertain record — a VUS or a ClinVar-*Conflicting* call) →
+ *     `discordance: 'soft'`, usable — the lean is the representative, but the surface can flag the soft conflict;
+ *   - **concordant** (≥2 distinct calls in a single direction, e.g. LB + B, no uncertain record) →
+ *     `discordance: 'concordant'`, usable, representative by star tiebreak;
+ *   - the distinct calls flow through as `classifications`, and `directional` records whether any confident
+ *     P/LP or B/LB call is present, so the histogram can drop VUS when a directional call dominates.
  *
  * Returns `null` when no *classified* control reaches the variant.
  */
@@ -103,9 +141,27 @@ export function reduceControlPlacement(
     }
   }
 
-  const pathogenicPresent = classifications.some((c) => isPathogenic(c.significance))
-  const benignPresent = classifications.some((c) => isBenign(c.significance))
-  const directional = pathogenicPresent || benignPresent
+  const pathogenicCalls = classifications.filter((c) => isPathogenic(c.significance))
+  const benignCalls = classifications.filter((c) => isBenign(c.significance))
+  const directional = pathogenicCalls.length > 0 || benignCalls.length > 0
+  // Any non-directional call is "uncertain" — a VUS *or* ClinVar's own aggregate Conflicting value.
+  const uncertainPresent = classifications.some((c) => !isDirectional(c.significance))
+
+  // Grade the disagreement. Opposite directions is hard (unusable). Otherwise, with a single direction:
+  // a co-occurring uncertain record (VUS/Conflicting) is a *soft conflict* — the lean stands but the direction
+  // may not be settled; ≥2 distinct calls in that one direction (no uncertain record) is merely concordant.
+  if (pathogenicCalls.length > 0 && benignCalls.length > 0) {
+    // Hard: opposing directional assertions break the projection premise, so there is no single winning call.
+    // No representative is computed, and the type withholds those fields so no surface can read a fake one.
+    return {discordance: 'hard', classifications, projected}
+  }
+  // soft > concordant > none.
+  const discordance: 'none' | 'concordant' | 'soft' =
+    directional && uncertainPresent
+      ? 'soft'
+      : pathogenicCalls.length > 1 || benignCalls.length > 1
+        ? 'concordant'
+        : 'none'
 
   // Representative for one-label surfaces (search dot, notables, tooltip): a directional call is more
   // informative than a co-occurring VUS, so prefer directional calls when present, then highest star.
@@ -119,9 +175,82 @@ export function reduceControlPlacement(
     [DEFAULT_CLNREVSTAT_FIELD]: representative.reviewStatus,
     dbIdentifier: representative.dbIdentifier,
     classifications,
-    excluded: pathogenicPresent && benignPresent,
+    discordance,
     directional,
     alleleDigest: representative.alleleDigest,
     projected
   }
 }
+
+/**
+ * A note qualifying a representative `call` — what, beyond the call itself, the headline should say.
+ * - `none` — a lone, unambiguous call; show it plainly.
+ * - `concordant` — the call represents ≥2 agreeing same-direction records; a quiet "representative of concordant
+ *   records" aside.
+ * - `soft-vus` — a soft conflict where the co-occurring uncertain record is a plain VUS.
+ * - `soft-conflicting` — a soft conflict where ClinVar itself marks a related record *Conflicting*.
+ *
+ * The two `soft-*` values are split so the surface can word the two soft conflicts differently; `soft-conflicting`
+ * wins when both a VUS and a Conflicting record co-occur (ClinVar's explicit conflict verdict is the stronger flag).
+ */
+export type ClinvarCallNote = 'none' | 'concordant' | 'soft-vus' | 'soft-conflicting'
+
+/**
+ * What a one-headline ClinVar surface should display for a measurement — a discriminated union so the
+ * component switches on `kind` instead of re-deriving a precedence ladder in its template.
+ * - `conflicting` — hard-discordant winning set; no single call to show.
+ * - `call` — the representative usable call (assayed-level or a projection sibling), with a {@link ClinvarCallNote}
+ *   qualifying it (concordant aside, or a soft-conflict flag). The lib owns that decision so the template renders it.
+ * - `presence` — no usable call, but a ClinVar record exists (a `-` germline-less submission); link out.
+ * - `none` — nothing reaches the measurement.
+ */
+export type ClinvarHeadline =
+  | {kind: 'conflicting'; placement: HardDiscordantPlacement}
+  | {kind: 'call'; clinvar: ClinvarAnnotation; placement: UsableControlPlacement; note: ClinvarCallNote}
+  | {kind: 'presence'; record: MeasurementClinvarRecord}
+  | {kind: 'none'}
+
+/** Derive the {@link ClinvarCallNote} for a usable placement — the lib's single display decision for a call. */
+function resolveCallNote(placement: UsableControlPlacement): ClinvarCallNote {
+  if (placement.discordance === 'concordant') return 'concordant'
+  if (placement.discordance === 'soft') {
+    return placement.classifications.some((c) => isConflicting(c.significance)) ? 'soft-conflicting' : 'soft-vus'
+  }
+  return 'none'
+}
+
+/** Pick the germline-less record to represent a measurement when the fold yields no call: the measured
+ *  allele's own record wins, then any linkable one, else first-seen. */
+function selectPresence(records: MeasurementClinvarRecord[]): MeasurementClinvarRecord | null {
+  if (records.length === 0) return null
+  return records.find((r) => r.onAssayed) ?? records.find((r) => Boolean(clinvarVariantUrl(r.clinvar))) ?? records[0]
+}
+
+/**
+ * Resolve what a one-headline ClinVar surface shows, over a resolved walk. Runs the fold and, when it yields
+ * no usable call, falls back to a `-` presence record — the single precedence decision every such surface
+ * reads, so the stat cell and variant screen agree.
+ */
+export function resolveClinvarHeadline(
+  records: MeasurementClinvarRecord[],
+  assayLevelDigest: string | null | undefined
+): ClinvarHeadline {
+  const placement = reduceControlPlacement(
+    records.map((r) => ({
+      significance: r.clinvar.clinicalSignificance,
+      reviewStatus: r.clinvar.clinicalReviewStatus,
+      alleleDigest: r.digest
+    })),
+    assayLevelDigest
+  )
+  if (placement?.discordance === 'hard') return {kind: 'conflicting', placement}
+  if (placement) {
+    const representative = records.find((r) => r.digest === placement.alleleDigest)
+    if (representative) {
+      return {kind: 'call', clinvar: representative.clinvar, placement, note: resolveCallNote(placement)}
+    }
+  }
+  // No usable call — a real classification would have folded above, so any surviving record is a `-`.
+  const presence = selectPresence(records)
+  return presence ? {kind: 'presence', record: presence} : {kind: 'none'}
+}
diff --git a/src/lib/clinvar-control-series.test.ts b/src/lib/clinvar-control-series.test.ts
new file mode 100644
index 00000000..d794294f
--- /dev/null
+++ b/src/lib/clinvar-control-series.test.ts
@@ -0,0 +1,117 @@
+import {describe, expect, test} from 'vitest'
+
+import {reduceControlPlacement, type ControlLink} from '@/lib/clinvar-control-placement'
+import {resolveControlSeries, type ControlSeriesOptions} from '@/lib/clinvar-control-series'
+
+// Review statuses and their star ratings (mirrors CLINVAR_REVIEW_STATUS_STARS).
+const ONE_STAR = 'criteria provided, single submitter' // 1★
+const TWO_STAR = 'criteria provided, multiple submitters, no conflicts' // 2★
+
+const ASSAY = 'assayed-level-digest'
+const SIB = 'sibling-digest'
+const SIB2 = 'sibling-digest-2'
+
+const P = 'Pathogenic'
+const LP = 'Likely pathogenic'
+const PLP = 'Pathogenic/Likely pathogenic'
+const B = 'Benign'
+const LB = 'Likely benign'
+const BLB = 'Benign/Likely benign'
+const VUS = 'Uncertain significance'
+const CONFLICTING = 'Conflicting classifications of pathogenicity'
+
+function link(significance: string, alleleDigest?: string, reviewStatus: string = ONE_STAR): ControlLink {
+  return {significance, reviewStatus, alleleDigest, dbIdentifier: `${significance}@${alleleDigest ?? '?'}`}
+}
+
+describe('resolveControlSeries — single-membership histogram placement', () => {
+  // Everything selected (all directional + both uncertain calls) and no star floor, unless a test overrides it,
+  // so membership is decided by the placement/toggle, not filtered out by selection or stars.
+  const ALL_SELECTED = [P, LP, PLP, B, LB, BLB, VUS, CONFLICTING]
+  const opts = (softConflictsEnabled: boolean, over: Partial<ControlSeriesOptions> = {}): ControlSeriesOptions => ({
+    softConflictsEnabled,
+    selectedSignificances: ALL_SELECTED,
+    minStars: Number.NEGATIVE_INFINITY,
+    ...over
+  })
+  const place = (...links: ControlLink[]) => reduceControlPlacement(links, ASSAY)
+
+  test('no placement → null in either mode', () => {
+    expect(resolveControlSeries(null, opts(true))).toBeNull()
+    expect(resolveControlSeries(undefined, opts(false))).toBeNull()
+  })
+
+  test('hard discordance → null in either mode (never a valid home)', () => {
+    const hard = place(link(P, SIB), link(B, SIB2))
+    expect(resolveControlSeries(hard, opts(true))).toBeNull()
+    expect(resolveControlSeries(hard, opts(false))).toBeNull()
+  })
+
+  describe('clean/concordant directional → its directional series, in either mode', () => {
+    test.each([
+      ['single P', [link(P, ASSAY)], 'pathogenic'],
+      ['single LB', [link(LB, ASSAY)], 'benign'],
+      ['concordant {P, LP}', [link(P, SIB), link(LP, SIB2)], 'pathogenic'],
+      ['concordant {B, LB}', [link(B, SIB), link(LB, SIB2)], 'benign']
+    ])('%s → %s', (_label, links, expected) => {
+      const p = place(...links)
+      expect(resolveControlSeries(p, opts(true))).toBe(expected)
+      expect(resolveControlSeries(p, opts(false))).toBe(expected)
+    })
+  })
+
+  describe('soft conflict → directional lean only while the fold is on', () => {
+    test.each([
+      ['directional + VUS', [link(LP, SIB), link(VUS, SIB2)], 'pathogenic'],
+      ['directional + Conflicting', [link(B, SIB), link(CONFLICTING, SIB2)], 'benign']
+    ])('%s → %s when on, null when off', (_label, links, expected) => {
+      const p = place(...links)
+      expect(p!.discordance).toBe('soft')
+      expect(resolveControlSeries(p, opts(true))).toBe(expected)
+      expect(resolveControlSeries(p, opts(false))).toBeNull()
+    })
+  })
+
+  describe('pure uncertain → its uncertain series only while the fold is off (mutual exclusion)', () => {
+    test('single VUS → uncertain when off, null when on', () => {
+      const p = place(link(VUS, ASSAY))
+      expect(resolveControlSeries(p, opts(false))).toBe('uncertain')
+      expect(resolveControlSeries(p, opts(true))).toBeNull()
+    })
+
+    test('lone Conflicting → conflicting when off, null when on', () => {
+      const p = place(link(CONFLICTING, ASSAY))
+      expect(resolveControlSeries(p, opts(false))).toBe('conflicting')
+      expect(resolveControlSeries(p, opts(true))).toBeNull()
+    })
+
+    test('{VUS, Conflicting} → exactly one uncertain series (its representative), never both', () => {
+      const p = place(link(VUS, SIB, TWO_STAR), link(CONFLICTING, SIB2, ONE_STAR))
+      // Representative is the higher-star uncertain call (VUS @ 2★), so it lands in the VUS series alone.
+      expect(resolveControlSeries(p, opts(false))).toBe('uncertain')
+      expect(resolveControlSeries(p, opts(true))).toBeNull()
+    })
+  })
+
+  describe('the star gate is on the representative', () => {
+    test('representative below minStars → null', () => {
+      const p = place(link(P, ASSAY, ONE_STAR))
+      expect(resolveControlSeries(p, opts(true, {minStars: 2}))).toBeNull()
+    })
+
+    test('representative clearing minStars → placed', () => {
+      const p = place(link(P, ASSAY, TWO_STAR))
+      expect(resolveControlSeries(p, opts(true, {minStars: 2}))).toBe('pathogenic')
+    })
+  })
+
+  describe('selection gates on the representative (single-representative membership)', () => {
+    // Concordant {P@2★, LP@1★}: representative is the higher-star P. It is placed once, by P — not by both
+    // filters. So an "LP-only" selection excludes it even though LP is in the winning set.
+    test('representative P dropped when only LP is selected', () => {
+      const p = place(link(P, SIB, TWO_STAR), link(LP, SIB2, ONE_STAR))
+      expect(resolveControlSeries(p, opts(true, {selectedSignificances: [LP]}))).toBeNull()
+      expect(resolveControlSeries(p, opts(true, {selectedSignificances: [P]}))).toBe('pathogenic')
+    })
+  })
+})
diff --git a/src/lib/clinvar-control-series.ts b/src/lib/clinvar-control-series.ts
new file mode 100644
index 00000000..62ad422a
--- /dev/null
+++ b/src/lib/clinvar-control-series.ts
@@ -0,0 +1,88 @@
+/**
+ * @fileoverview
+ * How the score-set histogram bins a ClinVar {@link ClinvarControlPlacement} into a single filtered series.
+ *
+ * This is the histogram's clinical control visualization of placements ({@link module:clinvar-control-placement}):
+ * Given a ClinVar placement, this module answers which of the four clinical histogram series it belongs to, or null
+ * if it is excluded by the user's filters.
+ *
+ */
+
+import {
+  BENIGN_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS,
+  CLINVAR_REVIEW_STATUS_STARS,
+  CONFLICTING_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS,
+  DEFAULT_CLNREVSTAT_FIELD,
+  DEFAULT_CLNSIG_FIELD,
+  PATHOGENIC_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS,
+  UNCERTAIN_SIGNIFICANCE_CLASSIFICATIONS
+} from '@/lib/clinvar-controls'
+import type {ClinvarControlPlacement} from '@/lib/clinvar-control-placement'
+
+const isPathogenic = (significance: string) => PATHOGENIC_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS.includes(significance)
+const isBenign = (significance: string) => BENIGN_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS.includes(significance)
+const isDirectional = (significance: string) => isPathogenic(significance) || isBenign(significance)
+const isConflicting = (significance: string) => CONFLICTING_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS.includes(significance)
+const starsOf = (reviewStatus: string) => CLINVAR_REVIEW_STATUS_STARS[reviewStatus] ?? -1
+
+/** The clinical-control histogram series a variant can be placed in — exactly one, or none. */
+export type ClinvarControlSeriesKey = 'pathogenic' | 'benign' | 'uncertain' | 'conflicting'
+
+/** How the histogram should read a placement into a series: the soft-conflict fold, the selection, the star gate. */
+export interface ControlSeriesOptions {
+  softConflictsEnabled: boolean
+  /** The significances the user has selected to include; membership gates on the *representative's* own value. */
+  selectedSignificances: string[]
+  /** Minimum review-status stars the representative must clear. */
+  minStars: number
+}
+
+/** Map a directional representative to its aggregate series, gated on it being a selected significance. */
+function directionalSeries(representative: string, selected: string[]): ClinvarControlSeriesKey | null {
+  if (!selected.includes(representative)) return null
+  if (isPathogenic(representative)) return 'pathogenic'
+  return isBenign(representative) ? 'benign' : null
+}
+
+/** Map an uncertain representative (VUS or Conflicting) to its series, gated on it being selected. */
+function uncertainSeries(representative: string, selected: string[]): ClinvarControlSeriesKey | null {
+  if (!selected.includes(representative)) return null
+  if (UNCERTAIN_SIGNIFICANCE_CLASSIFICATIONS.includes(representative)) return 'uncertain'
+  return isConflicting(representative) ? 'conflicting' : null
+}
+
+/**
+ * The single clinical-control series a placement belongs to — or null (excluded). **Never two:** membership is
+ * fixed by the placement's representative call, so a variant is placed once, not once per granularity filter it
+ * happens to intersect (this guarantees we don't "double count" controls).
+ *
+ *   - no placement / hard discordance → null (no representative; never a valid home);
+ *   - representative below `minStars` → null (the star gate is on the *representative*, not "any winning call");
+ *   - soft conflict (a directional lean beside an uncertain/Conflicting record) → its directional series, but only
+ *     while `softConflictsEnabled`; off, it is excluded so the uncertain series stay genuinely uncertain;
+ *   - a pure uncertain representative (VUS / lone Conflicting) → its uncertain series, but only while
+ *     `softConflictsEnabled` is OFF (the soft-fold and uncertain-series are mutually exclusive modes);
+ *   - a clean or concordant directional representative → its directional series.
+ *
+ * `selectedSignificances` gates on the representative's own significance, so e.g. a variant whose representative
+ * is `Pathogenic` drops out when only `Likely pathogenic` is selected.
+ */
+export function resolveControlSeries(
+  placement: ClinvarControlPlacement | null | undefined,
+  opts: ControlSeriesOptions
+): ClinvarControlSeriesKey | null {
+  if (!placement || placement.discordance === 'hard') return null
+  if (starsOf(placement[DEFAULT_CLNREVSTAT_FIELD]) < opts.minStars) return null
+
+  const representative = placement[DEFAULT_CLNSIG_FIELD]
+  // soft conflict: place by the directional lean, but only while the soft-fold is on.
+  if (placement.discordance === 'soft') {
+    return opts.softConflictsEnabled ? directionalSeries(representative, opts.selectedSignificances) : null
+  }
+  // none/concordant: place by the representative's own bucket.
+  if (isDirectional(representative)) {
+    return directionalSeries(representative, opts.selectedSignificances)
+  }
+  // A pure uncertain representative shows only in the uncertain-series mode.
+  return opts.softConflictsEnabled ? null : uncertainSeries(representative, opts.selectedSignificances)
+}
diff --git a/src/lib/clinvar-controls.test.ts b/src/lib/clinvar-controls.test.ts
index 592422e4..50912e84 100644
--- a/src/lib/clinvar-controls.test.ts
+++ b/src/lib/clinvar-controls.test.ts
@@ -1,10 +1,43 @@
 import {describe, expect, test} from 'vitest'
 
-import {clinicalSignificanceColor} from '@/lib/clinvar-controls'
+import {
+  clinicalSignificanceColor,
+  clinvarVersionKey,
+  enumerateUnderlyingClinvar,
+  isUncertainSignificance,
+  type MeasurementClinvarRecord,
+  resolveClinvarRecords,
+  selectClinvar
+} from '@/lib/clinvar-controls'
+import type {components} from '@/schema/openapi'
+
+type ClinvarAnnotation = components['schemas']['ClinvarAnnotation']
 
 const PATHOGENIC = 'var(--color-badge-pathogenic)'
 const BENIGN = 'var(--color-badge-benign)'
 
+// A ClinVar annotation with sensible defaults; only the fields a test cares about need overriding.
+function clinvar(overrides: Partial<ClinvarAnnotation> & {clinvarAlleleId: string}): ClinvarAnnotation {
+  return {
+    clinicalSignificance: 'Uncertain significance',
+    clinicalReviewStatus: 'criteria provided, single submitter',
+    clinvarVariationId: null,
+    dbVersion: '03_2024',
+    ...overrides
+  }
+}
+
+/** The ClinVar record ids in a resolved/enumerated list, in returned order. */
+const ids = (list: MeasurementClinvarRecord[]) =>
+  list.map((item) => item.clinvar.clinvarVariationId ?? item.clinvar.clinvarAlleleId)
+
+/** Enumerate the underlying popover records from a raw annotations map (the real walk → project path). */
+const enumerate = (
+  annotations: Parameters<typeof resolveClinvarRecords>[0],
+  alleles: Parameters<typeof resolveClinvarRecords>[1],
+  version?: string | null
+) => enumerateUnderlyingClinvar(resolveClinvarRecords(annotations, alleles, null, version))
+
 describe('clinicalSignificanceColor', () => {
   test.each([
     ['Pathogenic', PATHOGENIC],
@@ -34,3 +67,163 @@ describe('clinicalSignificanceColor', () => {
     expect(clinicalSignificanceColor('likely benign')).toBe(BENIGN)
   })
 })
+
+describe('resolveClinvarRecords — the single walk', () => {
+  test('nullish annotations → empty', () => {
+    expect(resolveClinvarRecords(null, null, null)).toEqual([])
+    expect(resolveClinvarRecords(undefined, undefined, undefined)).toEqual([])
+  })
+
+  test('keeps `-` records (tagged unclassified), skips alleles with no record', () => {
+    const annotations = {
+      a: {clinvar: [clinvar({clinvarAlleleId: 'a', clinicalSignificance: '-'})]},
+      b: {clinvar: [clinvar({clinvarAlleleId: 'b', clinicalSignificance: 'Pathogenic'})]},
+      c: {clinvar: null}
+    }
+    const records = resolveClinvarRecords(annotations, {}, null)
+    expect(ids(records)).toEqual(['a', 'b'])
+    expect(records.find((r) => r.digest === 'a')?.classified).toBe(false)
+    expect(records.find((r) => r.digest === 'b')?.classified).toBe(true)
+  })
+
+  test('tags onAssayed against the measured digest and pairs HGVS from the sidecar', () => {
+    const annotations = {
+      a: {clinvar: [clinvar({clinvarAlleleId: 'a', clinicalSignificance: 'Pathogenic'})]},
+      b: {clinvar: [clinvar({clinvarAlleleId: 'b', clinicalSignificance: 'Benign'})]}
+    }
+    const records = resolveClinvarRecords(annotations, {a: {hgvs: 'c.10A>G'}}, 'a')
+    expect(records.find((r) => r.digest === 'a')).toMatchObject({onAssayed: true, hgvs: 'c.10A>G'})
+    expect(records.find((r) => r.digest === 'b')).toMatchObject({onAssayed: false, hgvs: null})
+  })
+})
+
+describe('enumerateUnderlyingClinvar — the popover projection', () => {
+  test('nullish annotations → empty', () => {
+    expect(enumerate(null, null)).toEqual([])
+    expect(enumerate(undefined, undefined)).toEqual([])
+  })
+
+  test('keeps `-` records — only the fold drops them — sorted after classified calls', () => {
+    const annotations = {
+      a: {clinvar: [clinvar({clinvarAlleleId: 'a', clinicalSignificance: '-'})]},
+      b: {clinvar: [clinvar({clinvarAlleleId: 'b', clinicalSignificance: 'Pathogenic'})]},
+      c: {clinvar: null}
+    }
+    // b (directional) leads; a (`-`, non-directional) trails; c has no record.
+    expect(ids(enumerate(annotations, {}))).toEqual(['b', 'a'])
+  })
+
+  test('excludes the measured allele`s own record — the primary is not "underlying"', () => {
+    const annotations = {
+      assayed: {clinvar: [clinvar({clinvarAlleleId: 'assayed', clinicalSignificance: 'Pathogenic'})]},
+      sib: {clinvar: [clinvar({clinvarAlleleId: 'sib', clinicalSignificance: 'Uncertain significance'})]}
+    }
+    // Only the sibling is underlying; a lone assayed record would leave this empty (→ no popover).
+    expect(ids(enumerateUnderlyingClinvar(resolveClinvarRecords(annotations, {}, 'assayed')))).toEqual(['sib'])
+  })
+
+  test('keeps a projected headline`s source sibling (measured allele carries no record)', () => {
+    const annotations = {
+      assayed: {clinvar: null},
+      sib: {clinvar: [clinvar({clinvarAlleleId: 'sib', clinicalSignificance: 'Pathogenic'})]}
+    }
+    // The nucleotide sibling the protein-level headline was projected from is still an underlying record.
+    expect(ids(enumerateUnderlyingClinvar(resolveClinvarRecords(annotations, {}, 'assayed')))).toEqual(['sib'])
+  })
+
+  test('sorts directional calls ahead of VUS, then by descending star rating', () => {
+    const annotations = {
+      vus: {clinvar: [clinvar({clinvarAlleleId: 'vus', clinicalSignificance: 'Uncertain significance'})]},
+      lp1: {
+        clinvar: [
+          clinvar({
+            clinvarAlleleId: 'lp1',
+            clinicalSignificance: 'Likely pathogenic',
+            clinicalReviewStatus: 'criteria provided, single submitter'
+          })
+        ]
+      },
+      p3: {
+        clinvar: [
+          clinvar({
+            clinvarAlleleId: 'p3',
+            clinicalSignificance: 'Pathogenic',
+            clinicalReviewStatus: 'reviewed by expert panel'
+          })
+        ]
+      }
+    }
+    // p3 (directional, 3★) → lp1 (directional, 1★) → vus (non-directional, last).
+    expect(ids(enumerate(annotations, {}))).toEqual(['p3', 'lp1', 'vus'])
+  })
+
+  test('selects by version and dedupes by ClinVar record id (prefers a coding HGVS label)', () => {
+    const annotations = {
+      cDigest: {
+        clinvar: [
+          clinvar({clinvarAlleleId: 'x', clinvarVariationId: '123', clinicalSignificance: 'Benign', dbVersion: '03_2024'}),
+          clinvar({clinvarAlleleId: 'x', clinvarVariationId: '123', clinicalSignificance: 'Pathogenic', dbVersion: '06_2024'})
+        ]
+      },
+      gDigest: {
+        clinvar: [clinvar({clinvarAlleleId: 'x', clinvarVariationId: '123', clinicalSignificance: 'Benign', dbVersion: '03_2024'})]
+      }
+    }
+    const alleles = {cDigest: {hgvs: 'NM_1.2:c.10A>G'}, gDigest: {hgvs: 'NC_1.11:g.100A>G'}}
+    // Both digests select the 03_2024 record (same variation id) → one entry, coding HGVS wins as the label.
+    const result = enumerate(annotations, alleles, '03_2024')
+    expect(result).toHaveLength(1)
+    expect(result[0].hgvs).toBe('NM_1.2:c.10A>G')
+    expect(result[0].clinvar.clinicalSignificance).toBe('Benign')
+    // Pinning the newer release selects the pathogenic record from the allele that carries it.
+    const newer = enumerate(annotations, alleles, '06_2024')
+    expect(newer).toHaveLength(1)
+    expect(newer[0].clinvar.clinicalSignificance).toBe('Pathogenic')
+  })
+})
+
+describe('clinvarVersionKey — MM_YYYY ordered by year then month', () => {
+  test.each([
+    ['06_2024', '03_2024', true], // same year, later month is newer
+    ['01_2024', '12_2020', true], // the string-comparison trap: Jan 2024 beats Dec 2020
+    ['12_2020', '01_2024', false],
+    ['11_2023', '12_2020', true]
+  ])('%s newer than %s → %s', (a, b, aNewer) => {
+    expect(clinvarVersionKey(a) > clinvarVersionKey(b)).toBe(aNewer)
+  })
+
+  test('unrecognized versions sort to the bottom', () => {
+    expect(clinvarVersionKey('clinvar_2025')).toBe(-1)
+    expect(clinvarVersionKey('01_2000') > clinvarVersionKey('garbage')).toBe(true)
+  })
+})
+
+describe('selectClinvar — the release fallback', () => {
+  test('with no version pinned, returns the newest release (not the string-max)', () => {
+    // Old string comparison picked 12_2020 ('1' > '0'); the parsed key must pick 01_2024.
+    const annotations = [
+      clinvar({clinvarAlleleId: 'x', clinicalSignificance: 'Benign', dbVersion: '12_2020'}),
+      clinvar({clinvarAlleleId: 'x', clinicalSignificance: 'Pathogenic', dbVersion: '01_2024'})
+    ]
+    expect(selectClinvar(annotations)?.dbVersion).toBe('01_2024')
+    expect(selectClinvar(annotations)?.clinicalSignificance).toBe('Pathogenic')
+  })
+
+  test('with a version pinned, returns the exact match or null', () => {
+    const annotations = [clinvar({clinvarAlleleId: 'x', dbVersion: '03_2024'})]
+    expect(selectClinvar(annotations, '03_2024')?.dbVersion).toBe('03_2024')
+    expect(selectClinvar(annotations, '06_2024')).toBeNull()
+  })
+})
+
+describe('isUncertainSignificance', () => {
+  test.each([
+    ['Uncertain significance', true],
+    ['Conflicting classifications of pathogenicity', true],
+    ['Conflicting interpretations of pathogenicity', true],
+    ['Pathogenic', false],
+    ['Likely benign', false]
+  ])('%s → %s', (significance, expected) => {
+    expect(isUncertainSignificance(significance)).toBe(expected)
+  })
+})
diff --git a/src/lib/clinvar-controls.ts b/src/lib/clinvar-controls.ts
index a8b11938..1188337b 100644
--- a/src/lib/clinvar-controls.ts
+++ b/src/lib/clinvar-controls.ts
@@ -1,3 +1,4 @@
+import {hgvsLabelRank} from '@/lib/formats'
 import type {components} from '@/schema/openapi'
 
 export type ClinvarControlOption = components['schemas']['ClinicalControlOptions']
@@ -74,6 +75,8 @@ export const CONFLICTING_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS = [
   'Conflicting classifications of pathogenicity'
 ]
 
+export const UNCERTAIN_SIGNIFICANCE_CLASSIFICATIONS = ['Uncertain significance']
+
 export const CLINVAR_REVIEW_STATUS_STARS: {[status: string]: number} = {
   'no assertion criteria provided': 0,
   'criteria provided, conflicting interpretations': 1,
@@ -99,6 +102,9 @@ export const DEFAULT_MIN_STAR_RATING = 1
 
 export const DEFAULT_CLINVAR_CONTROL_DB = 'ClinVar'
 
+/** Germline-less (`-`) ClinVar records carry no call; renderers show this instead of a bare dash. */
+export const NO_GERMLINE_CLASSIFICATION_LABEL = 'No germline classification'
+
 /** Turn a ClinVar `dbVersion` like `03_2024` into "March 2024"; pass through anything unrecognized. */
 export function formatClinvarVersion(dbVersion: string): string {
   const match = dbVersion.match(/^(\d{2})_(\d{4})$/)
@@ -107,6 +113,18 @@ export function formatClinvarVersion(dbVersion: string): string {
   return new Date(Number(year), Number(month) - 1).toLocaleString('en-US', {month: 'long', year: 'numeric'})
 }
 
+/**
+ * A comparable sort key for a ClinVar `dbVersion` in `MM_YYYY` form, ordering by year then month — the
+ * frontend mirror of the API's `clinvar_version_sort_key`. `MM_YYYY` must NOT be compared as a raw string
+ * (month-first, so `"12_2020" > "01_2024"`); this parses it. Unrecognized versions sort to the bottom (`-1`).
+ */
+export function clinvarVersionKey(dbVersion: string): number {
+  const match = dbVersion.match(/^(\d{2})_(\d{4})$/)
+  if (!match) return -1
+  const [, month, year] = match
+  return Number(year) * 100 + Number(month)
+}
+
 /** Deep link to a ClinVar allele record, or null when the allele id is missing. */
 function clinvarAlleleUrl(alleleId: string | null | undefined): string | null {
   if (!alleleId) return null
@@ -149,11 +167,115 @@ export function clinicalSignificanceColor(significance: string | null | undefine
   return undefined
 }
 
+/**
+ * The ClinVar annotation for an allele at a given release, or null when it has none there. With no
+ * `version`, returns the most recent by `dbVersion` — the fallback used when a release isn't pinned.
+ */
+export function selectClinvar(
+  clinvar: ClinvarAnnotation[] | null | undefined,
+  version?: string | null
+): ClinvarAnnotation | null {
+  if (!clinvar?.length) return null
+  if (version) return clinvar.find((c) => c.dbVersion === version) ?? null
+  return clinvar.reduce((best, c) => (clinvarVersionKey(c.dbVersion) > clinvarVersionKey(best.dbVersion) ? c : best))
+}
+
 /** The most recent ClinVar annotation (by `dbVersion`), or null when there are none. */
 export function latestClinvar(annotations: AlleleAnnotations | null): ClinvarAnnotation | null {
-  const clinvar = annotations?.clinvar
-  if (!clinvar?.length) return null
-  return clinvar.reduce((best, c) => (c.dbVersion > best.dbVersion ? c : best))
+  return selectClinvar(annotations?.clinvar)
+}
+
+/**
+ * One ClinVar record reaching a measurement, resolved at a release. The single walk every ClinVar surface
+ * projects from: the fold reads `clinvar`/`digest`, the popover enumerates the `classified` subset, and the
+ * headline's `-` fallback reads `onAssayed` to prefer the measured allele's own record.
+ */
+export interface MeasurementClinvarRecord {
+  /** VRS digest of the allele this record annotates. */
+  digest: string
+  /** True when the record is on the measured allele itself (digest === assayLevelDigest), not a sibling. */
+  onAssayed: boolean
+  /** Reference-frame HGVS of the annotated allele, for labeling; null when the sidecar has none. */
+  hgvs: string | null
+  /** True for a real classification; false for a `-` germline-less (somatic/oncogenicity-only) placeholder. */
+  classified: boolean
+  clinvar: ClinvarAnnotation
+}
+
+/** Canonical identity of a ClinVar record: the variation id when present, else the allele id. Dedupes records
+ *  shared across reference frames, keys them in a list, and excludes the one already shown in a headline. */
+export function clinvarRecordId(clinvar: {clinvarVariationId?: string | null; clinvarAlleleId: string}): string {
+  return clinvar.clinvarVariationId ?? clinvar.clinvarAlleleId
+}
+
+/**
+ * Resolve the ClinVar records reaching one measurement at `version` — the single walk over the annotations
+ * map that the fold, the underlying-record popover, and the `-` headline fallback all project from, so no
+ * surface re-walks it. One record per annotated allele digest (unclassified `-` records included, tagged);
+ * downstream projections filter/fold as they need.
+ */
+export function resolveClinvarRecords(
+  annotations: Record<string, {clinvar?: ClinvarAnnotation[] | null}> | null | undefined,
+  alleles: Record<string, {hgvs?: string | null}> | null | undefined,
+  assayLevelDigest: string | null | undefined,
+  version?: string | null
+): MeasurementClinvarRecord[] {
+  if (!annotations) return []
+  const records: MeasurementClinvarRecord[] = []
+  for (const [digest, ann] of Object.entries(annotations)) {
+    const clinvar = selectClinvar(ann.clinvar, version)
+    if (!clinvar) continue
+    records.push({
+      digest,
+      onAssayed: digest === assayLevelDigest,
+      hgvs: alleles?.[digest]?.hgvs ?? null,
+      classified: isClassifiedSignificance(clinvar.clinicalSignificance),
+      clinvar
+    })
+  }
+  return records
+}
+
+/**
+ * The distinct *underlying* records for the popover, projected from a resolved walk — the records on sibling
+ * alleles the headline folded over. Excludes the measured allele's own record (`onAssayed`): that is the
+ * primary, already shown as the headline, not "underlying" — so a lone assayed record yields no popover, and
+ * a protein-level allele's projected headline still lists the nucleotide sibling it was drawn from.
+ *
+ * Germline-less `-` submissions are kept (a record that exists is worth linking to; only the control fold
+ * drops `-`). Dedupes by ClinVar record id across the DNA/protein frames that share one record (preferring a
+ * coding HGVS for the label), and sorts directional calls (P/LP, B/LB) ahead of VUS and `-`, then by stars.
+ */
+export function enumerateUnderlyingClinvar(records: MeasurementClinvarRecord[]): MeasurementClinvarRecord[] {
+  const byRecord = new Map<string, MeasurementClinvarRecord>()
+  for (const rec of records) {
+    if (rec.onAssayed) continue
+    const key = clinvarRecordId(rec.clinvar)
+    const existing = byRecord.get(key)
+    if (!existing) byRecord.set(key, {...rec})
+    else if (hgvsLabelRank(rec.hgvs) > hgvsLabelRank(existing.hgvs)) existing.hgvs = rec.hgvs
+  }
+  const isDirectional = (significance: string) =>
+    PATHOGENIC_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS.includes(significance) ||
+    BENIGN_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS.includes(significance)
+  return [...byRecord.values()].sort((a, b) => {
+    const dirDelta =
+      Number(isDirectional(b.clinvar.clinicalSignificance)) - Number(isDirectional(a.clinvar.clinicalSignificance))
+    if (dirDelta !== 0) return dirDelta
+    return (
+      (CLINVAR_REVIEW_STATUS_STARS[b.clinvar.clinicalReviewStatus] ?? 0) -
+      (CLINVAR_REVIEW_STATUS_STARS[a.clinvar.clinicalReviewStatus] ?? 0)
+    )
+  })
+}
+
+/**
+ * The label to render for a ClinVar `clinicalSignificance` — the classification itself, or, for a `-`
+ * germline-less (somatic/oncogenicity-only) placeholder, {@link NO_GERMLINE_CLASSIFICATION_LABEL} rather
+ * than a bare dash that reads as "no record". The single wording every ClinVar renderer shares.
+ */
+export function formatClinicalSignificance(significance: string | null | undefined): string {
+  return isClassifiedSignificance(significance) ? significance! : NO_GERMLINE_CLASSIFICATION_LABEL
 }
 
 /**
@@ -168,6 +290,14 @@ export function isClassifiedSignificance(significance: string | null | undefined
   return !!s && !/^-+$/.test(s)
 }
 
+/** Whether a significance is an uncertain call — a plain VUS or a ClinVar-*Conflicting* aggregate value. */
+export function isUncertainSignificance(significance: string): boolean {
+  return (
+    UNCERTAIN_SIGNIFICANCE_CLASSIFICATIONS.includes(significance) ||
+    CONFLICTING_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS.includes(significance)
+  )
+}
+
 /**
  * Returns an array of ClinVar clinical significance classifications,
  * appending a "Conflicting" classification with a description that
diff --git a/src/lib/notables.test.ts b/src/lib/notables.test.ts
index de669172..7f4dd57b 100644
--- a/src/lib/notables.test.ts
+++ b/src/lib/notables.test.ts
@@ -13,13 +13,16 @@ import type {DisplayVariant} from '@/lib/variants'
 function v(
   urn: string,
   score: number | null,
-  extras: {consequence?: string | null; clnsig?: string; stars?: keyof typeof STARS} = {}
+  extras: {consequence?: string | null; clnsig?: string; stars?: keyof typeof STARS; discordance?: string} = {}
 ): DisplayVariant {
   const variant = {variantUrn: urn, score, consequence: extras.consequence ?? null} as DisplayVariant
   if (extras.clnsig) {
     variant.control = {
       clinicalSignificance: extras.clnsig,
-      clinicalReviewStatus: extras.stars ?? '1-star'
+      clinicalReviewStatus: extras.stars ?? '1-star',
+      // Notables only headline clean/concordant controls; default to a clean call so the star/class logic
+      // is exercised, and let a test opt into 'soft'/'hard' to assert exclusion.
+      discordance: extras.discordance ?? 'none'
     } as DisplayVariant['control']
   }
   return variant
@@ -34,9 +37,11 @@ const STARS = {
 
 // Rewrite the factory's star shorthand into the real review-status strings.
 function withStars(variant: DisplayVariant): DisplayVariant {
-  const shorthand = variant.control?.clinicalReviewStatus as keyof typeof STARS | undefined
+  const control = variant.control
+  if (!control || control.discordance === 'hard') return variant
+  const shorthand = control.clinicalReviewStatus as keyof typeof STARS | undefined
   if (shorthand && STARS[shorthand]) {
-    ;(variant.control as {clinicalReviewStatus: string}).clinicalReviewStatus = STARS[shorthand]
+    ;(control as {clinicalReviewStatus: string}).clinicalReviewStatus = STARS[shorthand]
   }
   return variant
 }
@@ -88,6 +93,25 @@ describe('clinicalExtremesPerClass', () => {
     expect(result.map((r) => r.variantUrn)).toEqual(['b-ok'])
   })
 
+  it('excludes soft-conflict controls — a directional lean beside an uncertain record is not definitive', () => {
+    const variants = [
+      // Both carry a directional representative at a passing star, but the soft one is a soft conflict and
+      // must not headline; only the clean pathogenic exemplar survives (single-class fallback).
+      v('p-soft', -3, {clnsig: 'Pathogenic', stars: '2-star', discordance: 'soft'}),
+      v('p-clean', -1, {clnsig: 'Pathogenic', stars: '2-star', discordance: 'none'})
+    ].map(withStars)
+    expect(clinicalExtremesPerClass(variants, 1).map((r) => r.variantUrn)).toEqual(['p-clean'])
+  })
+
+  it('includes concordant controls — a same-direction agreement is still definitive', () => {
+    const variants = [
+      v('p-concordant', -4, {clnsig: 'Pathogenic', stars: '2-star', discordance: 'concordant'}),
+      v('b-ok', 3, {clnsig: 'Benign', stars: '1-star'})
+    ].map(withStars)
+    // Both classes present and usable → one exemplar each, pathogenic-then-benign.
+    expect(clinicalExtremesPerClass(variants, 1).map((r) => r.variantUrn)).toEqual(['p-concordant', 'b-ok'])
+  })
+
   it('returns nothing when no definitive controls clear the star gate', () => {
     const variants = [v('vus', 1, {clnsig: 'Uncertain significance', stars: '2-star'}), v('plain', 2)].map(withStars)
     expect(clinicalExtremesPerClass(variants)).toEqual([])
diff --git a/src/lib/notables.ts b/src/lib/notables.ts
index d83d9829..e314cf1c 100644
--- a/src/lib/notables.ts
+++ b/src/lib/notables.ts
@@ -1,4 +1,5 @@
 /**
+ * @fileoverview
  * Notable-variant samplers for the score-set variant search's empty state.
  *
  * When the search box is empty the dropdown offers a few "interesting" variants to jump to instead of a
@@ -18,6 +19,7 @@ import {
   DEFAULT_MIN_STAR_RATING,
   PATHOGENIC_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS
 } from '@/lib/clinvar-controls'
+import type {UsableControlPlacement} from '@/lib/clinvar-control-placement'
 import {consequenceBucket, EFFECT_BUCKETS} from '@/lib/consequences'
 import type {DisplayVariant} from '@/lib/variants'
 
@@ -26,9 +28,19 @@ function scored(variants: DisplayVariant[]): DisplayVariant[] {
   return variants.filter((v) => typeof v.score === 'number')
 }
 
+/**
+ * A control clean enough to headline a notables row: an unambiguous or concordant call. Soft conflicts (a
+ * directional lean beside an uncertain/Conflicting record) and hard discordance are excluded. Notables should
+ * be "definitive" exemplars, so we don't front a call we are hedging.
+ */
+function isDefinitiveControl(control: DisplayVariant['control']): control is UsableControlPlacement {
+  return control != null && (control.discordance === 'none' || control.discordance === 'concordant')
+}
+
 /** Star rating of a control's review status; -1 when the status is absent/unknown (never passes a ≥ gate). */
 function controlStars(variant: DisplayVariant): number {
-  const status = variant.control?.[DEFAULT_CLNREVSTAT_FIELD]
+  const control = variant.control
+  const status = isDefinitiveControl(control) ? control[DEFAULT_CLNREVSTAT_FIELD] : undefined
   return status != null ? (CLINVAR_REVIEW_STATUS_STARS[status] ?? -1) : -1
 }
 
@@ -46,11 +58,10 @@ export function clinicalExtremesPerClass(
   minStar: number = DEFAULT_MIN_STAR_RATING
 ): DisplayVariant[] {
   const definitive = (classes: string[]) =>
-    scored(variants).filter(
-      (v) =>
-        // Skip hard-discordant variants: they carry ClinVar data but aren't usable controls.
-        !v.control?.excluded && classes.includes(v.control?.[DEFAULT_CLNSIG_FIELD] ?? '') && controlStars(v) >= minStar
-    )
+    scored(variants).filter((v) => {
+      if (!isDefinitiveControl(v.control)) return false
+      return classes.includes(v.control[DEFAULT_CLNSIG_FIELD]) && controlStars(v) >= minStar
+    })
   const pathogenic = definitive(PATHOGENIC_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS)
   const benign = definitive(BENIGN_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS)
   if (!pathogenic.length && !benign.length) return []

From 1b5676e32a0b3b080a97e2a82b7a894629e9115b Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 16 Jul 2026 15:02:02 -0700
Subject: [PATCH 38/84] feat(score-set-histogram): bin clinical controls via
 resolveControlSeries

Drive the clinical control series off the new resolveControlSeries fold
so each control lands in exactly one of the pathogenic, benign,
uncertain, and conflicting series.

- Add a soft-conflicts toggle: on, a directional lean beside an
  uncertain or conflicting record folds into its directional series and
  the uncertain series are hidden; off, soft conflicts drop and
  uncertain and conflicting records show as their own series
- Consolidate the clinical-control state (database, version, options,
  refreshed, associated) into a single clinical object
- Add a projected-control legend note
---
 .../score-set/ScoreSetHistogram.vue           | 542 ++++++++----------
 1 file changed, 238 insertions(+), 304 deletions(-)

diff --git a/src/components/score-set/ScoreSetHistogram.vue b/src/components/score-set/ScoreSetHistogram.vue
index d4dcae31..78b67b39 100644
--- a/src/components/score-set/ScoreSetHistogram.vue
+++ b/src/components/score-set/ScoreSetHistogram.vue
@@ -47,26 +47,26 @@
   <div v-if="showControls" class="mavedb-histogram-custom-controls">
     <fieldset class="mavedb-histogram-controls-panel">
       <legend>Clinical Series Options</legend>
-      <div v-if="showClinicalControlOptions" class="mavedb-histogram-control">
+      <div v-if="clinical.showOptions" class="mavedb-histogram-control">
         <label class="mavedb-histogram-control-label" for="mavedb-histogram-db-select"
           >Clinical control database:
         </label>
         <PSelect
-          v-model="controlDb"
-          :disabled="!refreshedClinicalControls"
+          v-model="clinical.controlDb"
+          :disabled="!clinical.refreshed"
           input-id="mavedb-histogram-db-select"
           option-label="dbName"
-          :options="clinicalControlOptions"
+          :options="clinical.options"
           style="align-items: center; height: 1.5rem"
         />
         <label class="mavedb-histogram-control-label" for="mavedb-histogram-version-select"
           >Clinical control version:
         </label>
         <PSelect
-          v-model="controlVersion"
-          :disabled="!refreshedClinicalControls"
+          v-model="clinical.controlVersion"
+          :disabled="!clinical.refreshed"
           input-id="mavedb-histogram-version-select"
-          :options="controlDb?.availableVersions"
+          :options="clinical.controlDb?.availableVersions"
           style="align-items: center; height: 1.5rem"
         />
       </div>
@@ -76,7 +76,7 @@
         </label>
         <Rating
           v-model="customMinStarRating"
-          :disabled="!refreshedClinicalControls"
+          :disabled="!clinical.refreshed"
           input-id="mavedb-histogram-star-select"
           :stars="4"
           style="display: inline"
@@ -88,7 +88,7 @@
           <div v-for="typeOption of variantTypeOptions" :key="typeOption.name" class="flex gap-1 align-items-center">
             <Checkbox
               v-model="customSelectedControlVariantTypeFilters"
-              :disabled="!refreshedClinicalControls"
+              :disabled="!clinical.refreshed"
               :name="scopedId('variant-type-inputs')"
               :value="typeOption.name"
             />
@@ -96,6 +96,23 @@
           </div>
         </div>
       </div>
+      <div class="mavedb-histogram-control">
+        <div class="flex gap-1 align-items-center">
+          <Checkbox
+            v-model="customSoftConflictsEnabled"
+            binary
+            :disabled="!clinical.refreshed"
+            input-id="mavedb-histogram-soft-conflicts"
+          />
+          <label class="mavedb-histogram-control-label" for="mavedb-histogram-soft-conflicts">
+            Fold soft conflicts into their directional call
+          </label>
+        </div>
+        <span class="block text-xs italic text-text-muted">
+          A directional call with a related uncertain or conflicting record is shown in its directional series. Turn off
+          to view uncertain and conflicting records as their own series.
+        </span>
+      </div>
       <div class="mavedb-histogram-control">
         <span class="mavedb-histogram-control-label">Include variants with classification: </span>
         <div class="flex flex-wrap gap-3">
@@ -106,7 +123,9 @@
           >
             <Checkbox
               v-model="customSelectedClinicalSignificanceClassifications"
-              :disabled="!refreshedClinicalControls"
+              :disabled="
+                !clinical.refreshed || (customSoftConflictsEnabled && isUncertainSignificance(classification.name))
+              "
               :name="scopedId('clinical-significance-inputs')"
               :value="classification.name"
             />
@@ -123,7 +142,7 @@
           <div v-for="typeOption of variantTypeOptions" :key="typeOption.name" class="flex gap-1 align-items-center">
             <Checkbox
               v-model="customSelectedVariantTypeFilters"
-              :disabled="!refreshedClinicalControls"
+              :disabled="!clinical.refreshed"
               :name="scopedId('variant-type-inputs')"
               :value="typeOption.name"
             />
@@ -133,12 +152,9 @@
       </div>
     </fieldset>
   </div>
-  <div
-    v-if="clinicalControlsEnabled && (!refreshedClinicalControls || !associatedClinicalControls)"
-    style="font-size: small"
-  >
+  <div v-if="clinvarControlsEnabled && (!clinical.refreshed || !clinical.associated)" style="font-size: small">
     <ProgressSpinner style="height: 24px; width: 24px" />
-    Loading clinical control options in the background. Additional histogram views will be available once loaded.
+    Loading clinvar control options in the background. Additional histogram views will be available once loaded.
   </div>
   <div v-if="isCalibrationClassViewActive && isLoadingActiveCalibrationVariants" style="font-size: small">
     <ProgressSpinner style="height: 24px; width: 24px" />
@@ -146,13 +162,17 @@
   </div>
   <div ref="histogramContainer" class="mavedb-histogram-container" />
   <span
-    v-if="vizOptions[activeViz]?.clinicalControlLegendNoteEnabled && refreshedClinicalControls"
+    v-if="vizOptions[activeViz]?.clinvarControlLegendNoteEnabled && clinical.refreshed"
     class="mt-1 block text-center text-xs italic leading-tight"
   >
     Note: The ClinVar annotations shown above are matched to variants in this score set and may not correspond to the
     control variants used to derive the displayed calibration. For details on which variants were used, refer to the
     sources associated with each calibration.
   </span>
+  <span v-if="hasProjectedControlPlotted" class="mt-1 block text-center text-xs italic leading-tight">
+    Note: Some ClinVar controls shown (marked *) are carried over from a sibling allele that shares the protein
+    consequence — the assayed variant itself has no ClinVar record.
+  </span>
   <span v-if="selectedCalibrationIsClassBased" class="mavedb-class-based-calibration-note">
     *Class-based calibrations may not be visualized as thresholds. To view the distribution of variants within each
     class, select the
@@ -188,20 +208,24 @@ import useScopedId from '@/composables/scoped-id'
 import config from '@/config'
 import {saveChartAsSvg, saveChartAsPng} from '@/lib/chart-export'
 import {
-  BENIGN_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS,
   CLINVAR_REVIEW_STATUS_STARS,
   CONFLICTING_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS,
   DEFAULT_CLNREVSTAT_FIELD,
   DEFAULT_CLNSIG_FIELD,
-  DEFAULT_CLINICAL_CONTROL_DB,
   DEFAULT_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS,
   DEFAULT_MIN_STAR_RATING,
-  PATHOGENIC_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS,
+  UNCERTAIN_SIGNIFICANCE_CLASSIFICATIONS,
   clinvarClinicalSignificanceClassifications,
   clinvarConflictingSignificanceClassificationForVersion,
-  conflictingClinicalSignificanceSeriesLabelForVersion
-} from '@/lib/clinical-controls'
-import type {ClinicalControl, ClinicalControlOption} from '@/lib/clinical-controls'
+  conflictingClinicalSignificanceSeriesLabelForVersion,
+  isUncertainSignificance
+} from '@/lib/clinvar-controls'
+import {
+  resolveControlSeries,
+  type ClinvarControlSeriesKey,
+  type ControlSeriesOptions
+} from '@/lib/clinvar-control-series'
+import type {ClinvarControlsStore} from '@/composables/use-clinvar-controls'
 import makeHistogram, {
   DEFAULT_SERIES_COLOR,
   Histogram,
@@ -213,6 +237,7 @@ import makeHistogram, {
 } from '@/lib/histogram'
 import {getScoreCalibrationVariants} from '@/api/mavedb'
 import {
+  chooseDefaultCalibration,
   prepareCalibrationsForHistogram,
   shaderOverlapsBin,
   functionalClassificationContainsVariant,
@@ -222,6 +247,8 @@ import type {FunctionalClassificationVariant} from '@/lib/calibrations'
 import {
   tooltipBadgeBlock,
   tooltipCountRow,
+  tooltipEmptyLine,
+  tooltipFootnote,
   tooltipKeyValue,
   tooltipLink,
   tooltipNote,
@@ -254,7 +281,7 @@ interface Margins {
 interface VizOption {
   label: string
   view: 'distribution' | 'clinical' | 'effect' | 'custom' | 'calibration-classes'
-  clinicalControlLegendNoteEnabled: boolean
+  clinvarControlLegendNoteEnabled: boolean
 }
 
 export default defineComponent({
@@ -264,8 +291,8 @@ export default defineComponent({
 
   props: {
     coordinates: {
-      type: String as PropType<'raw' | 'mapped'>,
-      default: 'raw'
+      type: String as PropType<'submitted' | 'reference'>,
+      default: 'submitted'
     },
     defaultHistogram: {
       type: String,
@@ -308,6 +335,13 @@ export default defineComponent({
     lockSelection: {
       type: Boolean,
       default: false
+    },
+    // Shared clinical-control state (fetch + db/version selection + variant.control associations), owned by
+    // the parent via the `useClinvarControls`. Guarantees that the histogram and other components agree on
+    // the same control version and variant associations.
+    clinical: {
+      type: Object as PropType<ClinvarControlsStore>,
+      required: true
     }
   },
 
@@ -335,20 +369,12 @@ export default defineComponent({
       },
       defaultVizApplied: false,
 
-      clinicalControls: [] as ClinicalControl[],
-      clinicalControlOptions: [] as ClinicalControlOption[],
-      clinicalControlCache: {} as Record<string, Record<string, ClinicalControl[]>>,
-      someVariantsHaveClinicalSignificance: false,
-      clinicalControlsEnabled: true,
-      refreshedClinicalControls: false,
-      associatedClinicalControls: false,
+      clinvarControlsEnabled: true,
 
-      controlDb: null as ClinicalControlOption | null,
-      controlVersion: null as string | null,
-
-      clinicalSignificanceClassificationOptions: clinvarClinicalSignificanceClassifications(null),
       variantTypeOptions: EFFECT_TYPE_FILTER_OPTIONS,
       customMinStarRating: DEFAULT_MIN_STAR_RATING,
+
+      customSoftConflictsEnabled: true,
       customSelectedClinicalSignificanceClassifications: DEFAULT_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS,
       customSelectedVariantTypeFilters: [] as EffectBucketName[],
       customSelectedControlVariantTypeFilters: DEFAULT_EFFECT_TYPE_FILTERS.concat(
@@ -361,8 +387,13 @@ export default defineComponent({
   },
 
   computed: {
+    // The ClinVar significance labels track the selected control version (the "Conflicting" wording
+    // changed in 2025). Was previously a data field reassigned from the controlDbAndVersion watcher.
+    clinicalSignificanceClassificationOptions() {
+      return clinvarClinicalSignificanceClassifications(this.clinical.controlVersion)
+    },
+    // Worth offering as soon as some variant carries a VEP consequence (anything but 'No consequence').
     proteinEffectOptionsAvailable: function () {
-      // Worth offering as soon as some variant carries a VEP consequence (anything but 'No consequence').
       return this.variants.some((v) => consequenceBucket(v.consequence) !== 'No consequence')
     },
     selectedCalibrationIsClassBased: function () {
@@ -371,6 +402,14 @@ export default defineComponent({
         this.activeCalibration.value.functionalClassifications?.every((fc) => fc.class != null)
       )
     },
+    // True when a clinical-control view is active and at least one plotted control is a projection from a
+    // sibling allele. Gates the passthrough note.
+    hasProjectedControlPlotted: function (): boolean {
+      if (!this.vizOptions[this.activeViz]?.clinvarControlLegendNoteEnabled || !this.clinical.refreshed) {
+        return false
+      }
+      return (this.variants as DisplayVariant[]).some((v) => v.control?.projected)
+    },
     selectedCalibrationClassMap: function () {
       if (!this.selectedCalibrationIsClassBased) {
         return null
@@ -410,12 +449,12 @@ export default defineComponent({
       return calibrationUrn != null && this.calibrationClassVariantsLoadingByUrn[calibrationUrn] === true
     },
     series: function () {
-      if (!this.refreshedClinicalControls) {
+      if (!this.clinical.refreshed) {
         return null
       }
 
-      this.assureActiveVizIsAvailable()
-
+      // NOTE: keep this getter pure — clamping `activeViz` (a side effect) lives in the `vizOptions` watcher.
+      // An out-of-range index simply yields `undefined` here, which we treat as "no series".
       if (!this.vizOptions[this.activeViz]) {
         return null
       }
@@ -442,31 +481,31 @@ export default defineComponent({
             }
           }))
         }
-        case 'clinical':
+        case 'clinical': {
+          // The fixed clinical view: all directional classes, no star gate, soft conflicts folded into their
+          // directional lean (there are no uncertain series in the default).
+          const opts = {
+            softConflictsEnabled: true,
+            selectedSignificances: DEFAULT_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS,
+            minStars: Number.NEGATIVE_INFINITY
+          }
           return [
             {
-              classifier: (d: HistogramDatum) =>
-                _.intersection(
-                  PATHOGENIC_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS,
-                  this.selectedClinicalSignificanceClassifications
-                ).includes(d.control?.[DEFAULT_CLNSIG_FIELD]),
+              classifier: (d: HistogramDatum) => this.controlSeries(d, opts) === 'pathogenic',
               options: {
                 color: '#e41a1c',
                 title: 'Pathogenic/Likely Pathogenic'
               }
             },
             {
-              classifier: (d: HistogramDatum) =>
-                _.intersection(
-                  BENIGN_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS,
-                  this.selectedClinicalSignificanceClassifications
-                ).includes(d.control?.[DEFAULT_CLNSIG_FIELD]),
+              classifier: (d: HistogramDatum) => this.controlSeries(d, opts) === 'benign',
               options: {
                 color: '#377eb8',
                 title: 'Benign/Likely Benign'
               }
             }
           ]
+        }
 
         case 'effect': {
           // The dedicated effect view shows every annotated bucket (Start/Stop Loss omitted for
@@ -478,15 +517,15 @@ export default defineComponent({
         }
 
         case 'custom': {
+          const opts = {
+            softConflictsEnabled: this.customSoftConflictsEnabled,
+            selectedSignificances: this.customSelectedClinicalSignificanceClassifications,
+            minStars: this.customMinStarRating
+          }
           const series = [
             {
               classifier: (d: HistogramDatum) =>
-                _.intersection(
-                  PATHOGENIC_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS,
-                  this.selectedClinicalSignificanceClassifications
-                ).includes(d.control?.[DEFAULT_CLNSIG_FIELD]) &&
-                CLINVAR_REVIEW_STATUS_STARS[d.control?.[DEFAULT_CLNREVSTAT_FIELD]] >= this.minStarRating &&
-                this.filterControlVariantByEffect(d),
+                this.controlSeries(d, opts) === 'pathogenic' && this.filterControlVariantByEffect(d),
               options: {
                 color: '#e41a1c',
                 title: 'Pathogenic/Likely Pathogenic'
@@ -494,12 +533,7 @@ export default defineComponent({
             },
             {
               classifier: (d: HistogramDatum) =>
-                _.intersection(
-                  BENIGN_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS,
-                  this.selectedClinicalSignificanceClassifications
-                ).includes(d.control?.[DEFAULT_CLNSIG_FIELD]) &&
-                CLINVAR_REVIEW_STATUS_STARS[d.control?.[DEFAULT_CLNREVSTAT_FIELD]] >= this.minStarRating &&
-                this.filterControlVariantByEffect(d),
+                this.controlSeries(d, opts) === 'benign' && this.filterControlVariantByEffect(d),
               options: {
                 color: '#377eb8',
                 title: 'Benign/Likely Benign'
@@ -507,37 +541,40 @@ export default defineComponent({
             }
           ]
 
-          if (this.selectedClinicalSignificanceClassifications.includes('Uncertain significance')) {
-            series.push({
-              classifier: (d: DisplayVariant) =>
-                d.control?.[DEFAULT_CLNSIG_FIELD] == 'Uncertain significance' &&
-                (CLINVAR_REVIEW_STATUS_STARS[d.control?.[DEFAULT_CLNREVSTAT_FIELD]] ?? -1) >= this.minStarRating &&
-                this.filterControlVariantByEffect(d),
-              options: {
-                color: '#999999',
-                title: 'Uncertain significance'
-              }
-            })
-          }
+          // Uncertain series exist only when the soft-conflict fold is off (the two modes are mutually
+          // exclusive) — and then only for the uncertain classes the user has selected. controlSeries already
+          // returns null for uncertain records while the fold is on, so this gate keeps the empty series hidden.
+          if (!this.customSoftConflictsEnabled) {
+            if (
+              this.customSelectedClinicalSignificanceClassifications.some((c) =>
+                UNCERTAIN_SIGNIFICANCE_CLASSIFICATIONS.includes(c)
+              )
+            ) {
+              series.push({
+                classifier: (d: HistogramDatum) =>
+                  this.controlSeries(d, opts) === 'uncertain' && this.filterControlVariantByEffect(d),
+                options: {
+                  color: '#999999',
+                  title: 'Uncertain significance'
+                }
+              })
+            }
 
-          // Account for both possible conflicting classifications.
-          if (
-            this.selectedClinicalSignificanceClassifications.includes('Conflicting classifications of pathogenicity') ||
-            this.selectedClinicalSignificanceClassifications.includes('Conflicting interpretations of pathogenicity')
-          ) {
-            series.push({
-              classifier: (d: HistogramDatum) =>
-                _.intersection(
-                  CONFLICTING_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS,
-                  this.selectedClinicalSignificanceClassifications
-                ).includes(d.control?.[DEFAULT_CLNSIG_FIELD]) &&
-                CLINVAR_REVIEW_STATUS_STARS[d.control?.[DEFAULT_CLNREVSTAT_FIELD]] >= this.minStarRating &&
-                this.filterControlVariantByEffect(d),
-              options: {
-                color: '#984ea3',
-                title: conflictingClinicalSignificanceSeriesLabelForVersion(this.controlVersion)
-              }
-            })
+            // Account for both possible conflicting classifications.
+            if (
+              this.customSelectedClinicalSignificanceClassifications.some((c) =>
+                CONFLICTING_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS.includes(c)
+              )
+            ) {
+              series.push({
+                classifier: (d: HistogramDatum) =>
+                  this.controlSeries(d, opts) === 'conflicting' && this.filterControlVariantByEffect(d),
+                options: {
+                  color: '#984ea3',
+                  title: conflictingClinicalSignificanceSeriesLabelForVersion(this.clinical.controlVersion)
+                }
+              })
+            }
           }
 
           if (this.proteinEffectOptionsAvailable) {
@@ -554,29 +591,28 @@ export default defineComponent({
 
     vizOptions: function () {
       const options: VizOption[] = [
-        {label: 'Overall Distribution', view: 'distribution', clinicalControlLegendNoteEnabled: false}
+        {label: 'Overall Distribution', view: 'distribution', clinvarControlLegendNoteEnabled: false}
       ]
 
-      if (this.someVariantsHaveClinicalSignificance) {
-        options.push({label: 'Clinical View', view: 'clinical', clinicalControlLegendNoteEnabled: true})
+      if (this.clinical.someVariantsHaveClinicalSignificance) {
+        options.push({label: 'Clinical View', view: 'clinical', clinvarControlLegendNoteEnabled: true})
       }
 
       if (this.selectedCalibrationIsClassBased) {
         options.push({
           label: 'Calibration Class View',
           view: 'calibration-classes',
-          clinicalControlLegendNoteEnabled: false
+          clinvarControlLegendNoteEnabled: false
         })
       }
 
-      // crude to be based on clinical significance. may be a better option for viz control
       if (this.proteinEffectOptionsAvailable) {
-        options.push({label: 'Protein Effect View', view: 'effect', clinicalControlLegendNoteEnabled: false})
+        options.push({label: 'Protein Effect View', view: 'effect', clinvarControlLegendNoteEnabled: false})
       }
 
       // custom view should always come last
-      if (this.someVariantsHaveClinicalSignificance) {
-        options.push({label: 'Custom', view: 'custom', clinicalControlLegendNoteEnabled: true})
+      if (this.clinical.someVariantsHaveClinicalSignificance) {
+        options.push({label: 'Custom', view: 'custom', clinvarControlLegendNoteEnabled: true})
       }
       return options
     },
@@ -604,14 +640,6 @@ export default defineComponent({
       }
     },
 
-    showClinicalControlOptions: function () {
-      const hasMultipleDbs = this.clinicalControlOptions.length > 1
-      const hasSingleDbWithMultipleVersions =
-        this.clinicalControlOptions.length == 1 && this.clinicalControlOptions[0].availableVersions.length > 1
-
-      return hasMultipleDbs || hasSingleDbWithMultipleVersions
-    },
-
     activeCalibrationOptions: function () {
       if (!this.scoreCalibrations) return []
 
@@ -686,10 +714,6 @@ export default defineComponent({
       return this.customSelectedVariantTypeFilters
     },
 
-    controlDbAndVersion() {
-      return `${this.controlDb?.dbName}|${this.controlVersion}`
-    },
-
     tooltipHtmlGetter: function () {
       return (
         variant: DisplayVariant | null,
@@ -707,12 +731,9 @@ export default defineComponent({
 
   watch: {
     scoreSet: {
-      handler: async function () {
+      handler: function () {
         this.calibrationClassVariantsByUrn = {}
         this.calibrationClassVariantsLoadingByUrn = {}
-
-        await this.loadClinicalControlOptions()
-        // Changes to clinical control options will trigger loading of clinical controls.
       },
       immediate: true
     },
@@ -787,7 +808,7 @@ export default defineComponent({
         this.customSelectedClinicalSignificanceClassifications =
           this.customSelectedClinicalSignificanceClassifications.map((classification) => {
             if (CONFLICTING_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS.includes(classification)) {
-              return clinvarConflictingSignificanceClassificationForVersion(this.controlVersion).name
+              return clinvarConflictingSignificanceClassificationForVersion(this.clinical.controlVersion).name
             }
             return classification
           })
@@ -798,47 +819,31 @@ export default defineComponent({
         this.renderOrRefreshHistogram()
       }
     },
-    selectedVariantTypeFilters: {
-      handler: function () {
+    customSoftConflictsEnabled: {
+      handler: function (enabled: boolean) {
+        // The two modes are mutually exclusive: folding soft conflicts in hides the uncertain series, so drop
+        // any uncertain significances from the selection.
+        if (enabled) {
+          this.customSelectedClinicalSignificanceClassifications =
+            this.customSelectedClinicalSignificanceClassifications.filter((c) => !this.isUncertainSignificance(c))
+        }
         this.renderOrRefreshHistogram()
       }
     },
-    selectedControlVariantTypeFilters: {
+    selectedVariantTypeFilters: {
       handler: function () {
         this.renderOrRefreshHistogram()
       }
     },
-    clinicalControlOptions: {
-      handler: function () {
-        if (!this.controlDb) {
-          const defaultControlDb = this.clinicalControlOptions.find(
-            (option) => option.dbName == DEFAULT_CLINICAL_CONTROL_DB
-          )
-          this.controlDb = defaultControlDb ? defaultControlDb : this.clinicalControlOptions[0]
-        }
-        if (!this.controlVersion) {
-          this.controlVersion = this.controlDb?.availableVersions[0]
-        }
-        const cache: Record<string, Record<string, ClinicalControl[]>> = {}
-        for (const dbOption of this.clinicalControlOptions) {
-          cache[dbOption.dbName] = {}
-          for (const version of dbOption.availableVersions) {
-            cache[dbOption.dbName][version] = []
-          }
-        }
-        this.clinicalControlCache = cache
-      }
-    },
-    controlDbAndVersion: {
+    selectedControlVariantTypeFilters: {
       handler: function () {
-        this.clinicalSignificanceClassificationOptions = clinvarClinicalSignificanceClassifications(this.controlVersion)
-        this.loadClinicalControls()
+        this.renderOrRefreshHistogram()
       }
     },
-    clinicalControls: {
+    // The store re-associates `variant.control` off the main thread; re-render once it settles so the
+    // clinical series pick up any new annotations.
+    'clinical.associated': {
       handler: function () {
-        this.disassociateClinicalControlsWithVariants()
-        this.associateClinicalControlsWithVariants()
         this.renderOrRefreshHistogram()
       }
     },
@@ -857,6 +862,11 @@ export default defineComponent({
     },
     vizOptions: {
       handler(newOptions: VizOption[]) {
+        // Clamp first: if the available views shrank (e.g. the clinical view disappeared), keep `activeViz`
+        // in range.
+        if (this.activeViz >= newOptions.length) {
+          this.activeViz = 0
+        }
         if (this.defaultVizApplied) return
         const idx = newOptions.findIndex((opt: VizOption) => opt.view === this.defaultHistogram)
         if (idx >= 0) {
@@ -901,9 +911,9 @@ export default defineComponent({
       if (underlyingNt && underlyingNt !== label) {
         identity.push(tooltipNote(underlyingNt))
       }
-      // In the mapped frame an unmapped variant's label is its submitted (target-frame) HGVS; flag it so
-      // the string isn't mistaken for a mapped coordinate.
-      if (this.coordinates == 'mapped' && this.isUnmapped(variant)) {
+      // In the reference frame an unmapped variant's label is its submitted (target-frame) HGVS; flag it
+      // so the string isn't mistaken for a reference coordinate.
+      if (this.coordinates == 'reference' && this.isUnmapped(variant)) {
         identity.push(tooltipNote('Could not be mapped'))
       }
 
@@ -916,7 +926,7 @@ export default defineComponent({
       }
 
       if (variant.clingenAlleleId) {
-        identity.push(tooltipVariantDetailsLink(variant.clingenAlleleId))
+        identity.push(tooltipVariantDetailsLink(variant.clingenAlleleId, variant.variantUrn))
       }
 
       const sections = [tooltipSection(identity)]
@@ -937,7 +947,30 @@ export default defineComponent({
       if (!control) {
         return null
       }
+      // Hard discordance: the DNA variants encoding this change carry both pathogenic and benign
+      // calls, so there is no single call to show and it is excluded from the controls. Say so, rather
+      // than surfacing one side's call as if it were the answer.
+      if (control.discordance === 'hard') {
+        return tooltipSection([
+          tooltipSectionLabel('ClinVar'),
+          tooltipText('Conflicting classifications across DNA variants — excluded from controls')
+        ])
+      }
       const significance = control[DEFAULT_CLNSIG_FIELD]
+      // Soft conflict: the representative directional call stands, but a related record is uncertain/Conflicting.
+      // Flag it beneath the call so the fold isn't silent (differentiating a VUS from ClinVar's own verdict).
+      const softConflictNote =
+        control.discordance === 'soft'
+          ? control.classifications.some((c) =>
+              CONFLICTING_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS.includes(c.significance)
+            )
+            ? tooltipFootnote(
+                'A related variant with the same protein consequence is conflicting — the directional call is shown.'
+              )
+            : tooltipFootnote(
+                'A related variant with the same protein consequence is of uncertain significance — the directional call is shown.'
+              )
+          : null
       const reviewStatus = control[DEFAULT_CLNREVSTAT_FIELD]
       const hasSignificance = Boolean(significance) && significance != 'NA'
       const hasReviewStatus = Boolean(reviewStatus) && reviewStatus != 'NA'
@@ -946,20 +979,33 @@ export default defineComponent({
       }
 
       const description =
-        clinvarClinicalSignificanceClassifications(this.controlVersion).find((c) => c.name == significance)
+        clinvarClinicalSignificanceClassifications(this.clinical.controlVersion).find((c) => c.name == significance)
           ?.description ?? significance
       const numStars = hasReviewStatus ? CLINVAR_REVIEW_STATUS_STARS[reviewStatus] : null
       const stars = numStars != null ? ` ${tooltipReviewStars(numStars)}` : ''
 
+      // A projected placement: the measured allele has no ClinVar record, so this call
+      // is about a related variant at a different level. Say so — otherwise the histogram appears to
+      // contradict the assay-facts card, which shows this variant's own (empty) measured-level ClinVar.
+      const projectedAsterisk = control.projected ? '*' : ''
+      const projectedNote = control.projected
+        ? tooltipFootnote(
+            'For a related variant with the same protein consequence — the measured variant has no ClinVar record.'
+          )
+        : null
+
       return tooltipSection([
         tooltipSectionLabel('ClinVar'),
-        tooltipText(`${description}${stars}`),
+        tooltipText(`${description}${stars}${projectedAsterisk}`),
         hasReviewStatus
           ? tooltipLink(
               `http://www.ncbi.nlm.nih.gov/clinvar/?term=${control.dbIdentifier}[alleleid]`,
               'View in ClinVar'
             )
-          : null
+          : null,
+        tooltipEmptyLine(),
+        softConflictNote,
+        projectedNote
       ])
     },
 
@@ -1072,6 +1118,15 @@ export default defineComponent({
         options: {color: bucket.color, title: bucket.name}
       }))
     },
+    /**
+     * The single clinical-control series a variant belongs to — a thin wrapper over the pure
+     * {@link resolveControlSeries}, reading the placement off `variant.control`.
+     */
+    controlSeries(variant: DisplayVariant, opts: ControlSeriesOptions): ClinvarControlSeriesKey | null {
+      return resolveControlSeries(variant.control, opts)
+    },
+    /** Whether a significance string is an uncertain call — used to gate the mutually-exclusive filters. */
+    isUncertainSignificance,
     filterControlVariantByEffect(variant: DisplayVariant) {
       // Keep a control variant only when its effect bucket is among the selected filters.
       if (!this.proteinEffectOptionsAvailable) {
@@ -1109,9 +1164,19 @@ export default defineComponent({
     },
 
     renderOrRefreshHistogram: function () {
+      // Reactive triggers (now driven by a shared clinical-controls store) can fire before this instance is
+      // mounted — e.g. the second histogram on a page is created after the store has already settled, so its
+      // creation-time watchers run before `mounted()`. Building the chart with an absent container permanently
+      // poisons it: the lib records `svg = null` and every later refresh() no-ops, leaving an empty container.
+      // Short-circuit until the DOM exists; `mounted()` re-invokes this once the ref is available.
+      const container = this.$refs.histogramContainer as HTMLElement | undefined
+      if (!container) {
+        return
+      }
+
       if (!this.histogram) {
         this.histogram = makeHistogram()
-          .render(this.$refs.histogramContainer)
+          .render(container)
           .bottomAxisLabel('Functional Score')
           .leftAxisLabel('Number of Variants')
           .numBins(30)
@@ -1141,8 +1206,8 @@ export default defineComponent({
         .seriesClassifier(seriesClassifier)
         .title('Distribution of Functional Scores')
         .legendNote(
-          this.vizOptions[this.activeViz]?.clinicalControlLegendNoteEnabled && this.refreshedClinicalControls
-            ? `${this.controlDb?.dbName} data from version ${this.controlVersion}`
+          this.vizOptions[this.activeViz]?.clinvarControlLegendNoteEnabled && this.clinical.refreshed
+            ? `${this.clinical.controlDb?.dbName} data from version ${this.clinical.controlVersion}`
             : null
         )
         .shaders(this.histogramShaders)
@@ -1243,112 +1308,6 @@ export default defineComponent({
         }
       }
     },
-    loadClinicalControls: async function () {
-      if (
-        this.controlDb &&
-        this.controlVersion &&
-        this.clinicalControlCache[this.controlDb.dbName]?.[this.controlVersion].length > 0
-      ) {
-        this.clinicalControls = this.clinicalControlCache[this.controlDb.dbName][this.controlVersion]
-        this.refreshedClinicalControls = true
-        return
-      }
-
-      this.refreshedClinicalControls = false
-      let queryString = ''
-      if (this.controlDb) {
-        queryString += `?db=${encodeURIComponent(this.controlDb.dbName)}`
-      }
-      if (this.controlVersion) {
-        queryString += queryString
-          ? `&version=${encodeURIComponent(this.controlVersion)}`
-          : `?version=${encodeURIComponent(this.controlVersion)}`
-      }
-
-      if (this.scoreSet) {
-        try {
-          const response = await axios.get(
-            `${config.apiBaseUrl}/score-sets/${this.scoreSet.urn}/clinical-controls${queryString}`
-          )
-          if (response.data) {
-            this.clinicalControls = response.data
-
-            if (this.controlDb && this.controlVersion) {
-              this.clinicalControlCache[this.controlDb.dbName][this.controlVersion] = response.data
-            }
-          }
-        } catch {
-          // this.$toast.add({
-          //   severity: 'warn',
-          //   summary:
-          //     'No clinical control variants are associated with variants belonging to this score set. Clinical features are disabled.',
-          //   detail: error.detail,
-          //   life: 3000
-          // })
-          this.associatedClinicalControls = true
-        }
-      }
-      this.refreshedClinicalControls = true
-    },
-
-    loadClinicalControlOptions: async function () {
-      if (this.scoreSet) {
-        try {
-          const response = await axios.get(
-            `${config.apiBaseUrl}/score-sets/${this.scoreSet.urn}/clinical-controls/options`
-          )
-          if (response.status == 200) {
-            this.clinicalControlOptions = response.data
-          }
-        } catch {
-          // this.$toast.add({
-          //   severity: 'warn',
-          //   summary:
-          //     'No clinical control variants are associated with variants belonging to this score set. Clinical features are disabled.',
-          //   detail: error.detail,
-          //   life: 3000
-          // })
-          // We still want to set the refreshed flag to true so that the loading spinner goes away.
-          this.refreshedClinicalControls = true
-          this.associatedClinicalControls = true
-        }
-      }
-    },
-
-    disassociateClinicalControlsWithVariants: function () {
-      this.associatedClinicalControls = false
-      this.someVariantsHaveClinicalSignificance = false
-
-      for (const variant of this.variants) {
-        variant.control = null
-      }
-    },
-
-    associateClinicalControlsWithVariants: function () {
-      let associatedAnyControlsWithVariants = false
-
-      for (const clinicalControl of this.clinicalControls) {
-        clinicalControl.mappedVariants.forEach((mappedVariant) => {
-          const variant = this.variants.find((variant) => variant.variantUrn === mappedVariant.variantUrn)
-          if (variant) {
-            associatedAnyControlsWithVariants = true
-            variant.control = clinicalControl
-          }
-        })
-      }
-
-      this.associatedClinicalControls = true
-      this.someVariantsHaveClinicalSignificance = associatedAnyControlsWithVariants
-
-      //   if (!this.someVariantsHaveClinicalSignificance) {
-      //     this.$toast.add({
-      //       severity: 'warn',
-      //       summary:
-      //         'No clinical control variants are associated with variants belonging to this score set. Clinical features are disabled.'
-      //     })
-      //   }
-    },
-
     chooseDefaultCalibration: function () {
       if (this.activeCalibration.value) {
         return this.activeCalibration
@@ -1358,54 +1317,29 @@ export default defineComponent({
         return {label: 'None', value: null}
       }
 
+      // Honor an externally-selected calibration when it matches an available option (e.g. the
+      // VariantScreen composable defaults one before this histogram mounts).
       if (this.selectedCalibration) {
         const matchingCalibration = this.activeCalibrationOptions.find(
           (option) => option.value?.urn === this.selectedCalibration
         )
         if (matchingCalibration) {
-          return {
-            ...matchingCalibration
-          }
+          return {...matchingCalibration}
         }
       }
 
-      // Always default to showing the primary calibration if none is selected and one exists.
-      const primaryCalibration = this.activeCalibrationOptions.find((option) => option.value?.primary === true)
-      if (primaryCalibration) {
-        return primaryCalibration
-      }
-
-      // If no primary, prefer investigator provided calibrations
-      const investigatorProvided = this.activeCalibrationOptions.find(
-        (option) => option.value?.investigatorProvided === true
-      )
-      if (investigatorProvided) {
-        return investigatorProvided
-      }
-
-      // Next, prefer any calibration that is not research use only
-      const nonResearchUseOnly = this.activeCalibrationOptions.find(
-        (option) => option.value != null && option.value.researchUseOnly !== true
-      )
-      if (nonResearchUseOnly) {
-        return nonResearchUseOnly
-      }
-
-      // Next, prefer any calibration that has any functional ranges defined
-      const anyWithRanges = this.activeCalibrationOptions.find(
-        (option) => option.value?.functionalClassifications && option.value.functionalClassifications.length > 0
+      // Otherwise fall back to the shared default precedence, applied over the sorted options so ties break
+      // the same way the dropdown orders them.
+      const sortedCalibrations = this.activeCalibrationOptions
+        .map((option) => option.value)
+        .filter((value): value is NonNullable<typeof value> => value != null)
+      const defaultUrn = chooseDefaultCalibration(sortedCalibrations)?.urn ?? null
+      return (
+        this.activeCalibrationOptions.find((option) => option.value?.urn === defaultUrn) || {
+          label: 'None',
+          value: null
+        }
       )
-      if (anyWithRanges) {
-        return anyWithRanges
-      }
-
-      // Next, prefer any calibration at all
-      const anyCalibration = this.activeCalibrationOptions.find((option) => option.value != null)
-      if (anyCalibration) {
-        return anyCalibration
-      }
-
-      return {label: 'None', value: null}
     },
 
     titleCase(s: string) {

From c131d2299f3241ddd9c72d9cd3a7096641873b5b Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 16 Jul 2026 15:06:14 -0700
Subject: [PATCH 39/84] feat(gnomad): add frequency collection lib and variant
 surfaces

- Add collectGnomadFrequencies to gather the distinct gnomAD
  frequencies across a variant's alleles, deduped by variant id with a
  coding-HGVS-preferred label and sorted by descending allele frequency
- Add gnomadVariantUrl (version-matched dataset) and formatFrequency
- Add MvGnomadSummary and VariantGnomadStat to surface these on the
  variant page
---
 src/components/variant/MvGnomadSummary.vue   |  60 +++++++++
 src/components/variant/VariantGnomadStat.vue | 117 ++++++++++++++++++
 src/lib/gnomad.test.ts                       | 121 +++++++++++++++++++
 src/lib/gnomad.ts                            |  60 +++++++++
 4 files changed, 358 insertions(+)
 create mode 100644 src/components/variant/MvGnomadSummary.vue
 create mode 100644 src/components/variant/VariantGnomadStat.vue
 create mode 100644 src/lib/gnomad.test.ts
 create mode 100644 src/lib/gnomad.ts

diff --git a/src/components/variant/MvGnomadSummary.vue b/src/components/variant/MvGnomadSummary.vue
new file mode 100644
index 00000000..7a55c024
--- /dev/null
+++ b/src/components/variant/MvGnomadSummary.vue
@@ -0,0 +1,60 @@
+<template>
+  <div class="flex h-full flex-col gap-0.5 leading-snug">
+    <div class="flex flex-wrap items-center gap-x-2 gap-y-0.5">
+      <span class="text-text-primary"
+        >AF <span class="font-mono">{{ formatFrequency(gnomad.alleleFrequency) }}</span></span
+      >
+      <span class="text-sm text-text-muted"
+        >({{ gnomad.alleleCount.toLocaleString() }} / {{ gnomad.alleleNumber.toLocaleString() }})</span
+      >
+    </div>
+    <div class="flex flex-wrap items-center gap-x-2 gap-y-0.5">
+      <span v-if="gnomad.faf95Max !== null" class="text-text-primary"
+        >FAF95 <span class="font-mono text-text-muted">{{ formatFrequency(gnomad.faf95Max) }}</span></span
+      >
+      <span v-else class="text-text-muted">FAF95 —</span>
+    </div>
+    <div class="mt-auto text-[10px] text-text-muted">
+      As of gnomAD version {{ gnomad.dbVersion }}
+      <template v-if="url"
+        >·
+        <a
+          class="inline-flex items-center text-link hover:underline"
+          :href="url"
+          rel="noopener noreferrer"
+          target="_blank"
+        >
+          view in gnomAD
+        </a></template
+      >
+    </div>
+  </div>
+</template>
+
+<script lang="ts">
+import {defineComponent, type PropType} from 'vue'
+
+import {gnomadVariantUrl, formatFrequency} from '@/lib/gnomad'
+import type {components} from '@/schema/openapi'
+
+type GnomadAnnotation = components['schemas']['GnomadAnnotation']
+
+/** Rich display of one gnomAD annotation: allele frequency, the AC/AN behind it, FAF95, and a deep link. */
+export default defineComponent({
+  name: 'MvGnomadSummary',
+
+  props: {
+    gnomad: {type: Object as PropType<GnomadAnnotation>, required: true}
+  },
+
+  computed: {
+    url(): string {
+      return gnomadVariantUrl(this.gnomad)
+    }
+  },
+
+  methods: {
+    formatFrequency
+  }
+})
+</script>
diff --git a/src/components/variant/VariantGnomadStat.vue b/src/components/variant/VariantGnomadStat.vue
new file mode 100644
index 00000000..fbb6c094
--- /dev/null
+++ b/src/components/variant/VariantGnomadStat.vue
@@ -0,0 +1,117 @@
+<template>
+  <div :class="plain ? 'flex h-full flex-col gap-0.5' : 'stat'">
+    <!-- Label defaults to the score-set stat label; callers (e.g. the variant screen) inject their own. -->
+    <slot name="label"><span class="stat-label">gnomAD</span></slot>
+    <!-- The measured allele's own frequency (a nucleotide-level assay): the canonical stat, straight up. -->
+    <MvGnomadSummary v-if="assayGnomad" :gnomad="assayGnomad" />
+    <!-- No gnomAD on the measured allele itself, but sibling variants carry frequencies (protein level assay). 
+         Enumerate them: a max-AF headline + a popover of full allele-level frequencies. -->
+    <template v-else-if="underlyingGnomad.length">
+      <span class="stat-value font-semibold">Up to AF {{ formatFrequency(underlyingGnomadMaxAf) }}</span>
+      <button class="mt-auto text-left text-xs text-link hover:underline" type="button" @click="toggleGnomadPopover">
+        {{ underlyingGnomad.length }}
+        {{ underlyingGnomad.length === 1 ? 'underlying frequency' : 'underlying frequencies' }}
+      </button>
+      <Popover ref="gnomadPopoverRef">
+        <div class="flex max-w-xs flex-col gap-2">
+          <span class="text-xs text-text-muted">{{ underlyingGnomadNote }}</span>
+          <div
+            v-for="item in underlyingGnomad"
+            :key="item.gnomad.dbIdentifier"
+            class="flex flex-col gap-1 border-t border-border-light pt-2 first:border-t-0 first:pt-0"
+          >
+            <span v-if="item.hgvs" class="font-mono text-xs font-semibold text-text-primary">{{ item.hgvs }}</span>
+            <MvGnomadSummary :gnomad="item.gnomad" />
+          </div>
+        </div>
+      </Popover>
+    </template>
+    <span v-else class="stat-value">—</span>
+  </div>
+</template>
+
+<script lang="ts">
+import {defineComponent, type PropType} from 'vue'
+import Popover from 'primevue/popover'
+
+import MvGnomadSummary from '@/components/variant/MvGnomadSummary.vue'
+import {collectGnomadFrequencies, formatFrequency, type UnderlyingGnomad} from '@/lib/gnomad'
+import type {components} from '@/schema/openapi'
+
+type GnomadAnnotation = components['schemas']['GnomadAnnotation']
+type AlleleAnnotations = components['schemas']['AlleleAnnotations']
+type AlleleIdentity = components['schemas']['AlleleIdentity']
+
+/**
+ * The score-set variant panel's gnomAD stat cell. Shows the measured allele's own frequency when it has one;
+ * for a protein-level assay (where gnomAD annotates the *genomic* encoding variants, not the protein allele)
+ * it enumerates the codon siblings' distinct frequencies behind a popover along with a note that it isn't
+ * established which underlies the measurement.
+ */
+export default defineComponent({
+  name: 'VariantGnomadStat',
+
+  components: {Popover, MvGnomadSummary},
+
+  props: {
+    // Drop the score-set `.stat` chrome (bg/padding) so the cell can be embedded on its own (e.g. the
+    // variant screen's evidence panel), where the caller supplies the wrapper and a `#label` slot.
+    plain: {type: Boolean, default: false},
+    // The measured allele's own gnomAD annotation, or null (e.g. a protein-level assay).
+    assayGnomad: {type: Object as PropType<GnomadAnnotation | null>, default: null},
+    // Digest-keyed annotations for the whole record. Source for the encoding-variant enumeration.
+    annotations: {type: Object as PropType<Record<string, AlleleAnnotations>>, default: () => ({})},
+    // Digest-keyed allele identities. Supplies each underlying frequency's HGVS label.
+    alleles: {type: Object as PropType<Record<string, AlleleIdentity>>, default: () => ({})}
+  },
+
+  computed: {
+    underlyingGnomad(): UnderlyingGnomad[] {
+      return collectGnomadFrequencies(this.annotations, this.alleles)
+    },
+    // Sorted highest-first, so the leading entry is the max. This becomes the headline stat in the cell,
+    // with the rest enumerated in the popover.
+    underlyingGnomadMaxAf(): number | null {
+      return this.underlyingGnomad[0]?.gnomad.alleleFrequency ?? null
+    },
+    // Nucleotide variants that *could* encode the measured protein change; only those present in gnomAD
+    // are shown, and it's not established which (if any) actually underly the measurement.
+    underlyingGnomadNote(): string {
+      return this.underlyingGnomad.length === 1
+        ? 'The frequency of any variants in gnomAD which can encode this protein change. This assay does not establish which one underlies the measurement.'
+        : 'Frequencies of any variants in gnomAD which can encode this protein change. This assay does not establish which of them underlie the measurement.'
+    }
+  },
+
+  methods: {
+    toggleGnomadPopover(event: Event) {
+      ;(this.$refs.gnomadPopoverRef as InstanceType<typeof Popover>)?.toggle(event)
+    },
+    formatFrequency
+  }
+})
+</script>
+
+<style scoped>
+/* Matches the panel's facts grid (see VariantDetailPanel). Each cell is a stacked stat on the shared surface. */
+.stat {
+  display: flex;
+  flex-direction: column;
+  gap: 3px;
+  background: var(--color-surface);
+  padding: 10px 14px;
+}
+
+.stat-label {
+  font-size: 10px;
+  font-weight: 700;
+  text-transform: uppercase;
+  letter-spacing: 0.5px;
+  color: var(--color-text-muted);
+}
+
+.stat-value {
+  font-size: 0.875rem;
+  color: var(--color-text-primary);
+}
+</style>
diff --git a/src/lib/gnomad.test.ts b/src/lib/gnomad.test.ts
new file mode 100644
index 00000000..00c0537c
--- /dev/null
+++ b/src/lib/gnomad.test.ts
@@ -0,0 +1,121 @@
+import {describe, expect, test} from 'vitest'
+
+import {collectGnomadFrequencies, formatFrequency, gnomadVariantUrl, type UnderlyingGnomad} from '@/lib/gnomad'
+
+type GnomadAnnotation = UnderlyingGnomad['gnomad']
+
+// A gnomAD annotation with sensible defaults; only the fields a test cares about need overriding.
+function gnomad(overrides: Partial<GnomadAnnotation> & {dbIdentifier: string}): GnomadAnnotation {
+  return {
+    alleleFrequency: 0.001,
+    alleleCount: 10,
+    alleleNumber: 10000,
+    faf95Max: null,
+    dbVersion: '4',
+    ...overrides
+  }
+}
+
+/** The gnomAD variant ids in a collected list, in returned order. */
+const ids = (list: UnderlyingGnomad[]) => list.map((item) => item.gnomad.dbIdentifier)
+
+describe('collectGnomadFrequencies — enumeration of encoding-variant frequencies', () => {
+  test('nullish annotations → empty', () => {
+    expect(collectGnomadFrequencies(null, null)).toEqual([])
+    expect(collectGnomadFrequencies(undefined, undefined)).toEqual([])
+  })
+
+  test('no allele carries gnomAD → empty', () => {
+    const annotations = {'protein-digest': {}, 'other-digest': {gnomad: null}}
+    expect(collectGnomadFrequencies(annotations, {})).toEqual([])
+  })
+
+  test('collects one measurement per annotated allele, pairing the HGVS from the alleles sidecar', () => {
+    const annotations = {
+      'digest-a': {gnomad: gnomad({dbIdentifier: '1-100-A-G', alleleFrequency: 0.002})},
+      'digest-b': {gnomad: gnomad({dbIdentifier: '1-200-C-T', alleleFrequency: 0.001})}
+    }
+    const alleles = {'digest-a': {hgvs: 'c.10A>G'}, 'digest-b': {hgvs: 'c.20C>T'}}
+    const result = collectGnomadFrequencies(annotations, alleles)
+    expect(result).toHaveLength(2)
+    expect(result.find((r) => r.gnomad.dbIdentifier === '1-100-A-G')?.hgvs).toBe('c.10A>G')
+    expect(result.find((r) => r.gnomad.dbIdentifier === '1-200-C-T')?.hgvs).toBe('c.20C>T')
+  })
+
+  test('sorts by descending allele frequency (max first — drives the headline)', () => {
+    const annotations = {
+      low: {gnomad: gnomad({dbIdentifier: 'low', alleleFrequency: 0.0001})},
+      high: {gnomad: gnomad({dbIdentifier: 'high', alleleFrequency: 0.05})},
+      mid: {gnomad: gnomad({dbIdentifier: 'mid', alleleFrequency: 0.01})}
+    }
+    expect(ids(collectGnomadFrequencies(annotations, {}))).toEqual(['high', 'mid', 'low'])
+  })
+
+  test('missing HGVS is tolerated → null label', () => {
+    const annotations = {'digest-a': {gnomad: gnomad({dbIdentifier: '1-100-A-G'})}}
+    expect(collectGnomadFrequencies(annotations, {})[0]?.hgvs).toBeNull()
+    expect(collectGnomadFrequencies(annotations, {'digest-a': {hgvs: null}})[0]?.hgvs).toBeNull()
+  })
+
+  describe('deduplication by gnomAD variant id — the c/g members of one genomic variant share it', () => {
+    test('two digests, same dbIdentifier → one entry', () => {
+      const annotations = {
+        'c-digest': {gnomad: gnomad({dbIdentifier: '1-100-A-G'})},
+        'g-digest': {gnomad: gnomad({dbIdentifier: '1-100-A-G'})}
+      }
+      const alleles = {'c-digest': {hgvs: 'c.10A>G'}, 'g-digest': {hgvs: 'g.100A>G'}}
+      const result = collectGnomadFrequencies(annotations, alleles)
+      expect(result).toHaveLength(1)
+    })
+
+    test('coding HGVS is preferred as the label regardless of iteration order', () => {
+      // g-member seen first, c-member second.
+      const gFirst = {
+        'g-digest': {gnomad: gnomad({dbIdentifier: '1-100-A-G'})},
+        'c-digest': {gnomad: gnomad({dbIdentifier: '1-100-A-G'})}
+      }
+      // c-member seen first, g-member second.
+      const cFirst = {
+        'c-digest': {gnomad: gnomad({dbIdentifier: '1-100-A-G'})},
+        'g-digest': {gnomad: gnomad({dbIdentifier: '1-100-A-G'})}
+      }
+      const alleles = {'c-digest': {hgvs: 'NM_1.2:c.10A>G'}, 'g-digest': {hgvs: 'NC_1.11:g.100A>G'}}
+      expect(collectGnomadFrequencies(gFirst, alleles)[0]?.hgvs).toBe('NM_1.2:c.10A>G')
+      expect(collectGnomadFrequencies(cFirst, alleles)[0]?.hgvs).toBe('NM_1.2:c.10A>G')
+    })
+
+    test('genomic HGVS is preferred over a non-c/g label; a present label beats a missing one', () => {
+      const annotations = {
+        'n-digest': {gnomad: gnomad({dbIdentifier: 'X'})},
+        'g-digest': {gnomad: gnomad({dbIdentifier: 'X'})}
+      }
+      expect(collectGnomadFrequencies(annotations, {'n-digest': {hgvs: 'n.5A>G'}, 'g-digest': {hgvs: 'g.100A>G'}})[0]?.hgvs).toBe('g.100A>G')
+      expect(collectGnomadFrequencies(annotations, {'g-digest': {hgvs: 'g.100A>G'}})[0]?.hgvs).toBe('g.100A>G')
+    })
+  })
+})
+
+describe('formatFrequency', () => {
+  test('nullish → em dash', () => {
+    expect(formatFrequency(null)).toBe('—')
+    expect(formatFrequency(undefined)).toBe('—')
+  })
+
+  test('very rare (< 1e-4) → scientific notation, else 3 significant figures', () => {
+    expect(formatFrequency(0.00001)).toBe('1.00e-5')
+    expect(formatFrequency(0.0123456)).toBe('0.0123')
+    expect(formatFrequency(0)).toBe('0.00e+0')
+  })
+})
+
+describe('gnomadVariantUrl — dataset matches the annotation version', () => {
+  test.each([
+    ['4', 'gnomad_r4'],
+    ['3', 'gnomad_r3'],
+    ['2', 'gnomad_r2_1']
+  ])('major version %s → %s', (dbVersion, dataset) => {
+    const url = gnomadVariantUrl({dbIdentifier: '1-55051215-G-A', dbVersion})
+    expect(url).toContain(`dataset=${dataset}`)
+    expect(url).toContain('/variant/1-55051215-G-A')
+  })
+})
diff --git a/src/lib/gnomad.ts b/src/lib/gnomad.ts
new file mode 100644
index 00000000..ac468375
--- /dev/null
+++ b/src/lib/gnomad.ts
@@ -0,0 +1,60 @@
+/**
+ * @fileoverview
+ * gnomAD frequency annotations and related utilities.
+ *
+ * gnomAD is a population-scale variant frequency database. This module provides a type for the gnomAD
+ * annotation schema, and functions to collect the distinct frequencies across a variant's alleles, format them,
+ * and link to the gnomAD variant page.
+ */
+
+import {hgvsLabelRank} from '@/lib/formats'
+import type {components} from '@/schema/openapi'
+
+type GnomadAnnotation = components['schemas']['GnomadAnnotation']
+
+/** One underlying gnomAD measurement, tagged with the reference-frame HGVS of the allele it annotates. */
+export interface UnderlyingGnomad {
+  hgvs: string | null
+  gnomad: GnomadAnnotation
+}
+
+/**
+ * Collect the distinct gnomAD measurements across a variant record's alleles.
+ *
+ * A protein change is encoded by several genomic variants, each with its own gnomAD frequency. Enumerate
+ * this set of distinct frequencies, deduplicating by gnomAD variant id and preferring a coding HGVS for
+ * the label. Sort by descending allele frequency.
+ */
+export function collectGnomadFrequencies(
+  annotations: Record<string, {gnomad?: GnomadAnnotation | null}> | null | undefined,
+  alleles: Record<string, {hgvs?: string | null}> | null | undefined
+): UnderlyingGnomad[] {
+  if (!annotations) return []
+  const byVariant = new Map<string, UnderlyingGnomad>()
+  for (const [digest, ann] of Object.entries(annotations)) {
+    const gnomad = ann.gnomad
+    if (!gnomad) continue
+
+    const hgvs = alleles?.[digest]?.hgvs ?? null
+    const existing = byVariant.get(gnomad.dbIdentifier)
+    if (!existing) {
+      byVariant.set(gnomad.dbIdentifier, {hgvs, gnomad})
+    } else if (hgvsLabelRank(hgvs) > hgvsLabelRank(existing.hgvs)) {
+      existing.hgvs = hgvs
+    }
+  }
+  return [...byVariant.values()].sort((a, b) => b.gnomad.alleleFrequency - a.gnomad.alleleFrequency)
+}
+
+/** Deep link to a gnomAD variant page, choosing the dataset that matches the annotation's version. */
+export function gnomadVariantUrl(gnomad: {dbIdentifier: string; dbVersion: string}): string {
+  const major = parseInt(gnomad.dbVersion, 10)
+  const dataset = major === 3 ? 'gnomad_r3' : major === 2 ? 'gnomad_r2_1' : 'gnomad_r4'
+  return `https://gnomad.broadinstitute.org/variant/${encodeURIComponent(gnomad.dbIdentifier)}?dataset=${dataset}`
+}
+
+/** A frequency (e.g. gnomAD AF): scientific notation for the very rare, else 3 significant figures. */
+export function formatFrequency(value: number | null | undefined): string {
+  if (value == null) return '—'
+  return value < 0.0001 ? value.toExponential(2) : value.toPrecision(3)
+}

From 46d657f8255fb781cd235d6a91cb36539a3de725 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 16 Jul 2026 15:09:24 -0700
Subject: [PATCH 40/84] feat(variant): add ClinVar stat and summary components

- Add VariantClinvarStat, which resolves a measurement's ClinVar
  headline and renders per kind (conflicting, call, presence, none)
  with the underlying sibling records in a popover
- Add MvClinvarSummary to render a single ClinVar record with its
  significance label and link-out
---
 src/components/variant/MvClinvarSummary.vue   |  86 ++++++++++
 src/components/variant/VariantClinvarStat.vue | 155 ++++++++++++++++++
 2 files changed, 241 insertions(+)
 create mode 100644 src/components/variant/MvClinvarSummary.vue
 create mode 100644 src/components/variant/VariantClinvarStat.vue

diff --git a/src/components/variant/MvClinvarSummary.vue b/src/components/variant/MvClinvarSummary.vue
new file mode 100644
index 00000000..c28b1263
--- /dev/null
+++ b/src/components/variant/MvClinvarSummary.vue
@@ -0,0 +1,86 @@
+<template>
+  <div class="flex h-full flex-col gap-0.5 leading-snug">
+    <!-- A germline-less (`-`) record carries no call or review status — name the state; the link-out stays below. -->
+    <span v-if="!classified" class="text-sm italic text-text-muted">{{
+      formatClinicalSignificance(clinvar.clinicalSignificance)
+    }}</span>
+    <template v-else>
+      <div class="flex flex-wrap items-center gap-x-2 gap-y-0.5">
+        <span class="text-text-primary" :style="{color}">{{ clinvar.clinicalSignificance }}</span>
+        <span
+          :aria-label="`${stars} of 4 stars — ${clinvar.clinicalReviewStatus}`"
+          class="inline-flex items-center gap-px"
+          role="img"
+        >
+          <i
+            v-for="n in 4"
+            :key="n"
+            class="pi text-[10px]"
+            :class="n <= stars ? 'pi-star-fill text-amber-400' : 'pi-star text-border'"
+          />
+        </span>
+      </div>
+      <span class="flex text-[10px] text-text-muted">({{ clinvar.clinicalReviewStatus }})</span>
+    </template>
+    <template v-if="showProvenance">
+      <span class="flex mt-auto text-[10px] text-text-muted">
+        <span>As of ClinVar {{ formatClinvarVersion(clinvar.dbVersion) }} ·&nbsp</span>
+        <a
+          v-if="url"
+          class="text-link font-semibold hover:underline"
+          :href="url"
+          rel="noopener noreferrer"
+          target="_blank"
+        >
+          view in ClinVar
+        </a>
+      </span>
+    </template>
+  </div>
+</template>
+
+<script lang="ts">
+import {defineComponent, type PropType} from 'vue'
+
+import {
+  CLINVAR_REVIEW_STATUS_STARS,
+  clinicalSignificanceColor,
+  clinvarVariantUrl,
+  formatClinicalSignificance,
+  formatClinvarVersion,
+  isClassifiedSignificance
+} from '@/lib/clinvar-controls'
+import type {components} from '@/schema/openapi'
+
+type ClinvarAnnotation = components['schemas']['ClinvarAnnotation']
+
+/** Rich display of one ClinVar annotation: significance, gold-star review rating, and a deep link. */
+export default defineComponent({
+  name: 'MvClinvarSummary',
+
+  props: {
+    clinvar: {type: Object as PropType<ClinvarAnnotation>, required: true},
+    showProvenance: {type: Boolean, default: true}
+  },
+
+  computed: {
+    classified(): boolean {
+      return isClassifiedSignificance(this.clinvar.clinicalSignificance)
+    },
+    stars(): number {
+      return CLINVAR_REVIEW_STATUS_STARS[this.clinvar.clinicalReviewStatus] ?? 0
+    },
+    color(): string | undefined {
+      return clinicalSignificanceColor(this.clinvar.clinicalSignificance)
+    },
+    url(): string | null {
+      return clinvarVariantUrl(this.clinvar)
+    }
+  },
+
+  methods: {
+    formatClinvarVersion,
+    formatClinicalSignificance
+  }
+})
+</script>
diff --git a/src/components/variant/VariantClinvarStat.vue b/src/components/variant/VariantClinvarStat.vue
new file mode 100644
index 00000000..a9dc535d
--- /dev/null
+++ b/src/components/variant/VariantClinvarStat.vue
@@ -0,0 +1,155 @@
+<template>
+  <div :class="plain ? 'flex h-full flex-col gap-0.5' : 'stat'">
+    <!-- Label defaults to the score-set stat label; callers (e.g. the variant screen) inject their own. -->
+    <slot name="label"><span class="stat-label">ClinVar</span></slot>
+    <!-- Hard discordance: related variants carry both pathogenic and benign calls — no single call to show. -->
+    <span v-if="headline.kind === 'conflicting'" class="stat-value text-sm font-semibold">
+      Conflicting classifications
+    </span>
+    <!-- The winning placement's canonical call, plus the lib's `note`: a soft conflict keeps its directional
+         lean but flags a co-occurring uncertain record (differentiating a plain VUS from ClinVar's own
+         Conflicting verdict); a concordant call gets a quiet aside. Show the lean rather than hide it. -->
+    <template v-else-if="headline.kind === 'call'">
+      <MvClinvarSummary :clinvar="headline.clinvar" :show-provenance="false" />
+      <span v-if="headline.note === 'soft-conflicting'" class="text-xs italic text-text-muted">
+        ClinVar marks a record with the same protein consequence as conflicting.
+      </span>
+      <span v-else-if="headline.note === 'soft-vus'" class="text-xs italic text-text-muted">
+        ClinVar marks a record with the same protein consequence as uncertain.
+      </span>
+      <span v-else-if="headline.note === 'concordant'" class="text-xs italic text-text-muted">
+        Representative of concordant records with the same protein consequence.
+      </span>
+    </template>
+    <!-- No usable call, but a ClinVar record exists on an allele (a `-`, e.g. a somatic/oncogenicity-only
+         submission with no germline classification). MvClinvarSummary names the state and links out. -->
+    <MvClinvarSummary v-else-if="headline.kind === 'presence'" :clinvar="headline.record.clinvar" />
+    <span v-else class="stat-value">—</span>
+
+    <!-- The records on sibling alleles behind the headline — everything except the measured allele's own
+         record (germline-less `-` included), so a lone assayed record gets no popover. Mirrors gnomAD's. -->
+    <template v-if="underlyingClinvar.length">
+      <button class="mt-auto text-left text-xs text-link hover:underline" type="button" @click="toggleClinvarPopover">
+        {{ underlyingClinvar.length }}
+        {{ underlyingClinvar.length === 1 ? 'underlying record' : 'underlying records' }}
+      </button>
+      <Popover ref="clinvarPopoverRef">
+        <div class="flex max-w-xs flex-col gap-2">
+          <span class="text-xs text-text-muted">{{ underlyingClinvarNote }}</span>
+          <!-- Lean rows: the prioritized call is the headline above, so each underlying record shows only its
+               allele (HGVS), release, and a link out to ClinVar for the full classification. -->
+          <div
+            v-for="item in underlyingClinvar"
+            :key="clinvarRecordId(item.clinvar)"
+            class="flex flex-col gap-0.5 border-t border-border-light pt-2 first:border-t-0 first:pt-0"
+          >
+            <span v-if="item.hgvs" class="font-mono text-xs font-semibold text-text-primary">{{ item.hgvs }}</span>
+            <MvClinvarSummary :clinvar="item.clinvar" />
+          </div>
+        </div>
+      </Popover>
+    </template>
+  </div>
+</template>
+
+<script lang="ts">
+import {defineComponent, type PropType} from 'vue'
+import Popover from 'primevue/popover'
+
+import MvClinvarSummary from '@/components/variant/MvClinvarSummary.vue'
+import {
+  clinvarRecordId,
+  enumerateUnderlyingClinvar,
+  resolveClinvarRecords,
+  type MeasurementClinvarRecord
+} from '@/lib/clinvar-controls'
+import {resolveClinvarHeadline, type ClinvarHeadline} from '@/lib/clinvar-control-placement'
+import type {components} from '@/schema/openapi'
+
+type AlleleAnnotations = components['schemas']['AlleleAnnotations']
+type AlleleIdentity = components['schemas']['AlleleIdentity']
+
+/**
+ * The ClinVar stat cell shared by the score-set variant panel and the variant screen. Runs the
+ * concordant/discordant placement fold over the whole record so it agrees with the histogram:
+ * Prefer the assayed allele's own call wins, then...
+ * If the assayed allele is unannotated, a projected call from a sibling allele (same protein consequence) is used.
+ * If it is unannotated it falls through to a related-level projection sibling.
+ * If those siblings are discordant, note they are in conflict.
+ * If no germline record exists but the variant has a somatic/oncogenicity-only submission, link but note 'No germline classification'.
+ * Beneath the folded headline, a popover lists the sibling-allele records behind it (allele HGVS, release,
+ * link) — every record except the measured allele's own; germline-less `-` included, only the fold drops those.
+ * `clinvarVersion` is passed by the parent so this component resolves the same version as other histogram and stat cells.
+ * `plain` / the `#label` slot let a caller drop the `.stat` chrome and supply its own label.
+ */
+export default defineComponent({
+  name: 'VariantClinvarStat',
+
+  components: {MvClinvarSummary, Popover},
+
+  props: {
+    // Drop the score-set `.stat` chrome (bg/padding) so the cell can be embedded on its own (e.g. the
+    // variant screen's evidence panel), where the caller supplies the wrapper and a `#label` slot.
+    plain: {type: Boolean, default: false},
+    // Digest-keyed annotations for the whole record. Supply all ClinVar assertions so the placement can be reduced over the whole record.
+    annotations: {type: Object as PropType<Record<string, AlleleAnnotations>>, default: () => ({})},
+    // Digest-keyed allele identities. These supply a projected call's reference-frame HGVS.
+    alleles: {type: Object as PropType<Record<string, AlleleIdentity>>, default: () => ({})},
+    // The measured allele's digest.
+    assayLevelDigest: {type: String as PropType<string | null>, default: null},
+    // The ClinVar release to reduce over (raw `MM_YYYY`), so this cell agrees with all parents.
+    // `null` (store not ready / no controls) → fall back to the latest release per allele.
+    clinvarVersion: {type: String as PropType<string | null>, default: null}
+  },
+
+  computed: {
+    // The ClinVar records reaching this measurement at the selected release — walked once, projected below.
+    records(): MeasurementClinvarRecord[] {
+      return resolveClinvarRecords(this.annotations, this.alleles, this.assayLevelDigest, this.clinvarVersion)
+    },
+    // What the single headline shows: the fold's call, a `-` presence fallback, "conflicting", or nothing.
+    headline(): ClinvarHeadline {
+      return resolveClinvarHeadline(this.records, this.assayLevelDigest)
+    },
+    // The records on sibling alleles behind the headline — enumerateUnderlyingClinvar excludes the measured
+    // allele's own record (the primary), so a lone assayed record gets no popover.
+    underlyingClinvar(): MeasurementClinvarRecord[] {
+      return enumerateUnderlyingClinvar(this.records)
+    },
+    underlyingClinvarNote(): string {
+      return "ClinVar records for variants with this allele's protein consequence. Open each in ClinVar to view its full classification."
+    }
+  },
+
+  methods: {
+    clinvarRecordId,
+    toggleClinvarPopover(event: Event) {
+      ;(this.$refs.clinvarPopoverRef as InstanceType<typeof Popover>)?.toggle(event)
+    }
+  }
+})
+</script>
+
+<style scoped>
+/* Matches the panel's facts grid — each cell a stacked stat on the shared surface. */
+.stat {
+  display: flex;
+  flex-direction: column;
+  gap: 3px;
+  background: var(--color-surface);
+  padding: 10px 14px;
+}
+
+.stat-label {
+  font-size: 10px;
+  font-weight: 700;
+  text-transform: uppercase;
+  letter-spacing: 0.5px;
+  color: var(--color-text-muted);
+}
+
+.stat-value {
+  font-size: 0.875rem;
+  color: var(--color-text-primary);
+}
+</style>

From 5ec170c6fe7d595f0d5426924c13146d49a866c8 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 16 Jul 2026 15:10:12 -0700
Subject: [PATCH 41/84] feat(allele-grouping): add confidence badge axis

- Add ConfidenceBadge, the ALLELE_CONFIDENCE map (Measured, Resolved,
  Candidate), and confidenceBadge as the single source for the
  confidence badges and the Key drawer's confidence section
- Add a fileoverview header and condense the interface JSDoc to terse
  comments
---
 src/lib/allele-grouping.test.ts | 14 +++++++-
 src/lib/allele-grouping.ts      | 63 ++++++++++++++++++++++++---------
 2 files changed, 60 insertions(+), 17 deletions(-)

diff --git a/src/lib/allele-grouping.test.ts b/src/lib/allele-grouping.test.ts
index e4e89b9d..a4b27128 100644
--- a/src/lib/allele-grouping.test.ts
+++ b/src/lib/allele-grouping.test.ts
@@ -1,6 +1,6 @@
 import {describe, expect, it} from 'vitest'
 
-import {groupAlleles, type GroupAllelesInput} from '@/lib/allele-grouping'
+import {ALLELE_CONFIDENCE, confidenceBadge, groupAlleles, type GroupAllelesInput} from '@/lib/allele-grouping'
 import type {components} from '@/schema/openapi'
 
 type AlleleIdentity = components['schemas']['AlleleIdentity']
@@ -128,6 +128,18 @@ describe('groupAlleles — projection pairing + confidence', () => {
     expect(groups[0].measured).toBe(false)
   })
 
+  it('badges measured over derivation, maps projection→Resolved / candidate→Candidate, else null', () => {
+    // `measured` wins even if a derivation is also present (a stray measured sibling still reads "Measured").
+    expect(confidenceBadge({measured: true, derivation: 'projection'})).toBe(ALLELE_CONFIDENCE.measured)
+    expect(confidenceBadge({measured: false, derivation: 'projection'})).toBe(ALLELE_CONFIDENCE.projection)
+    expect(confidenceBadge({measured: false, derivation: 'candidate'})).toBe(ALLELE_CONFIDENCE.candidate)
+    // `authoritative` is only ever surfaced via `measured`; on its own it has no derived badge.
+    expect(confidenceBadge({measured: false, derivation: 'authoritative'})).toBeNull()
+    expect(confidenceBadge({measured: false, derivation: null})).toBeNull()
+    // The user-facing labels are decoupled from the enum keys.
+    expect(ALLELE_CONFIDENCE.projection.label).toBe('Resolved')
+  })
+
   it('surfaces distinct linked CAIDs, excluding the page anchor', () => {
     const groups = run({
       alleles: {
diff --git a/src/lib/allele-grouping.ts b/src/lib/allele-grouping.ts
index 15f6071a..f2663445 100644
--- a/src/lib/allele-grouping.ts
+++ b/src/lib/allele-grouping.ts
@@ -1,3 +1,10 @@
+/**
+ * @fileoverview
+ * Allele grouping: collapse a variant's alleles into one or more groups for display, pairing c↔g projections
+ * and deduplicating their annotations. The groups are the rendered entries in the variant detail's
+ * "alleles" section, and the source of truth for the histogram's per-allele controls.
+ */
+
 import _ from 'lodash'
 
 import type {components} from '@/schema/openapi'
@@ -5,49 +12,73 @@ import type {components} from '@/schema/openapi'
 type AlleleIdentity = components['schemas']['AlleleIdentity']
 type AlleleAnnotations = components['schemas']['AlleleAnnotations']
 
-/** Confidence/provenance axis (orthogonal to Cat-VRS `relation`); strongest first. */
+/** Confidence/provenance axis (orthogonal to Cat-VRS's `relation`); strongest confidence first. */
 export type Derivation = 'authoritative' | 'projection' | 'candidate'
 const DERIVATION_RANK: Record<string, number> = {authoritative: 0, projection: 1, candidate: 2}
 
 // Level display order (genomic → coding → protein) so a group reads bottom-up through the layer stack.
 const LEVEL_ORDER: Record<string, number> = {genomic: 0, cdna: 1, protein: 2}
 
+/** A member of an allele group: a single level's identity, its annotations, and whether it is the page root. */
 export interface AlleleMember extends AlleleIdentity {
   digest: string
   annotations: AlleleAnnotations | null
-  /** This allele is the CAID/PAID the page is anchored on. */
+  // Whether this allele is the CAID/PAID the page is anchored on.
   pageRoot: boolean
 }
 
 /**
  * A group of alleles rendered as one entry. Either a single allele (the protein apex, an unpaired
  * measured allele, or a projection-failed one-member candidate) or a c↔g projection pair collapsed into
- * one — the same change at two levels — with its annotations deduplicated.
+ * one (the same change at two levels).
  */
 export interface AlleleGroup {
   key: string
   members: AlleleMember[]
-  /** Contains the measured (authoritative) allele. */
+  // The measured (authoritative) allele.
   measured: boolean
-  /** Contains the page-anchor allele. */
+  // Whether this group contains the page-anchor allele.
   pageRoot: boolean
-  /** Grouped confidence: the strongest derivation among the members. */
+  // Grouped confidence: the strongest derivation among the members.
   derivation: Derivation | null
-  /**
-   * Whether the members' annotations can render as one block. Missingness is NOT a difference: a field
-   * present on one level and absent on the other coalesces to the present value. Only a genuine
-   * present-vs-present disagreement makes this false (→ render each level separately, with a note).
-   */
+  // Whether the members' annotations can render as one block.
   annotationsMatch: boolean
-  /**
-   * The per-field union of the members' annotations (present-wins). Used to render the single block when
-   * `annotationsMatch` — so a coalesced group shows every field any member has, not just member[0]'s.
-   */
+  // The per-field union of the members' annotations (present-wins).
   coalescedAnnotations: AlleleAnnotations | null
-  /** Distinct linked CAIDs to surface, excluding the page anchor (which is this page). */
+  // Distinct linked CAIDs to surface.
   clingenLinks: string[]
 }
 
+/** A provenance badge + its Key-drawer gloss: how a group's coordinate was established. */
+export interface ConfidenceBadge {
+  label: string
+  class: string
+  definition: string
+}
+
+// Single source for the confidence axis (badges + the Key drawer's "confidence" section). Keyed by
+// outcome, not raw `Derivation`: `measured` (authoritative) reads "Measured"; the two derived states map
+// straight from `derivation`. Insertion order is the drawer's display order.
+export const ALLELE_CONFIDENCE: Record<string, ConfidenceBadge> = {
+  measured: {label: 'Measured', class: 'bg-sage/15 text-sage', definition: 'Directly assayed in this score set.'},
+  projection: {
+    label: 'Resolved',
+    class: 'bg-nucleotide-light text-nucleotide',
+    definition: 'Derived from the measured allele by reverse translation — the same change expressed at another level.'
+  },
+  candidate: {
+    label: 'Candidate',
+    class: 'bg-amber-100 text-amber-700',
+    definition: 'A change that encodes the same protein change as your variant, but is a distinct nucleotide change.'
+  }
+}
+
+/** Confidence badge for a group: `measured` wins, else the derived state; null when neither applies. */
+export function confidenceBadge(group: Pick<AlleleGroup, 'measured' | 'derivation'>): ConfidenceBadge | null {
+  if (group.measured) return ALLELE_CONFIDENCE.measured
+  return group.derivation ? (ALLELE_CONFIDENCE[group.derivation] ?? null) : null
+}
+
 export interface GroupAllelesInput {
   alleles: Record<string, AlleleIdentity>
   annotations: Record<string, AlleleAnnotations>

From 95af0090d2f9c75bd9c43df0999906eac0f7c771 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 16 Jul 2026 15:25:00 -0700
Subject: [PATCH 42/84] feat(variant): restructure variant page around related
 alleles and evidence stats

- Add MvRelatedAlleles to render allele groups with their confidence
  badge and per-group ClinVar and gnomAD evidence
- Wire VariantClinvarStat, VariantGnomadStat, and MvRelatedAlleles into
  the variant screen, grouping alleles via groupAlleles
- Replace the detail panel's inline ClinVar and gnomAD markup with the
  new stat components
- Add a direct/related relationship badge, loading spinner, and score
  set urn to the measurement card, renaming studyTitle to scoreSetTitle
- Source the Key drawer's confidence section from ALLELE_CONFIDENCE
---
 src/components/screens/VariantScreen.vue      | 481 ++++++++++++++----
 src/components/variant/MvMeasurementCard.vue  | 112 ++--
 src/components/variant/MvRelatedAlleles.vue   | 147 ++++++
 src/components/variant/VariantDetailPanel.vue | 151 ++----
 src/components/variant/VariantInfoSection.vue |  19 +-
 .../variant/variant-key-sections.ts           |  18 +-
 6 files changed, 678 insertions(+), 250 deletions(-)
 create mode 100644 src/components/variant/MvRelatedAlleles.vue

diff --git a/src/components/screens/VariantScreen.vue b/src/components/screens/VariantScreen.vue
index d114af1e..951dabc3 100644
--- a/src/components/screens/VariantScreen.vue
+++ b/src/components/screens/VariantScreen.vue
@@ -27,7 +27,7 @@
             {{ lookup.variants.value.length }}
             {{ lookup.variants.value.length === 1 ? 'measurement' : 'measurements' }}
             <template v-if="lookup.uniqueAssayCount.value > 1">
-              across {{ lookup.uniqueAssayCount.value }} assays</template
+              across {{ lookup.uniqueAssayCount.value }} score sets</template
             >
           </p>
         </template>
@@ -35,6 +35,62 @@
     </template>
 
     <div class="mx-auto w-full px-4 tablet:px-6 py-6 tablet:py-8" style="max-width: 1000px">
+      <!-- ── CONTROL ROW (query axes: content valid-time + superseded scope) — always rendered so the
+           as_of / superseded controls stay reachable even when the query returns no measurements ── -->
+      <div
+        class="mave-gradient-bar relative overflow-hidden mb-4 flex flex-col gap-3 rounded-lg border border-border bg-surface px-4 py-3 tablet:flex-row tablet:flex-wrap tablet:items-center tablet:gap-x-5 tablet:gap-y-2 tablet:px-5 tablet:py-2.5"
+      >
+        <div class="flex flex-1 items-center gap-2 text-xs text-text-secondary">
+          <span v-key-term="'as-of'" class="font-semibold uppercase tracking-[0.3px] text-[#aaa]">MaveDB as of</span>
+          <DatePicker
+            v-model="asOfDate"
+            class="min-w-0 flex-1 tablet:w-72 tablet:flex-none"
+            date-format="yy-mm-dd"
+            fluid
+            icon-display="input"
+            :max-date="today"
+            placeholder="Current"
+            show-button-bar
+            show-icon
+            size="small"
+          />
+          <button
+            v-if="asOfDate"
+            class="cursor-pointer border-none bg-transparent text-xs font-semibold text-link hover:underline"
+            type="button"
+            @click="asOfDate = null"
+          >
+            Clear
+          </button>
+        </div>
+        <button
+          class="flex cursor-pointer items-center gap-1.5 rounded-md border px-2.5 py-1 text-xs font-semibold transition-colors tablet:ml-auto"
+          :class="
+            lookup.includeSuperseded.value
+              ? 'border-sage bg-sage text-white'
+              : 'border-border bg-surface text-text-secondary hover:border-sage hover:text-sage'
+          "
+          type="button"
+          @click="lookup.includeSuperseded.value = !lookup.includeSuperseded.value"
+        >
+          <i class="pi text-[11px]" :class="lookup.includeSuperseded.value ? 'pi-check' : 'pi-plus'" />
+          {{ lookup.includeSuperseded.value ? 'Hide superseded variants' : 'Show superseded variants' }}
+        </button>
+        <button
+          class="flex cursor-pointer items-center gap-1.5 rounded-md border px-2.5 py-1 text-xs font-semibold transition-colors"
+          :class="
+            keyDrawer.isOpen.value
+              ? 'border-sage bg-sage text-white'
+              : 'border-border bg-surface text-text-secondary hover:border-sage hover:text-sage'
+          "
+          type="button"
+          @click="keyDrawer.isOpen.value ? keyDrawer.close() : keyDrawer.open()"
+        >
+          <i class="pi pi-key text-[11px]" />
+          Key
+        </button>
+      </div>
+
       <!-- Error state -->
       <MvErrorState v-if="lookup.variantsStatus.value === 'Error'" @retry="lookup.fetchVariants" />
 
@@ -44,8 +100,8 @@
       <!-- Empty state -->
       <MvEmptyState
         v-else-if="lookup.variants.value.length === 0"
-        description="No variants were found for this allele."
-        title="No variants found"
+        :description="emptyStateDescription"
+        title="No measurements found"
       />
 
       <template v-else>
@@ -64,7 +120,7 @@
                 active-border="var(--color-nucleotide-border)"
                 color="var(--color-nucleotide)"
                 :count="lookup.nucleotideCount.value"
-                label="Nucleotide level"
+                label="Nucleotide"
               />
               <MvBadgeToggle
                 v-if="lookup.proteinCount.value > 0"
@@ -73,70 +129,146 @@
                 active-border="var(--color-protein-border)"
                 color="var(--color-protein)"
                 :count="lookup.proteinCount.value"
-                label="Protein level"
-              />
-              <MvBadgeToggle
-                v-if="lookup.associatedNucleotideCount.value > 0"
-                v-model="lookup.showAssociatedNucleotide.value"
-                active-background="var(--color-synonymous-nucleotide-light)"
-                active-border="var(--color-synonymous-nucleotide-border)"
-                color="var(--color-synonymous-nucleotide)"
-                :count="lookup.associatedNucleotideCount.value"
-                label="Synonymous nucleotide"
+                label="Protein"
               />
             </div>
           </div>
+          <!-- Anchor heading: names the frame of reference so the per-card relationship badges
+               ("Your variant" / "Its protein consequence" / "Encodes the protein consequence") read as
+               self-explaining rather than needing a per-badge tooltip. -->
+          <div class="px-4 tablet:px-5 pt-3.5 text-xs-minus text-text-muted">
+            What each result assayed, relative to your variant:
+          </div>
           <!-- Desktop: horizontal scroll strip -->
           <div class="measurement-switcher hidden tablet:flex gap-3 overflow-x-auto px-5 py-4">
             <MvMeasurementCard
-              v-for="variant in lookup.filteredVariants.value"
-              :key="'desktop-' + (variant.content.urn ?? variant.content.id)"
-              :abnormal-odds-path="lookup.getAbnormalOddsPath(variant.content.urn)"
-              :active="lookup.selectedVariantUrn.value === variant.content.urn"
-              :assay-type="lookup.getKeyword(variant.content, 'Phenotypic Assay Method')"
-              :classification="lookup.getVariantClassification(variant.content.urn)"
-              :evidence-code="lookup.getVariantEvidenceCode(variant.content.urn)"
-              :mechanism="lookup.getKeyword(variant.content, 'Molecular Mechanism Assessed')"
-              :model-system="lookup.getKeyword(variant.content, 'Phenotypic Assay Model System')"
-              :normal-odds-path="lookup.getNormalOddsPath(variant.content.urn)"
-              :study-title="variant.content.scoreSet?.title || 'Untitled score set'"
-              :type="variant.type"
-              @select="lookup.selectVariant(variant.content.urn)"
+              v-for="m in lookup.filteredVariants.value"
+              :key="'desktop-' + m.variantUrn"
+              :active="lookup.selectedVariantUrn.value === m.variantUrn"
+              :loading="lookup.selectedVariantUrn.value === m.variantUrn && lookup.selectedLoading.value"
+              :assay-level="m.assayLevel"
+              :assay-type="lookup.getKeyword(m.scoreSetUrn, 'Phenotypic Assay Method')"
+              :mechanism="lookup.getKeyword(m.scoreSetUrn, 'Molecular Mechanism Assessed')"
+              :model-system="lookup.getKeyword(m.scoreSetUrn, 'Phenotypic Assay Model System')"
+              :preferred-classification="m.preferredClassification ?? null"
+              :relationship="m.relationship"
+              :score="m.score ?? null"
+              :score-set-title="m.scoreSetTitle || 'Untitled score set'"
+              :score-set-urn="m.scoreSetUrn"
+              @select="lookup.selectVariant(m.variantUrn)"
             />
           </div>
           <!-- Mobile: dropdown selector -->
-          <div class="tablet:hidden px-4 py-3">
+          <div class="tablet:hidden flex items-center gap-2 px-4 py-3">
             <PSelect
-              class="w-full"
+              class="min-w-0 flex-1"
               :model-value="lookup.selectedVariantUrn.value"
               option-label="label"
               option-value="urn"
               :options="measurementOptions"
               @update:model-value="lookup.selectVariant($event)"
             />
+            <i
+              v-if="lookup.selectedLoading.value"
+              aria-label="Loading variant details"
+              class="pi pi-spin pi-spinner text-sage"
+            />
+          </div>
+        </div>
+
+        <!-- ── SUPERSESSION BANNER ───────────────────────────── -->
+        <div
+          v-if="lookup.selectedVariantDetail.value && !lookup.selectedVariantDetail.value.isCurrent"
+          class="mt-6 flex items-start gap-2 rounded-lg border border-amber-200 bg-amber-50 px-4 py-3 text-sm text-amber-800"
+        >
+          <i class="pi pi-exclamation-triangle mt-0.5 text-xs" />
+          <div>
+            This measurement is from a superseded version of its score set and may not reflect the current data.
+            <template v-if="lookup.selectedVariantDetail.value.supersededByScoreSet">
+              A newer version of this score set is available at
+              <router-link
+                class="font-semibold underline"
+                :to="{name: 'scoreSet', params: {urn: lookup.selectedVariantDetail.value.supersededByScoreSet}}"
+              >
+                {{ lookup.selectedVariantDetail.value.supersededByScoreSet }} </router-link
+              >. It is not guaranteed that it will contain a corresponding variant.
+            </template>
           </div>
         </div>
 
+        <!-- ── FUNCTIONAL EVIDENCE (MaveDB) ───────────────────── First-class: the functional measurement is
+             MaveDB's own contribution, so it leads the page. Descriptive annotations (VEP) sit in the identity 
+             section below; external reference evidence sits in its own card below. -->
+        <div
+          v-if="lookup.selectedVariantDetail.value"
+          class="relative mt-6 rounded-lg border bg-surface px-[18px] py-3.5"
+        >
+          <div class="mb-2.5 flex flex-wrap items-center gap-2">
+            <h3 class="mave-section-title !mb-0">Functional evidence</h3>
+            <span class="text-xs-minus text-text-muted">measured in this score set</span>
+            <span
+              v-if="primaryConfidenceBadge"
+              v-key-term="'confidence'"
+              class="ml-auto rounded-sm px-1.5 py-0.5 text-[10px] font-bold uppercase tracking-[0.3px]"
+              :class="primaryConfidenceBadge.class"
+              >{{ primaryConfidenceBadge.label }}</span
+            >
+          </div>
+          <div v-if="lookup.selectedVariantScore.value != null" class="flex flex-wrap gap-x-10 gap-y-3">
+            <div class="flex flex-col gap-0.5">
+              <span class="text-[10px] font-semibold uppercase tracking-[0.3px] text-[#aaa]">Functional impact</span>
+              <MvClassificationTag
+                v-if="lookup.calibrationResolution.classification.value"
+                v-key-term="'consequence'"
+                :classification="lookup.calibrationResolution.classification.value"
+              />
+              <span v-else class="text-sm text-text-muted">—</span>
+            </div>
+            <div class="flex flex-col gap-0.5">
+              <span class="text-[10px] font-semibold uppercase tracking-[0.3px] text-[#aaa]">Functional score</span>
+              <span class="text-sm font-semibold text-text-primary">{{
+                lookup.selectedVariantScore.value?.toPrecision(4)
+              }}</span>
+            </div>
+            <div class="flex flex-col gap-0.5">
+              <span class="text-[10px] font-semibold uppercase tracking-[0.3px] text-[#aaa]">ACMG code</span>
+              <MvEvidenceTag
+                v-if="lookup.calibrationResolution.formattedEvidenceCode.value"
+                v-key-term="'acmg'"
+                :code="lookup.calibrationResolution.formattedEvidenceCode.value"
+              />
+              <span v-else class="text-sm text-text-muted">—</span>
+            </div>
+            <div class="flex flex-col gap-0.5">
+              <span class="text-[10px] font-semibold uppercase tracking-[0.3px] text-[#aaa]">OddsPath ratio</span>
+              <span class="text-sm font-semibold text-text-primary">{{
+                lookup.calibrationResolution.scoreRange.value?.oddspathsRatio ?? '—'
+              }}</span>
+            </div>
+          </div>
+          <p v-else class="text-xs-plus italic text-text-muted">No score available</p>
+        </div>
+
         <!-- ── VARIANT & ASSAY DETAILS ──────────────────────── -->
         <template v-if="lookup.selectedVariantDetail.value">
           <!-- Desktop: single card with two columns -->
-          <div
-            class="mave-gradient-bar relative mt-6 hidden tablet:block rounded-lg border border-border bg-surface px-[18px] py-3.5"
-          >
+          <div class="relative mt-6 hidden tablet:block rounded-lg border border-border bg-surface px-[18px] py-3.5">
             <div class="grid grid-cols-2">
               <div class="border-r border-border-light pr-[18px]">
                 <VariantInfoSection
                   :allele-name="lookup.clingenAllele.alleleName.value"
-                  :classification="lookup.calibrationResolution.classification.value"
                   :clingen-allele-id="lookup.selectedClingenAlleleId.value"
                   :clinvar-allele-ids="lookup.clingenAllele.clinvarAlleleIds.value"
                   :genomic-locations="lookup.clingenAllele.genomicLocations.value"
+                  :molecular-consequence="primaryMolecularConsequence"
                 />
               </div>
               <div class="pl-[18px]">
                 <MvAssayFactsCard
+                  :assay-level="lookup.selectedVariantDetail.value?.assayLevel ?? null"
                   :columns="1"
                   :score-set="lookup.selectedScoreSet.value ?? undefined"
+                  show-urn
                   :variant-urn="lookup.selectedVariantDetail.value?.urn ?? undefined"
                 />
               </div>
@@ -144,80 +276,86 @@
           </div>
 
           <!-- Mobile: separate cards -->
-          <div
-            class="mt-6 tablet:hidden mave-gradient-bar relative rounded-lg border border-border bg-surface px-4 py-3.5"
-          >
+          <div class="mt-6 tablet:hidden relative rounded-lg border border-border bg-surface px-4 py-3.5">
             <VariantInfoSection
               :allele-name="lookup.clingenAllele.alleleName.value"
-              :classification="lookup.calibrationResolution.classification.value"
               :clingen-allele-id="lookup.selectedClingenAlleleId.value"
               :clinvar-allele-ids="lookup.clingenAllele.clinvarAlleleIds.value"
               :genomic-locations="lookup.clingenAllele.genomicLocations.value"
+              :molecular-consequence="primaryMolecularConsequence"
             />
           </div>
-          <div
-            class="mt-4 tablet:hidden mave-gradient-bar relative rounded-lg border border-border bg-surface px-4 py-3.5"
-          >
+          <div class="mt-4 tablet:hidden relative rounded-lg border border-border bg-surface px-4 py-3.5">
             <MvAssayFactsCard
+              :assay-level="lookup.selectedVariantDetail.value?.assayLevel ?? null"
               :columns="1"
               :score-set="lookup.selectedScoreSet.value ?? undefined"
+              show-urn
               :variant-urn="lookup.selectedVariantDetail.value?.urn ?? undefined"
             />
           </div>
         </template>
 
-        <!-- ── ANNOTATIONS CARD ──────────────────────────────── -->
+        <!-- ── EXTERNAL EVIDENCE ──────────────────────────────── Reference data pulled from other databases,
+             for comparison against the functional evidence above. Rendered only when there is at least one 
+             external annotation. -->
         <div
-          v-if="lookup.selectedVariantDetail.value && lookup.selectedVariantScore.value != null"
-          class="mave-gradient-bar relative mt-6 rounded-lg border border-border bg-surface px-[18px] py-3.5"
+          v-if="lookup.selectedVariantDetail.value && hasExternalEvidence"
+          class="relative mt-4 rounded-lg border border-border bg-surface px-[18px] py-3.5"
         >
-          <div class="annotations-columns grid grid-cols-1 tablet:grid-cols-3">
-            <!-- Classification -->
-            <div class="tablet:pr-[18px]">
-              <div class="mb-1.5 text-xs-minus font-bold uppercase tracking-[0.5px] text-black">Classification</div>
-              <MvDetailRow
-                label="Functional score"
-                :value="lookup.selectedVariantScore.value?.toPrecision(4)"
-              />
-              <MvDetailRow label="ACMG code">
-                <MvEvidenceTag
-                  v-if="lookup.calibrationResolution.formattedEvidenceCode.value"
-                  :code="lookup.calibrationResolution.formattedEvidenceCode.value"
-                />
-              </MvDetailRow>
-              <MvDetailRow
-                label="OddsPath ratio"
-                :value="lookup.calibrationResolution.scoreRange.value?.oddspathsRatio ?? undefined"
-              />
-            </div>
-            <!-- Placeholder columns for future data -->
-            <div
-              class="border-t border-border-light pt-4 tablet:border-t-0 tablet:pt-0 tablet:border-l tablet:border-border-light tablet:px-[18px]"
+          <div class="mb-2.5 flex flex-wrap items-center gap-2">
+            <h3 class="mave-section-title !mb-0">External evidence</h3>
+            <span class="text-xs-minus text-text-muted">from reference databases</span>
+            <span
+              v-if="primaryGroup && !primaryGroup.annotationsMatch"
+              class="ml-auto text-[10px] font-semibold uppercase tracking-[0.3px] text-amber-600"
+              >differ by level</span
             >
-              <div class="mb-1.5 text-xs-minus font-bold uppercase tracking-[0.5px] text-black">
-                Population Frequency
-              </div>
-              <template v-if="lookup.selectedGnomad.value">
-                <MvDetailRow label="gnomAD AF" :value="formatFrequency(lookup.selectedGnomad.value.alleleFrequency)" />
-                <MvDetailRow
-                  v-if="lookup.selectedGnomad.value.faf95Max != null"
-                  label="FAF95 max"
-                  :value="formatFrequency(lookup.selectedGnomad.value.faf95Max)"
-                />
+          </div>
+          <!-- Same fold + underlying-annotations popovers as the score-set variant panel, so both surfaces
+               apply identical placement rules and expose the precise underlying gnomAD/ClinVar records. -->
+          <div class="grid grid-cols-1 gap-x-8 gap-y-4 tablet:grid-cols-2">
+            <VariantGnomadStat
+              :alleles="lookup.selectedVariantDetail.value.alleles"
+              :annotations="lookup.selectedVariantDetail.value.annotations"
+              :assay-gnomad="assayGnomad"
+              plain
+            >
+              <template #label>
+                <span
+                  v-key-term="'population'"
+                  class="w-fit text-[10px] font-semibold uppercase tracking-[0.3px] text-[#aaa]"
+                  >Population frequency</span
+                >
               </template>
-              <p v-else class="text-xs-plus italic text-text-muted">No gnomAD data</p>
-            </div>
-            <div
-              class="border-t border-border-light pt-4 tablet:border-t-0 tablet:pt-0 tablet:border-l tablet:border-border-light tablet:pl-[18px]"
+            </VariantGnomadStat>
+            <VariantClinvarStat
+              :alleles="lookup.selectedVariantDetail.value.alleles"
+              :annotations="lookup.selectedVariantDetail.value.annotations"
+              :assay-level-digest="lookup.selectedVariantDetail.value.assayLevelDigest"
+              :clinvar-version="clinvarControls.controlVersion"
+              plain
             >
-              <div class="mb-1.5 text-xs-minus font-bold uppercase tracking-[0.5px] text-black">
-                Splicing Predictions
-              </div>
-              <p class="text-xs-plus italic text-text-muted">Data coming soon</p>
-            </div>
+              <template #label>
+                <span
+                  v-key-term="'clinical'"
+                  class="w-fit text-[10px] font-semibold uppercase tracking-[0.3px] text-[#aaa]"
+                  >Clinical significance</span
+                >
+              </template>
+            </VariantClinvarStat>
           </div>
         </div>
 
+        <!-- ── RELATED ALLELES ───────────────────────────────── Sibling alleles used as context;
+             subordinate to the evidence panel above (lighter, collapsed by default). -->
+        <div
+          v-if="lookup.selectedVariantDetail.value && siblingGroups.length > 0"
+          class="relative mt-4 rounded-lg border border-border-light bg-surface px-[18px] py-3.5"
+        >
+          <MvRelatedAlleles :groups="siblingGroups" :variant-urn="lookup.selectedVariantDetail.value.urn" />
+        </div>
+
         <!-- ── SCORE DISTRIBUTION CHART ──────────────────────── -->
         <div v-if="lookup.selectedScoreSet.value" class="mt-6 rounded-lg border border-border bg-surface">
           <div
@@ -241,7 +379,8 @@
               <ScoreSetHistogram
                 :key="lookup.selectedScoreSetUrn.value || ''"
                 ref="histogram"
-                :coordinates="'mapped'"
+                :clinical="clinvarControls"
+                :coordinates="'reference'"
                 :external-selection="lookup.variantScoreRow.value"
                 :lock-selection="true"
                 :score-set="lookup.selectedScoreSet.value"
@@ -264,18 +403,23 @@
         </div>
       </template>
     </div>
+
+    <!-- Vocabulary Key: mounted once; opened from the control-header trigger or deep-linked from a badge.
+         Generic drawer + variant-page content injected via props. -->
+    <MvKeyDrawer :docs-url="keyDocsUrl" :sections="keySections" />
   </MvLayout>
 </template>
 
 <script lang="ts">
+import DatePicker from 'primevue/datepicker'
 import Select from 'primevue/select'
 import SplitButton from 'primevue/splitbutton'
-import {defineComponent, toRef} from 'vue'
+import {defineComponent, toRef, type PropType} from 'vue'
+import {useRoute} from 'vue-router'
 import {useHead} from '@unhead/vue'
 import {useToast} from 'primevue/usetoast'
 
 import CalibrationTable from '@/components/calibration/CalibrationTable.vue'
-import MvDetailRow from '@/components/common/MvDetailRow.vue'
 import MvEmptyState from '@/components/common/MvEmptyState.vue'
 import MvErrorState from '@/components/common/MvErrorState.vue'
 import MvEvidenceTag from '@/components/common/MvEvidenceTag.vue'
@@ -286,21 +430,40 @@ import MvPageHeader from '@/components/layout/MvPageHeader.vue'
 import MvAssayFactsCard from '@/components/common/MvAssayFactsCard.vue'
 import MvBadgeToggle from '@/components/common/MvBadgeToggle.vue'
 import ScoreSetHistogram from '@/components/score-set/ScoreSetHistogram.vue'
+import {useClinvarControls} from '@/composables/use-clinvar-controls'
+import {useKeyDrawer} from '@/composables/use-key-drawer'
+import MvRelatedAlleles from '@/components/variant/MvRelatedAlleles.vue'
+import MvClassificationTag from '@/components/common/MvClassificationTag.vue'
+import VariantGnomadStat from '@/components/variant/VariantGnomadStat.vue'
+import VariantClinvarStat from '@/components/variant/VariantClinvarStat.vue'
+import MvKeyDrawer from '@/components/common/MvKeyDrawer.vue'
+import {VARIANT_KEY_SECTIONS, VARIANT_KEY_DOCS_URL} from '@/components/variant/variant-key-sections'
 import MvMeasurementCard from '@/components/variant/MvMeasurementCard.vue'
 import MvRowActionMenu, {type RowAction} from '@/components/common/MvRowActionMenu.vue'
 import VariantInfoSection from '@/components/variant/VariantInfoSection.vue'
 import {useVariantLookup} from '@/composables/use-variant-lookup'
-import {MEASUREMENT_TYPE_LABELS} from '@/lib/measurement-types'
+import {assayLevelBucket, LEVEL_BUCKET_LABELS} from '@/lib/measurement-types'
 import {hasFunctionalCalibrations, hasPathogenicityCalibrations} from '@/lib/calibrations'
+import {confidenceBadge, groupAlleles, type AlleleGroup, type ConfidenceBadge} from '@/lib/allele-grouping'
+import {formatConsequence} from '@/lib/formats'
+import type {components} from '@/schema/openapi'
+
+type AlleleAnnotations = components['schemas']['AlleleAnnotations']
+type GnomadAnnotation = components['schemas']['GnomadAnnotation']
 
 export default defineComponent({
   name: 'VariantScreen',
 
   components: {
     CalibrationTable,
+    DatePicker,
+    MvRelatedAlleles,
+    MvClassificationTag,
+    VariantGnomadStat,
+    VariantClinvarStat,
     MvAssayFactsCard,
     MvBadgeToggle,
-    MvDetailRow,
+    MvKeyDrawer,
     MvEmptyState,
     MvErrorState,
     MvEvidenceTag,
@@ -320,27 +483,125 @@ export default defineComponent({
     clingenAlleleId: {
       type: String,
       required: true
+    },
+    // The `?variant=` highlight URN — pre-selects a measurement card.
+    highlightVariantUrn: {
+      type: [String, null] as PropType<string | null>,
+      default: null
     }
   },
 
   setup(props) {
+    const route = useRoute()
+
+    const lookup = useVariantLookup(toRef(props, 'clingenAlleleId'), {
+      highlightUrn: toRef(props, 'highlightVariantUrn'),
+      // Seed the query-axis controls from the URL so shared links load in a single fetch.
+      initialIncludeSuperseded: (route.query.include_superseded as string)?.toLowerCase() === 'true',
+      initialAsOf: typeof route.query.as_of === 'string' ? route.query.as_of : null,
+      toast: useToast()
+    })
+
+    const clinvarControls = useClinvarControls(lookup.selectedScoreSetUrn, lookup.scores)
+
     return {
       head: useHead({title: 'Variant search results'}),
-      lookup: useVariantLookup(toRef(props, 'clingenAlleleId'), {toast: useToast()})
+      lookup,
+      clinvarControls,
+      keyDrawer: useKeyDrawer(),
+      keySections: VARIANT_KEY_SECTIONS,
+      keyDocsUrl: VARIANT_KEY_DOCS_URL
     }
   },
 
   computed: {
+    queryAxisState(): {includeSuperseded: boolean; asOf: string | null; selectedVariantUrn: string | null} {
+      return {
+        includeSuperseded: this.lookup.includeSuperseded.value,
+        asOf: this.lookup.asOf.value,
+        selectedVariantUrn: this.lookup.selectedVariantUrn.value
+      }
+    },
     pageTitle(): string {
       return this.lookup.clingenAllele.alleleName.value || this.lookup.selectedVariantName.value || 'Variant'
     },
+    // Allele groups for the selected measurement (c↔g projection pairs collapsed, annotations coalesced).
+    alleleGroups(): AlleleGroup[] {
+      const detail = this.lookup.selectedVariantDetail.value
+      if (!detail) return []
+      return groupAlleles({
+        alleles: detail.alleles ?? {},
+        annotations: detail.annotations ?? {},
+        pageClingenAlleleId: this.clingenAlleleId
+      })
+    },
+    // The subject of the page: the searched (page-root) allele, falling back to the measured allele. Its
+    // annotations are promoted into the evidence panel; everything else is a "related allele" control.
+    primaryGroup(): AlleleGroup | null {
+      const groups = this.alleleGroups
+      return groups.find((g) => g.pageRoot) ?? groups.find((g) => g.measured) ?? groups[0] ?? null
+    },
+    siblingGroups(): AlleleGroup[] {
+      const primary = this.primaryGroup
+      return this.alleleGroups.filter((g) => g !== primary)
+    },
+    primaryAnnotations(): AlleleAnnotations | null {
+      return this.primaryGroup?.coalescedAnnotations ?? null
+    },
+    // VEP molecular consequence for the primary allele.
+    primaryMolecularConsequence(): string | null {
+      const consequence = this.primaryAnnotations?.vep?.consequence
+      return consequence ? formatConsequence(consequence) : null
+    },
+    // The measured allele's own gnomAD annotation — the headline the gnomAD cell shows straight up (siblings
+    // are enumerated by the cell itself when the measured allele has none, e.g. a protein-level assay).
+    assayGnomad(): GnomadAnnotation | null {
+      const detail = this.lookup.selectedVariantDetail.value
+      const digest = detail?.assayLevelDigest
+      return (digest ? detail?.annotations?.[digest]?.gnomad : null) ?? null
+    },
+    // Whether any allele on the record carries a gnomAD or ClinVar annotation — gates the evidence card.
+    hasExternalEvidence(): boolean {
+      const annotations = this.lookup.selectedVariantDetail.value?.annotations
+      if (!annotations) return false
+      return Object.values(annotations).some((a) => a.gnomad || (a.clinvar?.length ?? 0) > 0)
+    },
+    // Confidence/provenance badge for the primary allele (Measured / Resolved / Candidate).
+    primaryConfidenceBadge(): ConfidenceBadge | null {
+      return this.primaryGroup ? confidenceBadge(this.primaryGroup) : null
+    },
+    today(): Date {
+      return new Date()
+    },
+    // Points the empty state back at the active query controls, since an as_of / superseded filter is a
+    // common reason a valid allele returns nothing.
+    emptyStateDescription(): string {
+      if (this.lookup.asOf.value) {
+        return this.lookup.includeSuperseded.value
+          ? `No measurements found as of ${this.lookup.asOf.value}. Try a more recent date.`
+          : `No measurements found as of ${this.lookup.asOf.value}. Try a more recent date, or include superseded versions.`
+      }
+      if (!this.lookup.includeSuperseded.value) {
+        return 'No current measurements were found for this allele. Try including superseded versions.'
+      }
+      return 'No measurements were found for this allele.'
+    },
+    // Maps the DatePicker's Date|null ⇄ the composable's `as_of` date string (null = current). A date-only
+    // string is valid ISO 8601; the API reconstructs the molecular/annotation layer at that instant.
+    // Built from local Y/M/D to avoid a UTC off-by-one.
+    asOfDate: {
+      get(): Date | null {
+        return this.lookup.asOf.value ? new Date(`${this.lookup.asOf.value}T00:00:00`) : null
+      },
+      set(value: Date | null) {
+        this.lookup.asOf.value = value ? this.toIsoDate(value) : null
+      }
+    },
     measurementOptions(): {label: string; urn: string}[] {
-      return this.lookup.filteredVariants.value
-        .filter((variant): variant is typeof variant & {content: {urn: string}} => !!variant.content.urn)
-        .map((variant) => ({
-          label: `${variant.content.scoreSet?.title || 'Untitled score set'} (${MEASUREMENT_TYPE_LABELS[variant.type]?.short ?? variant.type})`,
-          urn: variant.content.urn
-        }))
+      return this.lookup.filteredVariants.value.map((m) => ({
+        label: `${m.scoreSetTitle || 'Untitled score set'} (${LEVEL_BUCKET_LABELS[assayLevelBucket(m.assayLevel)].short})`,
+        urn: m.variantUrn
+      }))
     },
     downloadActions(): RowAction[] {
       return this.annotatedVariantDownloadOptions.map((opt) => ({
@@ -382,15 +643,37 @@ export default defineComponent({
   },
 
   watch: {
+    // Reflect the query-axis controls + selected measurement in the URL (shareable/citation). Guarded
+    // against redundant nav. Writing `variant` keeps the selection ↔ `?variant=` highlight in sync, so the
+    // URL always points at the card the user is on.
+    queryAxisState({includeSuperseded, asOf, selectedVariantUrn}: {includeSuperseded: boolean; asOf: string | null; selectedVariantUrn: string | null}) {
+      const query = {...this.$route.query}
+      if (includeSuperseded) query.include_superseded = 'true'
+      else delete query.include_superseded
+      if (asOf) query.as_of = asOf
+      else delete query.as_of
+      if (selectedVariantUrn) query.variant = selectedVariantUrn
+      else delete query.variant
+      if (JSON.stringify(query) !== JSON.stringify(this.$route.query)) this.$router.replace({query})
+    },
+    // Pull external URL changes (back/forward, edited link) back into the controls.
+    '$route.query'(query: Record<string, string | string[] | null | undefined>) {
+      const includeSuperseded = (query.include_superseded as string)?.toLowerCase() === 'true'
+      const asOf = typeof query.as_of === 'string' ? query.as_of : null
+      if (this.lookup.includeSuperseded.value !== includeSuperseded) this.lookup.includeSuperseded.value = includeSuperseded
+      if ((this.lookup.asOf.value ?? null) !== asOf) this.lookup.asOf.value = asOf
+    },
     'lookup.clingenAllele.alleleName.value'(name: string | undefined) {
       this.head!.patch({title: name ? `Variant ${name}` : 'Variant'})
     }
   },
 
   methods: {
-    formatFrequency(value: number | null | undefined): string {
-      if (value == null) return '—'
-      return value < 0.0001 ? value.toExponential(2) : value.toPrecision(3)
+    toIsoDate(date: Date): string {
+      const year = date.getFullYear()
+      const month = String(date.getMonth() + 1).padStart(2, '0')
+      const day = String(date.getDate()).padStart(2, '0')
+      return `${year}-${month}-${day}`
     }
   }
 })
diff --git a/src/components/variant/MvMeasurementCard.vue b/src/components/variant/MvMeasurementCard.vue
index 5126a97d..9dfc50cd 100644
--- a/src/components/variant/MvMeasurementCard.vue
+++ b/src/components/variant/MvMeasurementCard.vue
@@ -4,13 +4,34 @@
     :class="active ? 'border-sage shadow-[0_0_0_1px_var(--color-sage)]' : ''"
     @click="$emit('select')"
   >
-    <span
-      class="mb-2.5 inline-block self-start rounded-sm px-2 py-0.5 text-[10px] font-semibold uppercase tracking-[0.3px]"
-      :class="levelClass"
-    >
-      {{ levelLabel }}
-    </span>
-    <div class="mb-2 text-xs-plus font-semibold leading-[1.3] text-text-primary">{{ studyTitle }}</div>
+    <!-- Loading affordance for the active card while its detail/scores resolve — confirms the switch
+         registered even though the card body itself renders from already-loaded measurement data. -->
+    <i
+      v-if="loading"
+      aria-label="Loading variant details"
+      class="pi pi-spin pi-spinner absolute right-2.5 top-2.5 text-xs text-sage"
+    />
+    <div class="mb-2.5 flex flex-wrap items-center gap-1.5">
+      <span
+        v-key-term="'assay-level'"
+        class="inline-block rounded-sm px-2 py-0.5 text-[10px] font-semibold uppercase tracking-[0.3px]"
+        :class="levelClass"
+      >
+        {{ levelLabel }}
+      </span>
+      <span
+        v-key-term="'relationship'"
+        class="inline-block rounded-sm px-2 py-0.5 text-[10px] font-semibold uppercase tracking-[0.3px]"
+        :class="relationship === 'direct' ? 'bg-sage/15 text-sage' : 'bg-border-light text-text-muted'"
+      >
+        {{ relationshipLabel }}
+      </span>
+    </div>
+    <div class="text-xs-plus font-semibold leading-[1.3] text-text-primary">{{ scoreSetTitle }}</div>
+    <!-- The URN disambiguates correlated score sets whose title/assay facts are otherwise identical. -->
+    <div v-if="scoreSetUrn" class="mb-2 mt-0.5 font-mono text-[10px] text-text-muted">{{ scoreSetUrn }}</div>
+    <div v-else class="mb-2"></div>
+    <!-- Assay facts -->
     <div class="flex flex-col gap-[3px] text-xs-minus text-text-muted">
       <div class="flex items-baseline gap-1">
         <span class="fact-label min-w-[80px] shrink-0 font-semibold text-[#aaa]">Assay type</span>
@@ -25,27 +46,24 @@
         <span class="text-text-secondary">{{ modelSystem || 'Not specified' }}</span>
       </div>
     </div>
+    <!-- Variant facts -->
     <div class="mt-auto border-t border-border-light pt-3">
-      <div v-if="abnormalOddsPath || normalOddsPath" class="mb-2 flex items-center gap-2.5 text-xs-minus text-text-muted">
-        <span class="text-[10px] font-bold uppercase tracking-[0.3px] text-[#aaa]">Assay OddsPath</span>
-        <div>
-          <span class="text-[#666] text-xs-minus">
-            Abnormal: <strong class="font-mono font-bold text-text-secondary">{{ abnormalOddsPath ?? '\u2014' }}</strong>
-          </span>
-          <span class="text-[#666] text-xs-minus">
-            Normal: <strong class="font-mono font-bold text-text-secondary">{{ normalOddsPath ?? '\u2014' }}</strong>
-          </span>
-        </div>
+      <div v-if="score != null" class="mb-2 flex items-center gap-2.5 text-xs-minus text-text-muted">
+        <span class="text-[10px] font-bold uppercase tracking-[0.3px] text-[#aaa]">Functional score</span>
+        <strong class="font-mono font-bold text-text-secondary">{{ score.toPrecision(4) }}</strong>
       </div>
       <div v-if="classification || evidenceCode" class="mt-1.5">
         <span class="mb-1 block text-[10px] font-bold uppercase tracking-[0.3px] text-[#aaa]">Classified as</span>
-        <div class="flex items-center gap-1.5">
-          <MvClassificationTag v-if="classification" :classification="classification" />
-          <MvEvidenceTag v-if="evidenceCode" :code="evidenceCode" />
+        <div class="flex flex-wrap items-center gap-1.5">
+          <MvClassificationTag v-if="classification" v-key-term="'consequence'" :classification="classification" />
+          <MvEvidenceTag v-if="evidenceCode" v-key-term="'acmg'" :code="evidenceCode" />
+          <span v-if="oddspathsRatio != null" v-key-term="'acmg'" class="text-xs text-text-muted"
+            >(OddsPath {{ oddspathsRatio.toPrecision(3) }})</span
+          >
         </div>
       </div>
-      <div v-if="!abnormalOddsPath && !normalOddsPath && !classification" class="flex items-center gap-1.5">
-        <span class="text-xs italic text-text-muted">No calibration data</span>
+      <div v-if="!classification && !evidenceCode" class="flex items-center gap-1.5">
+        <span class="text-xs italic text-text-muted">No primary classification</span>
       </div>
     </div>
   </div>
@@ -56,7 +74,16 @@ import {defineComponent, type PropType} from 'vue'
 
 import MvClassificationTag from '@/components/common/MvClassificationTag.vue'
 import MvEvidenceTag from '@/components/common/MvEvidenceTag.vue'
-import {MEASUREMENT_TYPE_CLASSES, MEASUREMENT_TYPE_LABELS, type MeasurementType} from '@/lib/measurement-types'
+import {
+  assayLevelBucket,
+  LEVEL_BUCKET_CLASSES,
+  LEVEL_BUCKET_LABELS,
+  RELATIONSHIP_LABELS,
+  type MeasurementRelationship
+} from '@/lib/measurement-types'
+import type {components} from '@/schema/openapi'
+
+type SavedFunctionalClassification = components['schemas']['SavedFunctionalClassification']
 
 export default defineComponent({
   name: 'MvMeasurementCard',
@@ -68,26 +95,49 @@ export default defineComponent({
 
   props: {
     active: {type: Boolean, default: false},
-    type: {type: String as PropType<MeasurementType>, required: true},
-    studyTitle: {type: String, default: ''},
+    // Shown only on the active card, while the selected variant's detail/scores are still loading.
+    loading: {type: Boolean, default: false},
+    // The assayed level (AnnotationLayer: protein/cdna/genomic) — drives the level badge.
+    assayLevel: {type: [String, null] as PropType<string | null>, default: null},
+    // How the measurement relates to the queried ClinGen allele (direct / RT-related).
+    relationship: {type: String as PropType<MeasurementRelationship>, required: true},
+    // Score set attributes displayed on the card body.
+    scoreSetTitle: {type: String, default: ''},
+    scoreSetUrn: {type: [String, null] as PropType<string | null>, default: null},
+    score: {type: [Number, null] as PropType<number | null>, default: null},
     assayType: {type: [String, null] as PropType<string | null>, default: null},
     mechanism: {type: [String, null] as PropType<string | null>, default: null},
     modelSystem: {type: [String, null] as PropType<string | null>, default: null},
-    abnormalOddsPath: {type: [String, null] as PropType<string | null>, default: null},
-    normalOddsPath: {type: [String, null] as PropType<string | null>, default: null},
-    classification: {type: [String, null] as PropType<string | null>, default: null},
-    evidenceCode: {type: [String, null] as PropType<string | null>, default: null}
+    // The server-preferred functional classification, inline on the measurement (no scores fetch needed).
+    preferredClassification: {
+      type: [Object, null] as PropType<SavedFunctionalClassification | null>,
+      default: null
+    }
   },
 
   emits: ['select'],
 
   computed: {
     levelLabel(): string {
-      return MEASUREMENT_TYPE_LABELS[this.type]?.full ?? this.type
+      return LEVEL_BUCKET_LABELS[assayLevelBucket(this.assayLevel)].full
     },
     levelClass(): string {
-      return MEASUREMENT_TYPE_CLASSES[this.type] ?? ''
+      return LEVEL_BUCKET_CLASSES[assayLevelBucket(this.assayLevel)]
+    },
+    relationshipLabel(): string {
+      return RELATIONSHIP_LABELS[this.relationship] ?? this.relationship
+    },
+    classification(): string | null {
+      return this.preferredClassification?.functionalClassification ?? null
+    },
+    evidenceCode(): string | null {
+      const acmg = this.preferredClassification?.acmgClassification
+      if (!acmg?.evidenceStrength) return null
+      return `${acmg.criterion}_${acmg.evidenceStrength.toUpperCase()}`
     },
+    oddspathsRatio(): number | null {
+      return this.preferredClassification?.oddspathsRatio ?? null
+    }
   }
 })
 </script>
diff --git a/src/components/variant/MvRelatedAlleles.vue b/src/components/variant/MvRelatedAlleles.vue
new file mode 100644
index 00000000..d89fda72
--- /dev/null
+++ b/src/components/variant/MvRelatedAlleles.vue
@@ -0,0 +1,147 @@
+<template>
+  <div>
+    <div class="mb-1 flex flex-wrap items-baseline gap-x-2">
+      <span class="text-sm font-bold text-text-primary">Related alleles</span>
+      <span class="text-xs-minus text-text-muted">other variation sharing this variant's protein consequence</span>
+    </div>
+    <!-- Collapsed by default: these are additional context, secondary to the measured/selected allele shown in parallel. -->
+    <button
+      class="cursor-pointer border-none bg-transparent text-xs font-semibold text-link hover:underline"
+      type="button"
+      @click="expanded = !expanded"
+    >
+      {{
+        expanded
+          ? 'Hide related alleles'
+          : `Show ${groups.length} related ${groups.length === 1 ? 'allele' : 'alleles'}`
+      }}
+    </button>
+
+    <div v-if="expanded" class="mt-2 flex flex-col gap-2">
+      <div
+        v-for="group in groups"
+        :key="group.key"
+        class="rounded-md border border-border-light bg-surface px-3 py-2.5"
+      >
+        <!-- Confidence badge (Resolved/Candidate; a stray measured sibling still reads "Measured"). -->
+        <div class="mb-1.5 flex flex-wrap items-center gap-x-2 gap-y-1">
+          <span
+            v-if="confidenceBadge(group)"
+            v-key-term="'confidence'"
+            class="rounded-sm px-1.5 py-0.5 text-[10px] font-bold uppercase tracking-[0.3px]"
+            :class="confidenceBadge(group)!.class"
+            >{{ confidenceBadge(group)!.label }}</span
+          >
+          <router-link
+            v-for="caid in group.clingenLinks"
+            :key="caid"
+            class="ml-auto inline-flex items-center gap-0.5 font-mono text-xs font-semibold text-link hover:underline"
+            :to="{name: 'variant', params: {clingenAlleleId: caid}, query: variantUrn ? {variant: variantUrn} : {}}"
+          >
+            {{ caid }}<i class="pi pi-arrow-up-right text-xs" />
+          </router-link>
+        </div>
+
+        <!-- Identity: one line per level (a projection pair shows both), never the digest. -->
+        <div class="mb-1.5 flex flex-col gap-1">
+          <div v-for="m in group.members" :key="m.digest" class="flex flex-wrap items-center gap-x-2 gap-y-1">
+            <span
+              v-key-term="'assay-level'"
+              class="inline-block rounded-sm px-1.5 py-0.5 text-[10px] font-semibold uppercase tracking-[0.3px]"
+              :class="levelClass(m.level)"
+              >{{ levelLabel(m.level) }}</span
+            >
+            <span class="font-mono text-xs-plus font-semibold text-text-primary">{{ m.hgvs || '—' }}</span>
+          </div>
+        </div>
+
+        <!-- Annotations: one deduplicated block when the pair agrees, else per-level so divergence shows. -->
+        <div class="flex flex-col gap-1">
+          <div
+            v-if="!group.annotationsMatch"
+            class="text-[10px] font-semibold uppercase tracking-[0.3px] text-amber-600"
+          >
+            Annotations differ by level
+          </div>
+          <div v-for="line in annotationLines(group)" :key="line.label ?? 'shared'">
+            <div class="flex flex-col gap-0.5 text-xs-minus text-text-muted tablet:flex-row tablet:gap-5">
+              <span v-if="line.label" class="font-semibold text-[#aaa]">{{ line.label }}</span>
+              <span>
+                <span class="font-semibold text-[#aaa]">VEP:</span>
+                {{ line.annotations?.vep?.consequence ? formatConsequence(line.annotations.vep.consequence) : '—' }}
+              </span>
+              <span>
+                <span class="font-semibold text-[#aaa]">gnomAD:</span>
+                <template v-if="line.annotations?.gnomad">
+                  AF {{ formatFrequency(line.annotations.gnomad.alleleFrequency) }}</template
+                >
+                <template v-else> —</template>
+              </span>
+              <span>
+                <span class="font-semibold text-[#aaa]">ClinVar:</span>
+                <template v-if="latestClinvar(line.annotations)"
+                  >&nbsp;{{ formatClinicalSignificance(latestClinvar(line.annotations)!.clinicalSignificance) }}</template
+                >
+                <template v-else> —</template>
+              </span>
+            </div>
+          </div>
+        </div>
+      </div>
+    </div>
+  </div>
+</template>
+
+<script lang="ts">
+import {defineComponent, type PropType} from 'vue'
+
+import {type AlleleGroup, confidenceBadge} from '@/lib/allele-grouping'
+import {formatClinicalSignificance, latestClinvar} from '@/lib/clinvar-controls'
+import {formatConsequence} from '@/lib/formats'
+import {formatFrequency} from '@/lib/gnomad'
+import {ASSAY_LEVEL_LABELS, LEVEL_BUCKET_CLASSES, assayLevelBucket} from '@/lib/measurement-types'
+import type {components} from '@/schema/openapi'
+
+type AlleleAnnotations = components['schemas']['AlleleAnnotations']
+
+/**
+ * Subordinate "Related alleles" panel: the sibling allele groups (everything that is not the page's
+ * primary/selected allele — those are promoted into the evidence panel above). Collapsed by default and
+ * visually lighter, so they read as context rather than co-equal evidence. Grouping is done by the
+ * parent ({@link groupAlleles}); this component only renders the groups it is handed.
+ */
+export default defineComponent({
+  name: 'MvRelatedAlleles',
+
+  props: {
+    // Sibling allele groups (pre-grouped and filtered by the parent).
+    groups: {type: Array as PropType<AlleleGroup[]>, default: () => []},
+    // The selected measurement's URN. Carried as the `?variant=` highlight on each group's link-out.
+    variantUrn: {type: [String, null] as PropType<string | null>, default: null}
+  },
+
+  data() {
+    return {expanded: false}
+  },
+
+  methods: {
+    formatConsequence,
+    formatFrequency,
+    latestClinvar,
+    formatClinicalSignificance,
+    confidenceBadge,
+    // The annotation blocks to render: one coalesced block (present-wins union across levels) when there
+    // is no real divergence, else one per level so an actual present-vs-present disagreement shows.
+    annotationLines(group: AlleleGroup): Array<{label: string | null; annotations: AlleleAnnotations | null}> {
+      if (group.annotationsMatch) return [{label: null, annotations: group.coalescedAnnotations}]
+      return group.members.map((m) => ({label: this.levelLabel(m.level), annotations: m.annotations}))
+    },
+    levelLabel(level: string | null | undefined): string {
+      return ASSAY_LEVEL_LABELS[level as keyof typeof ASSAY_LEVEL_LABELS] ?? level ?? '—'
+    },
+    levelClass(level: string | null | undefined): string {
+      return LEVEL_BUCKET_CLASSES[assayLevelBucket(level)]
+    }
+  }
+})
+</script>
diff --git a/src/components/variant/VariantDetailPanel.vue b/src/components/variant/VariantDetailPanel.vue
index fd96bcdb..ba550c7c 100644
--- a/src/components/variant/VariantDetailPanel.vue
+++ b/src/components/variant/VariantDetailPanel.vue
@@ -10,7 +10,10 @@
     <div v-if="status === 'loading'" class="flex items-center justify-center px-5 py-4">
       <MvLoader text="Loading variant..." />
     </div>
-    <div v-else-if="status === 'error'" class="px-5 py-4 text-sm text-red-600">Could not load variant detail.</div>
+    <div v-else-if="status === 'error'" class="flex items-center justify-center gap-2 px-5 py-4 text-sm text-red-600">
+      <span class="flex items-center">Could not load variant detail.</span>
+      <button type="button" class="font-semibold text-link hover:underline" @click="fetchDetail(urn)">Retry</button>
+    </div>
 
     <template v-else-if="detail">
       <!-- Identity -->
@@ -28,8 +31,13 @@
       <!-- Facts -->
       <div class="grid grid-cols-2 gap-px border-t border-border-light bg-border-light tablet:grid-cols-4">
         <div class="stat">
-          <span class="stat-label">Consequence</span>
-          <span class="stat-value font-semibold">{{ consequence ? formatToken(consequence) : '—' }}</span>
+          <span class="stat-label">Molecular consequence</span>
+          <span class="stat-value font-semibold">{{
+            consequence?.consequence ? formatToken(consequence.consequence) : '—'
+          }}</span>
+          <span class="mt-auto text-[10px] text-text-muted">
+            As of VEP version {{ consequence?.sourceVersion ?? '—' }}</span
+          >
         </div>
 
         <div class="stat">
@@ -41,59 +49,21 @@
             <MvEvidenceTag v-if="acmgCode" :code="acmgCode" />
           </span>
           <span v-else class="stat-value font-semibold">—</span>
-          <span v-if="oddspathsRatio != null" class="mt-0.5 text-xs"> OddsPath {{ oddspathsRatio }} </span>
-        </div>
-
-        <div class="stat">
-          <span class="stat-label">gnomAD</span>
-          <a
-            v-if="gnomad"
-            class="stat-value font-semibold hover:underline"
-            :href="`https://gnomad.broadinstitute.org/variant/${gnomad.dbIdentifier}`"
-            target="_blank"
-            rel="noopener noreferrer"
-          >
-            AF {{ formatFrequency(gnomad.alleleFrequency) }}
-          </a>
-          <span v-else class="stat-value">—</span>
-          <span v-if="gnomad?.faf95Max != null" class="text-xs text-text-muted">
-            FAF95 {{ formatFrequency(gnomad.faf95Max) }}
-          </span>
+          <template v-if="oddspathsRatio != null">
+            <span class="stat-value font-semibold flex flex-wrap items-center mt-0.5 gap-x-1.5 gap-y-0.5">
+              <span class="text-text-muted">OddsPath</span>
+              <span class="text-text-muted">{{ oddspathsRatio }}</span>
+            </span>
+          </template>
         </div>
 
-        <div class="stat">
-          <span class="stat-label">ClinVar</span>
-          <a
-            v-if="latestClinvar?.clinvarVariationId"
-            class="stat-value font-semibold hover:underline"
-            :style="{color: clinvarColor}"
-            :href="`https://www.ncbi.nlm.nih.gov/clinvar/?term=${latestClinvar.clinvarAlleleId}[alleleId]`"
-            target="_blank"
-            rel="noopener noreferrer"
-          >
-            {{ latestClinvar.clinicalSignificance }}
-          </a>
-          <span v-else-if="latestClinvar" class="stat-value font-semibold" :style="{color: clinvarColor}">
-            {{ latestClinvar.clinicalSignificance }}
-          </span>
-          <span v-else class="stat-value">—</span>
-          <span
-            v-if="clinvarStars != null"
-            v-tooltip.top="latestClinvar?.clinicalReviewStatus"
-            class="flex items-center gap-0.5 text-amber-400"
-            aria-label="ClinVar review stars"
-          >
-            <i
-              v-for="n in 4"
-              :key="n"
-              :class="n <= clinvarStars ? 'pi pi-star-fill' : 'pi pi-star'"
-              class="text-[9px]"
-            />
-          </span>
-          <span v-if="latestClinvar" class="text-xs text-text-muted"
-            >As of {{ formatClinvarVersion(latestClinvar.dbVersion) }}</span
-          >
-        </div>
+        <VariantGnomadStat :alleles="detail.alleles" :annotations="detail.annotations" :assay-gnomad="gnomad" />
+        <VariantClinvarStat
+          :alleles="detail.alleles"
+          :annotations="detail.annotations"
+          :assay-level-digest="detail.assayLevelDigest"
+          :clinvar-version="clinvarVersion"
+        />
       </div>
 
       <!-- Status and Links -->
@@ -111,7 +81,7 @@
         <router-link
           v-if="detail.clingenAlleleId"
           class="ml-auto shrink-0 text-xs font-semibold text-link hover:underline"
-          :to="{name: 'variant', params: {clingenAlleleId: detail.clingenAlleleId}}"
+          :to="{name: 'variant', params: {clingenAlleleId: detail.clingenAlleleId}, query: {variant: detail.urn}}"
         >
           View full details <i class="pi pi-arrow-right text-[10px]" />
         </router-link>
@@ -125,9 +95,9 @@ import {defineComponent, type PropType} from 'vue'
 
 import MvEvidenceTag from '@/components/common/MvEvidenceTag.vue'
 import MvLoader from '@/components/common/MvLoader.vue'
+import VariantGnomadStat from '@/components/variant/VariantGnomadStat.vue'
+import VariantClinvarStat from '@/components/variant/VariantClinvarStat.vue'
 import {getVariantDetail} from '@/api/mavedb/variants'
-import {formatClinvarVersion} from '@/lib/formats'
-import {CLINVAR_REVIEW_STATUS_STARS} from '@/lib/clinical-controls'
 import type {components} from '@/schema/openapi'
 
 type VariantDetail = components['schemas']['VariantDetail']
@@ -137,29 +107,32 @@ type AlleleAnnotations = components['schemas']['AlleleAnnotations']
 /**
  * Compact selected-variant summary for the score-set page, consuming `GET /variants/{urn}`.
  *
- * Deliberately lean: the assay-level facts only (identity, consequence, the selected calibration's
- * classification, the assay allele's key annotations) as distinct, color-coded stats, plus a link out
- * to the full variant page. Coordinates follow the page's current frame; the classification follows the
- * page's selected calibration. The deep per-allele annotation breakdown and the Cat-VRS structure
- * belong on the dedicated variant page — VRS digests are join keys, never surfaced here.
+ * Deliberately lean: assay-level facts (identity, consequence, the selected calibration's classification)
+ * plus two annotation cells that reach past the assayed allele — {@link VariantGnomadStat} and
+ * {@link VariantClinvarStat}. These each own their own presentation and their fold/enumeration wiring to sibling
+ * alleles.
+ *
+ * Coordinates follow the page's current frame; the classification follows the page's selected calibration. A
+ * parent supplies `clinvarVersion` so the ClinVar cell reduces over the same release as any parent components.
  */
 export default defineComponent({
   name: 'VariantDetailPanel',
 
-  components: {MvEvidenceTag, MvLoader},
+  components: {MvEvidenceTag, MvLoader, VariantGnomadStat, VariantClinvarStat},
 
   props: {
     urn: {type: String, required: true},
-    // The display label for the variant in the page's current frame — the SAME string the search box
-    // and heatmap use (`labelForVariant`, protein-preferred). Passed in so the panel's identity never
-    // disagrees with the rest of the page (e.g. panel showing coding while the heatmap shows protein).
-    coordinate: {type: String, default: ''},
+    // The display label for the variant in the page's current frame.
+    coordinate: {type: String as PropType<string | null>, default: null},
     // The underlying nucleotide HGVS in the current frame. Shown muted beside the (protein-preferred)
-    // primary label to disambiguate distinct coding variants that collapse to the same protein change,
-    // and as provenance for the actually-measured coordinate. Empty when it equals the primary label.
-    underlyingCoordinate: {type: String, default: ''},
+    // primary label to disambiguate distinct coding variants that collapse to the same protein change.
+    // Empty when there is no underlying nucleotide coordinate.
+    underlyingCoordinate: {type: String as PropType<string | null>, default: null},
     // The calibration selected on the page (its numeric id); its classification is the one shown.
     selectedCalibrationId: {type: Number as PropType<number | null>, default: null},
+    // The ClinVar release the page's clinical-controls store has selected (raw `MM_YYYY`), passed through to
+    // the ClinVar cell so it reduces over the same release as parent components. Null → fall back to latest.
+    clinvarVersion: {type: String as PropType<string | null>, default: null},
     // When embedded inside another card (e.g. under the search box), drop the panel's own card chrome
     // and separate from the row above with just a top divider, so the two read as one unit.
     flush: {type: Boolean, default: false}
@@ -179,30 +152,12 @@ export default defineComponent({
       if (!this.detail?.annotations || !digest) return null
       return this.detail.annotations[digest] ?? null
     },
-    consequence(): string | null {
-      return this.assayAnnotations?.vep?.consequence ?? null
+    consequence(): AlleleAnnotations['vep'] | null {
+      return this.assayAnnotations?.vep ?? null
     },
     gnomad(): AlleleAnnotations['gnomad'] | null {
       return this.assayAnnotations?.gnomad ?? null
     },
-    latestClinvar(): NonNullable<AlleleAnnotations['clinvar']>[number] | null {
-      const clinvar = this.assayAnnotations?.clinvar
-      if (!clinvar?.length) return null
-      return clinvar.reduce((best, c) => (c.dbVersion > best.dbVersion ? c : best))
-    },
-    clinvarStars(): number | null {
-      const status = this.latestClinvar?.clinicalReviewStatus?.toLowerCase()
-      if (!status) return null
-      const stars = CLINVAR_REVIEW_STATUS_STARS[status] ?? null
-      return stars != null ? stars : null
-    },
-    clinvarColor(): string | undefined {
-      const s = this.latestClinvar?.clinicalSignificance?.toLowerCase() ?? ''
-      if (s.includes('conflicting')) return undefined
-      if (s.includes('pathogenic')) return 'var(--color-badge-pathogenic)'
-      if (s.includes('benign')) return 'var(--color-badge-benign)'
-      return undefined
-    },
     // The classification for the page's selected calibration; falls back to primary, then first.
     selectedClassification(): VariantClassification | null {
       const classifications = this.detail?.classifications ?? []
@@ -224,9 +179,11 @@ export default defineComponent({
       return `${acmg.criterion}_${acmg.evidenceStrength.toUpperCase()}`
     },
     supersededTooltip(): string {
+      // Supersession is anchored on the score set, not the variant: the newer version may not contain a
+      // corresponding variant, so we never imply a navigable superseding measurement.
       return this.detail?.supersededByScoreSet
-        ? `Superseded by score set ${this.detail.supersededByScoreSet}`
-        : 'This measurement has been superseded by a newer version.'
+        ? `Superseded by score set ${this.detail.supersededByScoreSet}. That version may not contain a corresponding variant.`
+        : 'This measurement is from a superseded version of its score set. The newer version may not contain a corresponding variant.'
     }
   },
 
@@ -253,18 +210,14 @@ export default defineComponent({
     formatToken(value: string | null | undefined): string {
       if (!value) return '—'
       return value.replace(/_/g, ' ').replace(/\b\w/g, (ch) => ch.toUpperCase())
-    },
-    formatFrequency(value: number | null | undefined): string {
-      if (value == null) return '—'
-      return value < 0.0001 ? value.toExponential(2) : value.toPrecision(3)
-    },
-    formatClinvarVersion
+    }
   }
 })
 </script>
 
 <style scoped>
-/* Each fact is its own cell on a shared light background; the 1px grid gap draws the dividers. */
+/* Each fact is its own cell on a shared light background; the 1px grid gap draws the dividers. The two
+   annotation cells ({@link VariantGnomadStat}/{@link VariantClinvarStat}) mirror this .stat styling. */
 .stat {
   display: flex;
   flex-direction: column;
diff --git a/src/components/variant/VariantInfoSection.vue b/src/components/variant/VariantInfoSection.vue
index 65ce374e..194edcb3 100644
--- a/src/components/variant/VariantInfoSection.vue
+++ b/src/components/variant/VariantInfoSection.vue
@@ -13,14 +13,16 @@
     </MvDetailRow>
     <MvDetailRow :label="`ClinVar allele ${clinvarAlleleIds.length > 1 ? 'IDs' : 'ID'}`">
       <template v-for="(cvId, i) in clinvarAlleleIds" :key="cvId">
-        <a class="text-link" :href="`http://www.ncbi.nlm.nih.gov/clinvar/?term=${cvId}[alleleid]`" target="_blank">{{
+        <a class="text-link" :href="clinvarVariantUrl({clinvarAlleleId: cvId}) ?? undefined" target="_blank">{{
           cvId
         }}</a>
         <template v-if="i < clinvarAlleleIds.length - 1">, </template>
       </template>
+      <template v-if="clinvarAlleleIds.length === 0"><span class="text-text-muted">—</span></template>
     </MvDetailRow>
-    <MvDetailRow label="Functional consequence">
-      <MvClassificationTag v-if="classification" :classification="classification" />
+    <MvDetailRow label="Molecular consequence">
+      <span v-if="molecularConsequence">{{ formatConsequence(molecularConsequence) }}</span>
+      <span v-else class="italic text-text-muted">—</span>
     </MvDetailRow>
     <MvDetailRow :align="'flex-start'" :label="`Genomic ${genomicLocations.length > 1 ? 'locations' : 'location'}`">
       <table v-if="genomicLocations.length > 0" class="border-collapse">
@@ -39,8 +41,9 @@
 <script lang="ts">
 import {defineComponent, type PropType} from 'vue'
 
-import MvClassificationTag from '@/components/common/MvClassificationTag.vue'
 import MvDetailRow from '@/components/common/MvDetailRow.vue'
+import {clinvarVariantUrl} from '@/lib/clinvar-controls'
+import {formatConsequence} from '@/lib/formats'
 
 type GenomicLocation = {chromosome: string; start: string | number; referenceGenome: string}
 
@@ -48,7 +51,6 @@ export default defineComponent({
   name: 'VariantInfoSection',
 
   components: {
-    MvClassificationTag,
     MvDetailRow
   },
 
@@ -56,8 +58,13 @@ export default defineComponent({
     alleleName: {type: [String, null] as PropType<string | null>, default: null},
     clingenAlleleId: {type: [String, null] as PropType<string | null>, default: null},
     clinvarAlleleIds: {type: Array as PropType<string[]>, default: () => []},
-    classification: {type: [String, null] as PropType<string | null>, default: null},
+    molecularConsequence: {type: [String, null] as PropType<string | null>, default: null},
     genomicLocations: {type: Array as PropType<GenomicLocation[]>, default: () => []}
+  },
+
+  methods: {
+    clinvarVariantUrl,
+    formatConsequence
   }
 })
 </script>
diff --git a/src/components/variant/variant-key-sections.ts b/src/components/variant/variant-key-sections.ts
index bbcb5883..f1519070 100644
--- a/src/components/variant/variant-key-sections.ts
+++ b/src/components/variant/variant-key-sections.ts
@@ -1,5 +1,6 @@
 import config from '@/config'
 import type {KeySection} from '@/composables/use-key-drawer'
+import {ALLELE_CONFIDENCE} from '@/lib/allele-grouping'
 
 /**
  * Variant-page content for the generic {@link MvKeyDrawer}. These are the tier-2 vocabulary glosses; the
@@ -47,21 +48,8 @@ export const VARIANT_KEY_SECTIONS: KeySection[] = [
   {
     id: 'confidence',
     title: 'How a coordinate was established',
-    terms: [
-      {label: 'Measured', definition: 'Directly assayed in this score set.', class: 'bg-sage/15 text-sage'},
-      {
-        label: 'Resolved',
-        definition:
-          'Derived from the measured allele by reverse translation — the same change expressed at another level.',
-        class: 'bg-nucleotide-light text-nucleotide'
-      },
-      {
-        label: 'Candidate',
-        definition:
-          'A change that encodes the same protein change as your variant, but is a distinct nucleotide change.',
-        class: 'bg-amber-100 text-amber-700'
-      }
-    ]
+    // Assembled from the shared confidence vocabulary so badges and this gloss can never drift apart.
+    terms: Object.values(ALLELE_CONFIDENCE).map((c) => ({label: c.label, definition: c.definition, class: c.class}))
   },
   {
     id: 'selected-allele',

From 7a8b4be3d39e3dcdfb10dc9529f43350b5776877 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 16 Jul 2026 15:50:02 -0700
Subject: [PATCH 43/84] feat(score-set): add search-and-jump variant picker

- Add ScoreSetVariantSearch, an autocomplete that jumps to a variant:
  a notables empty state grouped by rung, virtual-scrolled search over
  all scored variants when typing, and per-option leading dots,
  captions, coordinate labels, and clinical tags
- Add MvMeasurementRow for per-measurement result rows
- Rebuild cross-score-set search to list every related measurement as
  its own row rather than aggregating by score set, removing the now
  unused measurement-aggregation lib
- Embed ScoreSetVariantSearch in the score set view
---
 .../score-set/ScoreSetVariantSearch.vue       | 424 ++++++++++++++++++
 src/components/screens/ScoreSetView.vue       | 215 ++++-----
 .../screens/SearchVariantsScreen.vue          | 270 +++++------
 src/components/search/MvMeasurementRow.vue    |  57 +++
 src/lib/measurement-aggregation.test.ts       |  61 ---
 src/lib/measurement-aggregation.ts            |  76 ----
 6 files changed, 676 insertions(+), 427 deletions(-)
 create mode 100644 src/components/score-set/ScoreSetVariantSearch.vue
 create mode 100644 src/components/search/MvMeasurementRow.vue
 delete mode 100644 src/lib/measurement-aggregation.test.ts
 delete mode 100644 src/lib/measurement-aggregation.ts

diff --git a/src/components/score-set/ScoreSetVariantSearch.vue b/src/components/score-set/ScoreSetVariantSearch.vue
new file mode 100644
index 00000000..0e51e1d9
--- /dev/null
+++ b/src/components/score-set/ScoreSetVariantSearch.vue
@@ -0,0 +1,424 @@
+<template>
+  <div class="relative min-w-0 flex-1">
+    <MvFloatField label="Search variants">
+      <template #default="{id}">
+        <AutoComplete
+          :id="id"
+          v-model="localSelection"
+          class="w-full"
+          complete-on-focus
+          :delay="300"
+          dropdown
+          fluid
+          :input-style="hasSelection ? {paddingRight: '2.25rem'} : undefined"
+          option-group-label="label"
+          option-group-children="items"
+          :option-label="variantOptionLabel"
+          :scroll-height="variantSearchQuery ? '175px' : '320px'"
+          select-on-focus
+          :suggestions="variantSearchSuggestions"
+          :virtual-scroller-options="variantSearchQuery ? {itemSize: 50} : undefined"
+          @complete="variantSearch"
+        >
+          <!-- Group header: on the empty state each notable group names its rung; while typing the single
+               group's label carries the match count. -->
+          <!-- A standing note that the empty-box rows are a curated handful, not the whole set. -->
+          <template #header>
+            <div
+              v-if="!variantSearchQuery && variantSearchSuggestions.length"
+              class="border-b border-border-light px-3 py-1.5 text-xs text-text-muted"
+            >
+              Showing sample variants — type to search all {{ scoredVariants.length.toLocaleString() }}.
+            </div>
+          </template>
+          <template #optiongroup="{option}">
+            <div
+              class="px-3 py-1.5 text-[0.6875rem] font-semibold uppercase tracking-wide text-text-muted"
+              :class="{'border-t border-border-light': !variantSearchQuery}"
+            >
+              {{ option.label }}
+            </div>
+          </template>
+          <template #option="{option}">
+            <div class="flex w-full items-center justify-between gap-2">
+              <div class="flex min-w-0 items-center gap-2">
+                <!-- Leading dot. On the empty box it's the notable caption's (consequence palette or red/
+                     blue clinical call). While searching it flags the "interesting" hits — ClinVar controls,
+                     colored by classification — and is transparent (but reserves its width, so labels stay
+                     aligned) for everything else. -->
+                <span
+                  class="size-2 shrink-0 rounded-full"
+                  :style="{backgroundColor: optionDotColor(option) || 'transparent'}"
+                  :title="variantSearchQuery ? (clinicalTag(option) ?? undefined) : undefined"
+                />
+                <div class="flex min-w-0 flex-col justify-center leading-tight">
+                  <span class="truncate">{{ variantOptionLabel(option) }}</span>
+                  <!-- Empty box: the notable caption. Searching: the underlying coordinate, for
+                       disambiguating distinct coding variants that share a protein label. -->
+                  <span
+                    v-if="!variantSearchQuery && notableCaption(option)"
+                    class="truncate text-xs font-semibold text-text-secondary"
+                  >
+                    {{ notableCaption(option)?.label }}
+                  </span>
+                  <span
+                    v-else-if="variantSearchQuery && variantUnderlyingLabel(option)"
+                    class="truncate font-mono text-xs text-text-muted"
+                  >
+                    {{ variantUnderlyingLabel(option) }}
+                  </span>
+                  <span v-if="frame === 'reference' && isUnmapped(option)" class="text-xs italic text-text-muted">
+                    Variant could not be mapped
+                  </span>
+                </div>
+              </div>
+              <span v-if="typeof option.score === 'number'" class="shrink-0 text-xs text-text-muted">
+                {{ option.score.toFixed(2) }}
+              </span>
+            </div>
+          </template>
+          <template #empty>
+            <div v-if="!variantSearchQuery" class="p-3 text-sm text-text-muted">
+              Type a position or coordinate to find a variant.
+            </div>
+            <div v-else class="p-2.5 text-center text-sm text-text-muted">No matching variants found.</div>
+          </template>
+        </AutoComplete>
+      </template>
+    </MvFloatField>
+    <button
+      v-if="hasSelection"
+      aria-label="Clear"
+      class="absolute right-12 top-1/2 flex size-5 -translate-y-1/2 cursor-pointer items-center justify-center rounded-full text-text-muted hover:bg-red-50 hover:text-red-600"
+      @click="clearSelection"
+    >
+      <i class="pi pi-times text-[10px]" />
+    </button>
+  </div>
+</template>
+
+<script lang="ts">
+import AutoComplete from 'primevue/autocomplete'
+import {defineComponent, shallowRef, type PropType} from 'vue'
+
+import MvFloatField from '@/components/forms/MvFloatField.vue'
+import type {ClinvarControlsStore} from '@/composables/use-clinvar-controls'
+import {useVariantCoordinates, type CoordinateFrame} from '@/composables/use-variant-coordinates'
+import {
+  BENIGN_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS,
+  CLINVAR_REVIEW_STATUS_STARS,
+  DEFAULT_CLNREVSTAT_FIELD,
+  DEFAULT_CLNSIG_FIELD,
+  DEFAULT_MIN_STAR_RATING,
+  PATHOGENIC_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS
+} from '@/lib/clinvar-controls'
+import {consequenceBucket, EFFECT_BUCKETS} from '@/lib/consequences'
+import {
+  clinicalExtremesPerClass,
+  consequenceExemplars,
+  deviationsFromMedian,
+  medianAndMad,
+  scoreExtremes
+} from '@/lib/notables'
+import type {DisplayVariant} from '@/lib/variants'
+
+// A labeled block of suggestions. The AutoComplete is always grouped: an empty box shows the notable
+// groups (clinical / consequence / score extremes), typing collapses to a single group whose label
+// carries the match count.
+interface VariantGroup {
+  label: string
+  items: DisplayVariant[]
+}
+
+// The secondary line rendered under a notable row, framed for its group (a consequence name, a ClinVar
+// call, or a deviations-from-median readout). `color` drives the leading dot when present.
+interface NotableCaption {
+  label: string
+  color?: string
+}
+
+// How many most-extreme-score rows to sample on the empty state.
+const SCORE_EXTREME_COUNT = 4
+
+/**
+ * The score-set variant picker: a search-and-jump AutoComplete. An empty box offers "notable" variants to
+ * jump to (grouped by signal-richness: clinvar controls, then consequence exemplars, then score
+ * extremes); typing filters the whole set by coordinate. Both states are real grouped options, so both
+ * stay keyboard-navigable and select/jump natively. Selection is surfaced via `v-model` (the parent owns
+ * it — the histograms, heatmap, detail panel, and URL all two-way sync through it).
+ */
+export default defineComponent({
+  name: 'ScoreSetVariantSearch',
+
+  components: {AutoComplete, MvFloatField},
+
+  props: {
+    variants: {
+      type: Array as PropType<DisplayVariant[]>,
+      required: true
+    },
+    // Shared clinical-control store — gates and feeds the "Clinically classified" group once its
+    // associations settle.
+    clinical: {
+      type: Object as PropType<ClinvarControlsStore>,
+      required: true
+    },
+    // Coordinate frame the labels resolve in (reference in clinical mode, submitted otherwise).
+    frame: {
+      type: String as PropType<CoordinateFrame>,
+      required: true
+    },
+    // The selected variant (v-model). Null when nothing is selected.
+    modelValue: {
+      type: Object as PropType<DisplayVariant | null>,
+      default: null
+    }
+  },
+
+  emits: ['update:modelValue'],
+
+  setup() {
+    // shallowRef, not ref: the groups are replaced wholesale on each search, and a deep ref would lazily
+    // Proxy every option object the first time PrimeVue's AutoComplete touches it (its `ariaSetSize`
+    // computed filters the entire list on open) — which is what made the dropdown slow to appear.
+    const variantSearchSuggestions = shallowRef<VariantGroup[]>([])
+    return {
+      ...useVariantCoordinates(),
+      variantSearchSuggestions
+    }
+  },
+
+  data: () => ({
+    // The AutoComplete's own model: PrimeVue writes the typed string here while searching and the option
+    // object on select. Mirrored from `modelValue` and re-emitted, guarding against the transient string.
+    localSelection: null as DisplayVariant | string | null,
+    variantSearchQuery: ''
+  }),
+
+  computed: {
+    // Whether an actual variant (not a transient typed string) is selected — drives the clear button and
+    // the input's trailing padding.
+    hasSelection(): boolean {
+      return typeof this.localSelection === 'object' && this.localSelection !== null
+    },
+    // Only scored variants are selectable — the visualizations plot a score, so a variant without one has
+    // nothing to jump to.
+    scoredVariants(): DisplayVariant[] {
+      return this.variants.filter((v) => typeof v.score === 'number')
+    },
+    // Search index built once per loaded set: each scored variant paired with a lowercased haystack of all
+    // its coordinate strings (both frames) plus its URN. Filtering a keystroke is then one `includes` per
+    // variant instead of re-resolving ~7 coordinates and re-lowercasing them on every keypress.
+    variantSearchIndex(): {variant: DisplayVariant; haystack: string}[] {
+      return this.scoredVariants.map((v) => ({
+        variant: v,
+        haystack: [
+          v.hgvsNt?.hgvs,
+          v.hgvsPro?.hgvs,
+          v.hgvsSplice?.hgvs,
+          v.mapped?.cdna?.hgvs,
+          v.mapped?.genomic?.hgvs,
+          v.mapped?.protein?.hgvs,
+          v.variantUrn
+        ]
+          .filter(Boolean)
+          .join(' ')
+          .toLowerCase()
+      }))
+    },
+    // The "notables" shown when the box is empty — a useful entry point instead of a blank list. Three
+    // groups graded by signal-richness, each present only if it has data: clinvar controls (richest,
+    // needs the fetch — pops in once associations settle), consequence exemplars (intrinsic; empty on
+    // truly-unmapped sets), and score extremes (the universal floor). A variant appears in only its
+    // highest-signal group; the matching caption is stashed per URN for the #option slot.
+    notableData(): {groups: VariantGroup[]; captions: Map<string, NotableCaption>} {
+      const scored = this.scoredVariants
+      const groups: VariantGroup[] = []
+      const captions = new Map<string, NotableCaption>()
+      if (!scored.length) return {groups, captions}
+      const seen = new Set<string>()
+
+      // 1. Clinically classified — gated on the clinical-control fetch having associated; the group simply
+      // isn't there until then, so it pops in asynchronously.
+      const clinical = this.clinical.associated
+        ? clinicalExtremesPerClass(scored, DEFAULT_MIN_STAR_RATING).filter((v) => !seen.has(v.variantUrn))
+        : []
+      for (const v of clinical) {
+        seen.add(v.variantUrn)
+        captions.set(v.variantUrn, this.clinicalCaption(v))
+      }
+      if (clinical.length) groups.push({label: 'Clinically classified', items: clinical})
+
+      // 2. By consequence — one representative per effect bucket present.
+      const consequence = consequenceExemplars(scored).filter((v) => !seen.has(v.variantUrn))
+      for (const v of consequence) {
+        seen.add(v.variantUrn)
+        const bucket = consequenceBucket(v.consequence)
+        captions.set(v.variantUrn, {label: bucket, color: EFFECT_BUCKETS.find((b) => b.name === bucket)?.color})
+      }
+      if (consequence.length) groups.push({label: 'By consequence', items: consequence})
+
+      // 3. Most extreme scores — request a few extra to backfill any deduped against the groups above, then
+      // trim to the target count.
+      const spread = medianAndMad(scored.map((v) => v.score as number))
+      const extremes = scoreExtremes(scored, SCORE_EXTREME_COUNT + seen.size)
+        .filter((v) => !seen.has(v.variantUrn))
+        .slice(0, SCORE_EXTREME_COUNT)
+      for (const v of extremes) {
+        seen.add(v.variantUrn)
+        captions.set(v.variantUrn, this.scoreCaption(v, spread))
+      }
+      if (extremes.length) groups.push({label: 'Most extreme scores', items: extremes})
+
+      return {groups, captions}
+    }
+  },
+
+  watch: {
+    // Mirror parent-driven selections (histogram/heatmap/URL) into the local model, but never clobber the
+    // text the user is actively typing.
+    modelValue: {
+      handler(value: DisplayVariant | null) {
+        if (typeof this.localSelection !== 'string' && value !== this.localSelection) {
+          this.localSelection = value
+        }
+      },
+      immediate: true
+    },
+    // Surface only a real selection (an option object) or a clear (null); ignore the transient typed
+    // string PrimeVue writes while searching — which is how typing-over a selection unlocks the views.
+    localSelection(value: DisplayVariant | string | null) {
+      const next = typeof value === 'object' ? value : null
+      if (next !== this.modelValue) {
+        this.$emit('update:modelValue', next)
+      }
+    },
+    // Keep the empty-box suggestions live: the clinical group joins asynchronously once controls associate
+    // (and the intrinsic groups settle as variants load), so re-push the groups whenever they change while
+    // the box is empty. `@complete` only fires on open/keystroke, which would otherwise miss the pop-in.
+    notableData() {
+      if (!this.variantSearchQuery) {
+        this.variantSearchSuggestions = this.notableData.groups
+      }
+    },
+    // Warm the two heavy computeds once the variants land — the notables (built on first dropdown-open) and
+    // the coordinate haystack (built on first keystroke) — so those first interactions are instant instead
+    // of paying an O(n) build synchronously. Deferred to idle to keep it off the initial render path, which
+    // is why these stay lazy computeds rather than eager fields.
+    variants: {
+      handler(list: DisplayVariant[]) {
+        if (!list.length) return
+        const warm = () => {
+          void this.notableData
+          void this.variantSearchIndex
+        }
+        if (typeof window !== 'undefined' && 'requestIdleCallback' in window) {
+          window.requestIdleCallback(warm)
+        } else {
+          setTimeout(warm, 200)
+        }
+      },
+      immediate: true
+    }
+  },
+
+  methods: {
+    // The precomputed caption for a notable row (empty-box state), keyed by URN; null for search-result
+    // rows, which show the variant's annotation instead.
+    notableCaption(variant: DisplayVariant): NotableCaption | null {
+      return this.notableData.captions.get(variant.variantUrn) ?? null
+    },
+
+    // The leading dot color. On the empty box it's the notable caption's; while searching it's the
+    // ClinVar classification color for control hits (the "interesting" flag) and undefined otherwise.
+    optionDotColor(variant: DisplayVariant): string | undefined {
+      return this.variantSearchQuery ? this.clinicalColor(variant) : this.notableCaption(variant)?.color
+    },
+
+    // Classification color for a ClinVar control (red pathogenic, blue benign, grey otherwise), echoing
+    // the histogram's control colors; undefined when the variant isn't a control.
+    clinicalColor(variant: DisplayVariant): string | undefined {
+      const control = variant.control
+      // Hard-discordant placements carry no representative call — narrow before reading one.
+      const significance = control && control.discordance !== 'hard' ? control[DEFAULT_CLNSIG_FIELD] : undefined
+      if (!significance) return undefined
+      if (PATHOGENIC_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS.includes(significance)) return '#e41a1c'
+      if (BENIGN_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS.includes(significance)) return '#377eb8'
+      return '#999999'
+    },
+
+    // The ClinVar call + star rating for a control variant — the search-result dot's hover title; null
+    // when the variant isn't a control (or controls haven't been fetched yet).
+    clinicalTag(variant: DisplayVariant): string | null {
+      const control = variant.control
+      // Hard-discordant placements carry no representative call — narrow before reading one.
+      if (!control || control.discordance === 'hard') return null
+      const significance = control[DEFAULT_CLNSIG_FIELD]
+      if (!significance) return null
+      const stars = CLINVAR_REVIEW_STATUS_STARS[control[DEFAULT_CLNREVSTAT_FIELD] ?? ''] ?? 0
+      return stars ? `${significance} · ${stars}★` : significance
+    },
+
+    // Caption for a clinical-control notable row: the ClinVar call and star rating, dotted by class.
+    clinicalCaption(variant: DisplayVariant): NotableCaption {
+      return {label: this.clinicalTag(variant) ?? '', color: this.clinicalColor(variant)}
+    },
+
+    // Caption for a most-extreme-scores row: distance from the median in robust (MAD) units. Falls back to
+    // a bare label when the scale is degenerate (MAD 0, so the count is meaningless).
+    scoreCaption(variant: DisplayVariant, spread: {median: number; mad: number}): NotableCaption {
+      const deviations = deviationsFromMedian(variant.score as number, spread)
+      if (deviations == null) return {label: 'Extreme score'}
+      return {label: `${Math.abs(deviations).toFixed(1)} deviations ${deviations < 0 ? 'below' : 'above'} median`}
+    },
+
+    variantSearch(event: {query: string}) {
+      const query = event.query.trim().toLowerCase()
+      this.variantSearchQuery = query
+
+      // Search-and-jump: an empty box shows the notable groups (styled via #option), not the whole set —
+      // far too many to list usefully; browse the full set via the heatmap/histograms. Typing collapses to
+      // a single group of coordinate matches whose label carries the count.
+      if (!query) {
+        this.variantSearchSuggestions = this.notableData.groups
+        return
+      }
+
+      const matches: DisplayVariant[] = []
+      for (const entry of this.variantSearchIndex) {
+        if (entry.haystack.includes(query)) matches.push(entry.variant)
+      }
+      this.variantSearchSuggestions = matches.length
+        ? [
+            {
+              label: `${matches.length.toLocaleString()} of ${this.scoredVariants.length.toLocaleString()} variants match`,
+              items: matches
+            }
+          ]
+        : []
+    },
+
+    clearSelection() {
+      this.localSelection = null
+    },
+
+    // Label for the AutoComplete chip and suggestions. A function (not a materialized field) so it
+    // re-resolves from the current frame — flipping the clinical toggle re-labels reactively. PrimeVue
+    // may hand back the raw typed string before a selection is made, so tolerate that.
+    variantOptionLabel(variant: DisplayVariant | string): string {
+      return typeof variant === 'string' ? variant : this.labelForVariant(variant, this.frame)
+    },
+
+    // The underlying nucleotide coordinate in the current frame, when it differs from the (protein-
+    // preferred) display label — surfaced to disambiguate distinct coding variants that share a protein
+    // label, and as provenance. `getHgvsNt` is coding-preferred (NM_:c.), so a genomic-measured variant
+    // surfaces its coding key — the natural pair of the protein change — rather than the g. coordinate.
+    // Null when the label already is the nucleotide coordinate.
+    variantUnderlyingLabel(variant: DisplayVariant | string): string | null {
+      if (typeof variant === 'string') return null
+      const nt = this.getHgvsNt(variant, this.frame)
+      return nt && nt !== this.variantOptionLabel(variant) ? nt : null
+    }
+  }
+})
+</script>
diff --git a/src/components/screens/ScoreSetView.vue b/src/components/screens/ScoreSetView.vue
index 2b47f6eb..fa298dca 100644
--- a/src/components/screens/ScoreSetView.vue
+++ b/src/components/screens/ScoreSetView.vue
@@ -71,57 +71,20 @@
           class="mave-gradient-bar relative mb-4 overflow-hidden rounded-lg border border-border bg-surface"
         >
           <div class="flex flex-col gap-3 px-4 py-3 tablet:flex-row tablet:items-center">
-            <div class="relative min-w-0 flex-1 mt-2">
-              <MvFloatField label="Search variants">
-                <template #default="{id}">
-                  <AutoComplete
-                    :id="id"
-                    v-model="selectedVariant"
-                    class="w-full"
-                    :delay="300"
-                    dropdown
-                    fluid
-                    :input-style="variantToVisualize ? {paddingRight: '2.25rem'} : undefined"
-                    :option-label="variantOptionLabel"
-                    scroll-height="175px"
-                    select-on-focus
-                    :suggestions="variantSearchSuggestions"
-                    :virtual-scroller-options="{itemSize: 50}"
-                    @complete="variantSearch"
-                  >
-                    <template #option="{option}">
-                      <div class="flex flex-col justify-center leading-tight">
-                        <span>{{ variantOptionLabel(option) }}</span>
-                        <span v-if="variantUnderlyingLabel(option)" class="font-mono text-xs text-text-muted">
-                          {{ variantUnderlyingLabel(option) }}
-                        </span>
-                        <span v-if="frame === 'mapped' && isUnmapped(option)" class="text-xs italic text-text-muted">
-                          Variant could not be mapped
-                        </span>
-                      </div>
-                    </template>
-                    <template #empty>
-                      <div class="p-2.5 text-center text-sm text-text-muted">No matching variants found.</div>
-                    </template>
-                  </AutoComplete>
-                </template>
-              </MvFloatField>
-              <button
-                v-if="variantToVisualize"
-                aria-label="Clear"
-                class="absolute right-12 top-1/2 flex size-5 -translate-y-1/2 cursor-pointer items-center justify-center rounded-full text-text-muted hover:bg-red-50 hover:text-red-600"
-                @click="selectedVariant = null"
-              >
-                <i class="pi pi-times text-[10px]" />
-              </button>
-            </div>
+            <ScoreSetVariantSearch
+              v-model="selectedVariant"
+              class="mt-2"
+              :clinical="clinvarControls"
+              :frame="frame"
+              :variants="variants ?? []"
+            />
             <div class="flex items-center gap-2 text-sm text-text-secondary tablet:ml-auto">
               <span
                 :class="[
                   clinicalMode ? 'text-text-muted' : 'font-semibold text-sage',
                   {'opacity-50': coordinateSwitching}
                 ]"
-                >Raw variants</span
+                >Submitted variants</span
               >
               <!-- Wrapper so the tooltip fires even when the switch is disabled (a disabled control has
                  pointer-events: none and won't trigger a tooltip on itself). Only shown when mapped
@@ -132,7 +95,7 @@
                 :class="{'cursor-not-allowed': !mappedModeAvailable}"
               >
                 <ToggleSwitch
-                  :aria-label="`Click to change to ${clinicalMode ? 'raw data' : 'clinical view'}.`"
+                  :aria-label="`Click to change to ${clinicalMode ? 'submitted data' : 'clinical view'}.`"
                   :disabled="coordinateSwitching || !mappedModeAvailable"
                   :model-value="clinicalMode"
                   @update:model-value="toggleClinicalMode"
@@ -143,7 +106,7 @@
                   clinicalMode ? 'font-semibold text-sage' : 'text-text-muted',
                   {'opacity-50': coordinateSwitching}
                 ]"
-                >Mapped variants</span
+                >Reference variants</span
               >
               <i v-if="coordinateSwitching" class="pi pi-spinner pi-spin text-xs text-sage" />
               <span
@@ -158,6 +121,7 @@
           <VariantDetailPanel
             v-if="variantToVisualize?.variantUrn"
             :key="variantToVisualize.variantUrn"
+            :clinvar-version="clinvarControls.controlVersion"
             :coordinate="variantOptionLabel(variantToVisualize)"
             :flush="true"
             :identify="false"
@@ -196,6 +160,7 @@
             <div class="p-3 tablet:p-5">
               <ScoreSetHistogram
                 ref="distHistogram"
+                :clinical="clinvarControls"
                 :coordinates="frame"
                 :default-histogram="'distribution'"
                 :external-selection="variantToVisualize"
@@ -256,6 +221,7 @@
             <div class="p-3 tablet:p-5">
               <ScoreSetHistogram
                 ref="clinicalHistogram"
+                :clinical="clinvarControls"
                 :coordinates="frame"
                 :default-histogram="'clinical'"
                 :external-selection="variantToVisualize"
@@ -291,29 +257,32 @@
               class="relative z-10 flex flex-wrap items-center justify-between gap-3 border-b border-border-light bg-surface px-4 py-3.5 tablet:px-5"
             >
               <h3 class="mave-section-title">Variant Effect Heatmap</h3>
-              <div class="flex flex-wrap items-center gap-2">
-                <SelectButton
+              <div class="ml-auto flex flex-wrap items-center justify-end gap-2">
+                <Select
                   v-if="heatmapSequenceTypeOptions.length > 1"
-                  :allow-empty="false"
                   :model-value="heatmapSequenceType"
                   option-label="title"
                   option-value="value"
                   :options="heatmapSequenceTypeOptions"
                   size="small"
                   @update:model-value="heatmapSequenceType = $event"
-                />
-                <SelectButton
-                  :allow-empty="false"
+                >
+                  <template #value="{value}">
+                    Sequence: {{ heatmapSequenceTypeOptions.find((o) => o.value === value)?.title ?? value }}
+                  </template>
+                </Select>
+                <Select
                   :model-value="heatmapLayout"
                   option-label="title"
                   option-value="value"
-                  :options="[
-                    {title: 'Normal', value: 'normal'},
-                    {title: 'Compact', value: 'compact'}
-                  ]"
+                  :options="heatmapLayoutOptions"
                   size="small"
                   @update:model-value="heatmapLayout = $event"
-                />
+                >
+                  <template #value="{value}">
+                    Layout: {{ heatmapLayoutOptions.find((o) => o.value === value)?.title ?? value }}
+                  </template>
+                </Select>
                 <PButton
                   v-if="uniprotId != null"
                   icon="pi pi-box"
@@ -383,7 +352,7 @@
 
         <!-- Assay Facts -->
         <div class="mb-4 mave-gradient-bar relative overflow-hidden rounded-lg border border-border bg-white p-5">
-          <MvAssayFactsCard :link-title="false" :score-set="item" />
+          <MvAssayFactsCard :assay-level="assayLevel" :link-title="false" :score-set="item" />
         </div>
 
         <!-- Attribution -->
@@ -491,15 +460,13 @@
 <script lang="ts">
 import _ from 'lodash'
 import {markdownToHtml} from '@/lib/form-helpers'
-import AutoComplete from 'primevue/autocomplete'
 import PButton from 'primevue/button'
 import SplitButton from 'primevue/splitbutton'
-import MvFloatField from '@/components/forms/MvFloatField.vue'
-import SelectButton from 'primevue/selectbutton'
+import Select from 'primevue/select'
 import ToggleSwitch from 'primevue/toggleswitch'
 import PrimeDialog from 'primevue/dialog'
 import Drawer from 'primevue/drawer'
-import {ref} from 'vue'
+import {ref, toRef} from 'vue'
 import {useHead} from '@unhead/vue'
 
 import CalibrationEditor from '@/components/calibration/CalibrationEditor.vue'
@@ -522,6 +489,7 @@ import ScoreSetDownloads from '@/components/score-set/ScoreSetDownloads.vue'
 import ScoreSetMetadataCard from '@/components/score-set/ScoreSetMetadataCard.vue'
 import ScoreSetHeatmap from '@/components/score-set/ScoreSetHeatmap.vue'
 import ScoreSetHistogram from '@/components/score-set/ScoreSetHistogram.vue'
+import ScoreSetVariantSearch from '@/components/score-set/ScoreSetVariantSearch.vue'
 import MvVariantPreview from '@/components/common/MvVariantPreview.vue'
 import VariantDetailPanel from '@/components/variant/VariantDetailPanel.vue'
 import ScoreSetProcessingStatus from '@/components/score-set/ScoreSetProcessingStatus.vue'
@@ -532,13 +500,15 @@ import useItem from '@/composition/item.ts'
 import useRemoteData from '@/composition/remote-data'
 import {useDatasetPermissions} from '@/composables/use-dataset-permissions'
 import {useCalibrationDialog} from '@/composables/use-calibration-dialog'
+import {useClinvarControls} from '@/composables/use-clinvar-controls'
 import {useChartExport, type ChartExportFns} from '@/composables/use-chart-export'
-import {useVariantCoordinates, type CoordinateFrame} from '@/composables/use-variant-coordinates'
+import {useVariantCoordinates, type CoordinateFrame, type SequenceLevel} from '@/composables/use-variant-coordinates'
 import config from '@/config'
 import {hasPathogenicityCalibrations, hasFunctionalCalibrations} from '@/lib/calibrations'
 import {getScoreSetShortName} from '@/lib/score-sets'
+import {dominantAssayLevel} from '@/lib/measurement-types'
 import {type DisplayVariant} from '@/lib/variants'
-import {deleteScoreSet, publishScoreSet, getScoreSetClinicalControlOptions, leanScoreSetVariantsUrl} from '@/api/mavedb'
+import {deleteScoreSet, publishScoreSet, getScoreSetClinvarControlOptions, leanScoreSetVariantsUrl} from '@/api/mavedb'
 import {components} from '@/schema/openapi'
 import MvLoader from '@/components/common/MvLoader.vue'
 import MvEmptyState from '@/components/common/MvEmptyState.vue'
@@ -550,12 +520,10 @@ export default {
   name: 'ScoreSetView',
 
   components: {
-    AutoComplete,
     CalibrationEditor,
     CalibrationTable,
     Drawer,
     MvEmailPrompt,
-    MvFloatField,
     MvItemNotFound,
     MvAssayFactsCard,
     MvCollectionStrip,
@@ -578,10 +546,11 @@ export default {
     ScoreSetDownloads,
     ScoreSetHeatmap,
     ScoreSetHistogram,
+    ScoreSetVariantSearch,
     ScoreSetMetadataCard,
     ScoreSetProcessingStatus,
     ScoreSetVisualizer,
-    SelectButton,
+    Select,
     ToggleSwitch,
     VariantDetailPanel
   },
@@ -596,10 +565,14 @@ export default {
   setup(props) {
     const head = useHead()
     const variantsRemoteData = useRemoteData()
-    const variantSearchSuggestions = ref<DisplayVariant[]>([])
     const selectedCalibrations = ref<(string | null)[]>([null, null])
     const urnRef = ref(props.itemId)
 
+    // The score set's variants. Held in setup (not data) so the shared clinical-controls store can watch
+    // them and associate `variant.control` in one place for every consumer (both histograms + the search).
+    const variants = ref<DisplayVariant[] | null>(null)
+    const clinvarControls = useClinvarControls(toRef(props, 'itemId'), variants)
+
     const {permissions} = useDatasetPermissions('score-set', urnRef, ACTIONS)
 
     const distHistogramExportFn = ref<ChartExportFns | null>(null)
@@ -614,6 +587,8 @@ export default {
       config,
       permissions,
       selectedCalibrations,
+      variants,
+      clinvarControls,
 
       ...useCalibrationDialog(),
       ...useItem<ScoreSet>({itemTypeName: 'scoreSet'}),
@@ -623,7 +598,6 @@ export default {
       variantsDataStatus: variantsRemoteData.remoteDataStatus,
       setVariantsDataUrl: variantsRemoteData.setDataUrl,
       ensureVariantsDataLoaded: variantsRemoteData.ensureDataLoaded,
-      variantSearchSuggestions,
 
       distHistogramExportFn,
       clinicalHistogramExportFn,
@@ -643,13 +617,12 @@ export default {
   data: () => ({
     clinicalMode: true,
     coordinateSwitching: false,
-    variants: null as DisplayVariant[] | null,
     showHeatmap: true,
     isScoreSetVisualizerVisible: false,
     hasClinicalVariants: false,
     heatmapExists: false,
     selectedVariant: null as DisplayVariant | null,
-    heatmapSequenceType: 'protein' as 'dna' | 'protein',
+    heatmapSequenceType: 'protein' as SequenceLevel,
     heatmapLayout: 'normal' as 'normal' | 'compact',
     syncingBinSelection: false
   }),
@@ -657,12 +630,12 @@ export default {
   computed: {
     clinicalModeHelpText() {
       if (!this.mappedModeAvailable) {
-        return 'This score set has no mapped variants, so only raw (submitted) coordinates are available.'
+        return 'This score set has no mapped variants, so only submitted coordinates are available.'
       }
       if (this.item?.targetGenes?.[0]?.targetSequence) {
-        return 'In clinical mode, mapped variant coordinates are used when available, and start- and stop-loss codons are omitted because this score set was produced using a synthetic target sequence.'
+        return 'In clinical mode, reference coordinates are used when available, and start- and stop-loss codons are omitted because this score set was produced using a synthetic target sequence.'
       }
-      return 'In clinical mode, mapped variant coordinates are used when available. For experiments with endogenously-edited targets, raw and mapped data are usually identical.'
+      return 'In clinical mode, reference coordinates are used when available. For experiments with endogenously-edited targets, submitted and reference data are usually identical.'
     },
     contributors() {
       const creatorId = this.item?.createdBy?.orcidId
@@ -670,21 +643,32 @@ export default {
         .filter((c) => c.orcidId !== creatorId)
         .sort((a, b) => (a.familyName ?? '').localeCompare(b.familyName ?? ''))
     },
-    // The coordinate frame the page is displaying in: clinical mode reads the mapped (reference)
-    // numbering, non-clinical the raw (submitted/target) numbering.
+    // The coordinate frame the page is displaying in: clinical mode reads the reference numbering,
+    // non-clinical the submitted (target) numbering.
     frame(): CoordinateFrame {
-      return this.clinicalMode ? 'mapped' : 'raw'
+      return this.clinicalMode ? 'reference' : 'submitted'
     },
-    // Whether the mapped frame has anything to show — some variant carries a mapped coordinate at some
-    // level. When false the score set has no mapped data (unmapped or unmappable), so mapped mode is
-    // disabled and the page makes only the raw frame available.
+    // Whether the reference frame has anything to show — some variant carries a reference coordinate at
+    // some level. When false the score set has no mapped data (unmapped or unmappable), so reference mode
+    // is disabled and the page makes only the submitted frame available.
     mappedModeAvailable(): boolean {
-      return !!this.variants?.length && this.sequenceTypeOptions(this.variants, 'mapped').length > 0
+      return !!this.variants?.length && this.sequenceTypeOptions(this.variants, 'reference').length > 0
     },
     heatmapSequenceTypeOptions(): Array<{title: string; value: string}> {
       if (!this.variants?.length) return []
       return this.sequenceTypeOptions(this.variants, this.frame)
     },
+    heatmapLayoutOptions(): Array<{title: string; value: string}> {
+      return [
+        {title: 'Normal', value: 'normal'},
+        {title: 'Compact', value: 'compact'}
+      ]
+    },
+    // The level this score set's variants were assayed at (protein / cDNA / genomic), derived from the
+    // loaded variants since it isn't carried on the score-set metadata itself.
+    assayLevel(): SequenceLevel | null {
+      return this.variants?.length ? dominantAssayLevel(this.variants.map((v) => v.assayLevel)) : null
+    },
     hasCounts() {
       const allCountColumns = this.item?.datasetColumns?.countColumns ?? []
       return allCountColumns.filter((col) => col !== 'accession').length > 0
@@ -747,26 +731,36 @@ export default {
         ? _.get(this.item?.targetGenes, [0, 'uniprotIdFromMappedMetadata'], null)
         : null
     },
-    variantToVisualize() {
-      return typeof this.selectedVariant === 'object' ? this.selectedVariant : null
+    // The variant to drive the detail panel / histograms / heatmap with — the current selection. The
+    // search picker only ever emits an actual variant or null, so this is just the selection itself.
+    variantToVisualize(): DisplayVariant | null {
+      return this.selectedVariant
     }
   },
 
   watch: {
     item(newValue) {
       this.head.patch({title: newValue ? getScoreSetShortName(newValue) : undefined})
-      if (newValue) this.checkClinicalVariants()
+      if (newValue) {
+        this.checkClinicalVariants()
+        // Metadata is in and the shell can render, so now kick off the heavy variants load. The visuals
+        // area shows its own "variants loading" state while this resolves.
+        let variantsUrl = null
+        if (this.itemType?.restCollectionName && this.itemId) {
+          variantsUrl = leanScoreSetVariantsUrl(this.itemId)
+        }
+        this.setVariantsDataUrl(variantsUrl)
+        this.ensureVariantsDataLoaded()
+      }
     },
     itemId: {
       handler(newValue, oldValue) {
         if (newValue !== oldValue) {
+          // Fetch ONLY the score-set metadata here. The variants payload is large and, fired concurrently,
+          // starves the fast metadata request on the server — which keeps the full-page "loading" state up
+          // the whole time. Deferring variants to the `item` watcher lets the shell render as soon as
+          // metadata lands (~60ms), then the variants load behind it.
           this.setItemId(newValue)
-          let variantsUrl = null
-          if (this.itemType?.restCollectionName && this.itemId) {
-            variantsUrl = leanScoreSetVariantsUrl(this.itemId)
-          }
-          this.setVariantsDataUrl(variantsUrl)
-          this.ensureVariantsDataLoaded()
         }
       },
       immediate: true
@@ -833,7 +827,7 @@ export default {
     async checkClinicalVariants() {
       if (!this.item) return
       try {
-        await getScoreSetClinicalControlOptions(this.item.urn)
+        await getScoreSetClinvarControlOptions(this.item.urn)
         this.hasClinicalVariants = true
       } catch {
         // No clinical variants available
@@ -897,36 +891,7 @@ export default {
       this.heatmapExportFn = fns
     },
 
-    variantSearch(event: {query: string}) {
-      const query = event.query.toLowerCase()
-      const matches: DisplayVariant[] = []
-
-      for (const variant of this.variants || []) {
-        if (!_.isNumber(variant.score)) continue
-        // Empty query lists every scored variant; otherwise keep those whose coordinate strings match.
-        if (!query || this.variantMatchesQuery(variant, query)) {
-          matches.push(variant)
-        }
-      }
-      this.variantSearchSuggestions = matches
-    },
-
-    // Whether any of a variant's coordinate strings contains the query. Matches the current frame's
-    // coordinates plus the submitted (target-frame) strings, so a search finds the submitted HGVS the
-    // label falls back to for an unmapped variant — not just the mapped representation.
-    variantMatchesQuery(variant: DisplayVariant, query: string): boolean {
-      const candidates = [
-        this.getHgvsNt(variant, this.frame),
-        this.getHgvsPro(variant, this.frame),
-        variant.hgvsNt?.hgvs,
-        variant.hgvsPro?.hgvs,
-        variant.hgvsSplice?.hgvs,
-        variant.variantUrn
-      ]
-      return candidates.some((candidate) => candidate != null && candidate.toLowerCase().includes(query))
-    },
-
-    // Label for the AutoComplete chip and suggestions. A function (not a materialized field) so it
+    // Label for the selected-variant detail panel. A function (not a materialized field) so it
     // re-resolves from the current frame — flipping the clinical toggle re-labels reactively. PrimeVue
     // may hand back the raw typed string before a selection is made, so tolerate that.
     variantOptionLabel(variant: DisplayVariant | string): string {
@@ -934,8 +899,10 @@ export default {
     },
 
     // The underlying nucleotide coordinate in the current frame, when it differs from the (protein-
-    // preferred) display label — surfaced to disambiguate distinct coding variants that share a
-    // protein label, and as provenance. Null when the label already is the nucleotide coordinate.
+    // preferred) display label — surfaced to disambiguate distinct coding variants that share a protein
+    // label, and as provenance. `getHgvsNt` is coding-preferred (NM_:c.), so a genomic-measured variant
+    // surfaces its coding key — the natural pair of the protein change — rather than the g. coordinate.
+    // Null when the label already is the nucleotide coordinate.
     variantUnderlyingLabel(variant: DisplayVariant | string): string | null {
       if (typeof variant === 'string') return null
       const nt = this.getHgvsNt(variant, this.frame)
diff --git a/src/components/screens/SearchVariantsScreen.vue b/src/components/screens/SearchVariantsScreen.vue
index 07b2eaa7..cd01e80a 100644
--- a/src/components/screens/SearchVariantsScreen.vue
+++ b/src/components/screens/SearchVariantsScreen.vue
@@ -371,129 +371,50 @@
           </MvCollapsible>
         </div>
 
-        <!-- Card body: measurements -->
+        <!-- Card body: the searched change first, then the rest of its equivalence class, one row per
+             measurement so the whole class stays visible. -->
         <div
           v-if="
             allele.variantsStatus === 'Loaded' &&
-            (allele.variants.nucleotide.length > 0 ||
-              allele.variants.protein.length > 0 ||
-              allele.variants.associatedNucleotide.length > 0)
+            (searchedMeasurements(allele).length || relatedEvidence(allele).length)
           "
         >
-          <!-- Nucleotide measurements -->
-          <div v-if="allele.variants.nucleotide.length > 0" aria-label="Nucleotide level assays" role="group">
-            <div class="flex items-center gap-2 px-5 pt-3.5 pb-1">
-              <span class="text-sm font-bold uppercase tracking-wide text-gray-500">Nucleotide level assays</span>
+          <!-- Section 1: exactly what was searched, measured directly. -->
+          <div v-if="searchedMeasurements(allele).length" aria-label="Directly measured" role="group">
+            <div class="flex items-center gap-2 px-5 pt-3.5 pb-0.5">
+              <span class="text-sm font-bold uppercase tracking-wide text-gray-500">{{ searchedHeading(allele) }}</span>
               <span class="rounded-full bg-sage px-3 py-px text-[0.6875rem] font-semibold text-white">{{
-                allele.variants.nucleotide.length
+                searchedMeasurements(allele).length
               }}</span>
             </div>
-            <MvScoreSetRow
-              v-for="(variant, idx) in nucleotideScoreSetListIsExpanded[alleleIdx]
-                ? allele.variants.nucleotide
-                : allele.variants.nucleotide.slice(0, defaultNumScoreSetsToShow)"
-              :key="variant.urn ?? idx"
-              class="pl-8"
-              :score-set="variant.scoreSet"
-              :show-description="false"
-              :show-meta="false"
+            <MvMeasurementRow
+              v-for="(m, idx) in searchedMeasurements(allele)"
+              :key="m.variantUrn ?? idx"
+              class="pl-8 pr-5"
+              :measurement="m"
             />
-            <button
-              v-if="allele.variants.nucleotide.length > defaultNumScoreSetsToShow"
-              :aria-expanded="!!nucleotideScoreSetListIsExpanded[alleleIdx]"
-              class="mb-2 ml-5 mt-1 cursor-pointer border-none bg-transparent text-sm font-semibold text-link"
-              @click="nucleotideScoreSetListIsExpanded[alleleIdx] = !nucleotideScoreSetListIsExpanded[alleleIdx]"
-            >
-              {{
-                nucleotideScoreSetListIsExpanded[alleleIdx]
-                  ? 'Show less'
-                  : `Show ${allele.variants.nucleotide.length - defaultNumScoreSetsToShow} more`
-              }}
-            </button>
           </div>
 
           <div
-            v-if="allele.variants.nucleotide.length > 0 && allele.variants.protein.length > 0"
+            v-if="searchedMeasurements(allele).length && relatedEvidence(allele).length"
             class="mx-5 h-px bg-gray-100"
           ></div>
 
-          <!-- Protein measurements -->
-          <div v-if="allele.variants.protein.length > 0" aria-label="Protein level assays" role="group">
-            <div class="flex items-center gap-2 px-5 pt-3.5 pb-1">
-              <span class="text-sm font-bold uppercase tracking-wide text-gray-500">Protein level assays</span>
+          <!-- Section 2: the same functional change measured elsewhere, one row per measurement. -->
+          <div v-if="relatedEvidence(allele).length" :aria-label="relatedHeading(allele)" role="group">
+            <div class="flex items-center gap-2 px-5 pt-3.5 pb-0.5">
+              <span class="text-sm font-bold uppercase tracking-wide text-gray-500">{{ relatedHeading(allele) }}</span>
               <span class="rounded-full bg-sage px-3 py-px text-[0.6875rem] font-semibold text-white">{{
-                allele.variants.protein.length
-              }}</span>
-            </div>
-            <MvScoreSetRow
-              v-for="(variant, idx) in proteinScoreSetListIsExpanded[alleleIdx]
-                ? allele.variants.protein
-                : allele.variants.protein.slice(0, defaultNumScoreSetsToShow)"
-              :key="variant.urn ?? idx"
-              class="pl-8"
-              :score-set="variant.scoreSet"
-              :show-description="false"
-              :show-meta="false"
-            />
-            <button
-              v-if="allele.variants.protein.length > defaultNumScoreSetsToShow"
-              :aria-expanded="!!proteinScoreSetListIsExpanded[alleleIdx]"
-              class="mb-2 ml-5 mt-1 cursor-pointer border-none bg-transparent text-sm font-semibold text-link"
-              @click="proteinScoreSetListIsExpanded[alleleIdx] = !proteinScoreSetListIsExpanded[alleleIdx]"
-            >
-              {{
-                proteinScoreSetListIsExpanded[alleleIdx]
-                  ? 'Show less'
-                  : `Show ${allele.variants.protein.length - defaultNumScoreSetsToShow} more`
-              }}
-            </button>
-          </div>
-
-          <div
-            v-if="
-              allele.variants.associatedNucleotide.length > 0 &&
-              (allele.variants.nucleotide.length > 0 || allele.variants.protein.length > 0)
-            "
-            class="mx-5 h-px bg-gray-100"
-          ></div>
-
-          <!-- Associated nucleotide measurements -->
-          <div
-            v-if="allele.variants.associatedNucleotide.length > 0"
-            aria-label="Associated nucleotide assays"
-            role="group"
-          >
-            <div class="flex items-center gap-2 px-5 pt-3.5 pb-1">
-              <span class="text-xs font-bold uppercase tracking-wide text-gray-500">Associated nucleotide</span>
-              <span class="rounded-full bg-sage px-2 py-px text-[0.6875rem] font-semibold text-white">{{
-                allele.variants.associatedNucleotide.length
+                relatedEvidence(allele).length
               }}</span>
             </div>
-            <MvScoreSetRow
-              v-for="(variant, idx) in associatedNucleotideScoreSetListIsExpanded[alleleIdx]
-                ? allele.variants.associatedNucleotide
-                : allele.variants.associatedNucleotide.slice(0, defaultNumScoreSetsToShow)"
-              :key="variant.urn ?? idx"
-              class="pl-8"
-              :score-set="variant.scoreSet"
-              :show-description="false"
-              :show-meta="false"
+            <div class="px-5 pb-1.5 text-xs italic text-gray-400">{{ relatedDescription(allele) }}</div>
+            <MvMeasurementRow
+              v-for="(m, idx) in relatedEvidence(allele)"
+              :key="m.variantUrn ?? idx"
+              class="pl-8 pr-5"
+              :measurement="m"
             />
-            <button
-              v-if="allele.variants.associatedNucleotide.length > defaultNumScoreSetsToShow"
-              :aria-expanded="!!associatedNucleotideScoreSetListIsExpanded[alleleIdx]"
-              class="mb-2 ml-5 mt-1 cursor-pointer border-none bg-transparent text-sm font-semibold text-link"
-              @click="
-                associatedNucleotideScoreSetListIsExpanded[alleleIdx] =
-                  !associatedNucleotideScoreSetListIsExpanded[alleleIdx]
-              "
-            >
-              {{
-                associatedNucleotideScoreSetListIsExpanded[alleleIdx]
-                  ? 'Show less'
-                  : `Show ${allele.variants.associatedNucleotide.length - defaultNumScoreSetsToShow} more`
-              }}
-            </button>
           </div>
         </div>
 
@@ -670,7 +591,7 @@ import {useToast} from 'primevue/usetoast'
 import {useHead} from '@unhead/vue'
 
 import MvCollapsible from '@/components/common/MvCollapsible.vue'
-import MvScoreSetRow from '@/components/common/MvScoreSetRow.vue'
+import MvMeasurementRow from '@/components/search/MvMeasurementRow.vue'
 import MvLayout from '@/components/layout/MvLayout.vue'
 import {
   type AlleleResult,
@@ -680,7 +601,8 @@ import {
   vrsDigestRegex,
   scoreSetUrnFromVariantUrn,
   extractIdFromUrl,
-  createAlleleResult
+  createAlleleResult,
+  mergeAlleleSpellings
 } from '@/lib/mavemd'
 import {getTargetGeneName} from '@/lib/target-genes'
 import {components} from '@/schema/openapi'
@@ -696,14 +618,13 @@ import {
   ALLELE_OPTIONS
 } from '@/data/mavemd'
 import {getAlleleByCaId, getAlleleByHgvs, getAlleleByDbSnp, getAlleleByClinVar, getGeneBySymbol} from '@/api/clingen'
-import {getCollection, getErrorResponse, lookupVariantsByClingenId} from '@/api/mavedb'
-import {lookupVariantsByVrsDigest} from '@/api/mavedb/variants'
+import {getCollection, getErrorResponse} from '@/api/mavedb'
+import {getAlleleMeasurements, lookupVariantsByVrsDigest} from '@/api/mavedb/variants'
 import {useEntityCache} from '@/composables/entity-cache'
 import MvLoader from '@/components/common/MvLoader.vue'
 
-const SCORE_SETS_TO_SHOW = 5
-
 type ScoreSet = components['schemas']['ScoreSet']
+type AlleleMeasurement = components['schemas']['AlleleMeasurement']
 type TargetGene = components['schemas']['TargetGene']
 
 export default defineComponent({
@@ -713,10 +634,10 @@ export default defineComponent({
     MvEntityLink,
     InputText,
     MvCollapsible,
+    MvMeasurementRow,
     MvLayout,
     Message,
     MvLoader,
-    MvScoreSetRow,
     PSelect
   },
 
@@ -748,10 +669,6 @@ export default defineComponent({
       inputAlternateAllele: null as string | null,
       allAlleleOptions: ALLELE_OPTIONS,
       alleles: [] as AlleleResult[],
-      nucleotideScoreSetListIsExpanded: [] as Array<boolean>,
-      proteinScoreSetListIsExpanded: [] as Array<boolean>,
-      associatedNucleotideScoreSetListIsExpanded: [] as Array<boolean>,
-      defaultNumScoreSetsToShow: SCORE_SETS_TO_SHOW,
       guideExpanded: false,
       maveMdScoreSetUrns: [] as string[],
       maveMdScoreSets: {} as {[urn: string]: ScoreSet | undefined},
@@ -809,13 +726,6 @@ export default defineComponent({
   },
 
   watch: {
-    alleles: {
-      handler: function (newValue) {
-        this.nucleotideScoreSetListIsExpanded = newValue.map(() => false)
-        this.proteinScoreSetListIsExpanded = newValue.map(() => false)
-        this.associatedNucleotideScoreSetListIsExpanded = newValue.map(() => false)
-      }
-    },
     searchType: {
       handler(newVal, oldVal) {
         if (newVal !== oldVal && this.defaultSearchVisible) {
@@ -1048,7 +958,11 @@ export default defineComponent({
       this.loading = false
       await this.searchVariants()
     },
-    fetchDefaultSearchResults: async function (searchString: string, maneStatus: string | null = null, forcedSearchType?: string) {
+    fetchDefaultSearchResults: async function (
+      searchString: string,
+      maneStatus: string | null = null,
+      forcedSearchType?: string
+    ) {
       const searchType = forcedSearchType ?? this.searchType
       let searchStr = searchString.trim()
 
@@ -1130,7 +1044,7 @@ export default defineComponent({
                 transcriptAlleles: [],
                 maneCoordinates: [],
                 variantsStatus: 'Loaded',
-                variants: {nucleotide: [], protein: [], associatedNucleotide: []}
+                variants: {direct: [], proteinConsequence: [], nucleotideEncoding: []}
               })
             }
           }
@@ -1166,11 +1080,16 @@ export default defineComponent({
               if (searchType !== 'hgvs' || aminoAcidAlleles[i].hgvs?.includes(searchString)) {
                 const transcripts = aminoAcidAlleles[i]?.matchingRegisteredTranscripts || []
                 if (transcripts.length > 0) {
+                  // Policy: a protein change is ONE result, not one per transcript spelling. Anchor the card
+                  // on the PA (its equivalence-class query returns the protein-level evidence directly) and
+                  // merge every registered transcript's coordinates onto it so all spellings are listed.
+                  const card = createAlleleResult(result, maneStatus)
                   for (let j = 0; j < transcripts.length; j++) {
                     const associatedId = extractIdFromUrl(transcripts[j]?.['@id'])
-                    const associatedData = await getAlleleByCaId(associatedId!)
-                    this.alleles.push(createAlleleResult(associatedData, maneStatus))
+                    if (!associatedId) continue
+                    mergeAlleleSpellings(card, createAlleleResult(await getAlleleByCaId(associatedId), maneStatus))
                   }
+                  this.alleles.push(card)
                 } else {
                   const bareAllele = createAlleleResult(result, null)
                   bareAllele.canonicalAlleleName = searchStr
@@ -1199,58 +1118,77 @@ export default defineComponent({
         })
       }
     },
+    // ── Result composition ────────────────────────────────────
+    // Section 1: the searched change itself, measured directly (nucleotide for a CA, protein for a PA).
+    searchedMeasurements(allele: AlleleResult): AlleleMeasurement[] {
+      return allele.variants.direct
+    },
+    searchedHeading(allele: AlleleResult): string {
+      return allele.clingenAlleleId?.startsWith('PA')
+        ? 'Searched · measured directly (protein)'
+        : 'Searched · measured directly (nucleotide)'
+    },
+    // Section 2: the rest of the equivalence class (protein consequence + sibling encodings), one row per
+    // measurement so every representation stays visible.
+    relatedEvidence(allele: AlleleResult): AlleleMeasurement[] {
+      return [...allele.variants.proteinConsequence, ...allele.variants.nucleotideEncoding]
+    },
+    relatedHeading(allele: AlleleResult): string {
+      if (allele.clingenAlleleId?.startsWith('PA')) return 'Nucleotide-level evidence'
+      const label = this.proteinChangeLabel(allele)
+      return label ? `Same protein change (${label})` : 'Same protein change'
+    },
+    relatedDescription(allele: AlleleResult): string {
+      return allele.clingenAlleleId?.startsWith('PA')
+        ? 'DNA variants that produce this protein change'
+        : "Other studies that measured this variant's protein consequence"
+    },
+    // The consequence's protein HGVS, taken from any protein-level measurement in the class (for the heading).
+    proteinChangeLabel(allele: AlleleResult): string | null {
+      const proteinMeasurement = [...allele.variants.proteinConsequence, ...allele.variants.direct].find(
+        (m) => m.assayLevel === 'protein'
+      )
+      return proteinMeasurement?.assayLevelHgvs || proteinMeasurement?.submittedHgvs || null
+    },
     searchVariants: async function () {
       for (const allele of this.alleles) {
         const caId = allele.clingenAlleleId
         if (!caId) continue
         allele.variantsStatus = 'Loading'
         try {
-          const data = await lookupVariantsByClingenId([caId])
+          // A nucleotide query widens to its protein consequence's sibling nt changes (search discovery);
+          // a protein query already returns every encoding, so the flag is a no-op there.
+          const measurements = await getAlleleMeasurements(caId, {includeNucleotideSiblings: !caId.startsWith('PA')})
 
-          if (caId.startsWith('CA')) {
-            allele.variants.nucleotide = data[0]?.exactMatch?.variantEffectMeasurements || []
-            allele.variants.protein = (data[0]?.equivalentAa || []).flatMap(
-              (entry) => entry.variantEffectMeasurements || []
-            )
-            allele.variants.associatedNucleotide = (data[0]?.equivalentNt || []).flatMap(
-              (entry) => entry.variantEffectMeasurements || []
-            )
-          } else if (caId.startsWith('PA')) {
-            allele.variants.protein = data[0]?.exactMatch?.variantEffectMeasurements || []
-            allele.variants.nucleotide = (data[0]?.equivalentNt || []).flatMap(
-              (entry) => entry.variantEffectMeasurements || []
-            )
+          // Bucket each measurement by the API's relationship directly — the display labels (below) interpret
+          // each bucket for the searched level. Variant-level: every measurement is its own row (no score-set
+          // dedup), so the whole equivalence class stays visible even when one screen assayed many of it.
+          const buckets: AlleleResult['variants'] = {direct: [], proteinConsequence: [], nucleotideEncoding: []}
+          for (const m of measurements) {
+            const bucket =
+              m.relationship === 'direct'
+                ? 'direct'
+                : m.relationship === 'protein_consequence'
+                  ? 'proteinConsequence'
+                  : 'nucleotideEncoding'
+            buckets[bucket].push(m)
           }
+          allele.variants = buckets
           allele.variantsStatus = 'Loaded'
         } catch (error: unknown) {
-          allele.variants = {nucleotide: [], protein: [], associatedNucleotide: []}
+          allele.variants = {direct: [], proteinConsequence: [], nucleotideEncoding: []}
           console.log('Error while loading MaveDB search results for variant', error)
+          allele.variantsStatus = 'Error'
           const {status} = getErrorResponse(error)
-          if (status === 404) {
-            allele.variantsStatus = 'Loaded'
-            this.toast.add({
-              severity: 'info',
-              summary: 'No results found',
-              detail: 'No variants match the provided search criteria.',
-              life: 10000
-            })
-          } else if (status >= 500) {
-            allele.variantsStatus = 'Error'
-            this.toast.add({
-              severity: 'error',
-              summary: 'Server Error',
-              detail: 'The server encountered an unexpected error. Please try again later.',
-              life: 10000
-            })
-          } else {
-            allele.variantsStatus = 'Error'
-            this.toast.add({
-              severity: 'error',
-              summary: 'Error fetching results',
-              detail: 'An error occurred while fetching MaveDB variants.',
-              life: 10000
-            })
-          }
+          this.toast.add({
+            severity: 'error',
+            summary: status >= 500 ? 'Server Error' : 'Error fetching results',
+            detail:
+              status >= 500
+                ? 'The server encountered an unexpected error. Please try again later.'
+                : 'An error occurred while fetching MaveDB variants.',
+            life: 10000
+          })
         }
       }
     },
diff --git a/src/components/search/MvMeasurementRow.vue b/src/components/search/MvMeasurementRow.vue
new file mode 100644
index 00000000..ec37cf3d
--- /dev/null
+++ b/src/components/search/MvMeasurementRow.vue
@@ -0,0 +1,57 @@
+<template>
+  <div class="flex flex-wrap items-baseline gap-x-3 gap-y-0.5 border-b border-gray-50 py-1.5 text-sm last:border-b-0">
+    <span
+      class="inline-block rounded-sm px-1.5 py-0.5 text-[10px] font-semibold uppercase tracking-[0.3px]"
+      :class="levelClass"
+      >{{ levelLabel }}</span
+    >
+    <span class="font-mono text-xs-plus font-semibold text-gray-700">{{ hgvs }}</span>
+    <span v-if="measurement.score != null" class="text-xs-minus text-gray-500"
+      >score <strong class="font-mono text-gray-700">{{ measurement.score.toPrecision(4) }}</strong></span
+    >
+    <MvClassificationTag v-if="classification" :classification="classification" />
+    <router-link
+      v-if="showScoreSet"
+      class="ml-auto max-w-[45%] truncate text-xs-minus text-link hover:underline"
+      :title="measurement.scoreSetTitle"
+      :to="{name: 'scoreSet', params: {urn: measurement.scoreSetUrn}}"
+      >{{ measurement.scoreSetTitle }}</router-link
+    >
+  </div>
+</template>
+
+<script lang="ts">
+import {defineComponent, type PropType} from 'vue'
+
+import MvClassificationTag from '@/components/common/MvClassificationTag.vue'
+import {ASSAY_LEVEL_LABELS, LEVEL_BUCKET_CLASSES, assayLevelBucket} from '@/lib/measurement-types'
+import type {components} from '@/schema/openapi'
+
+type AlleleMeasurement = components['schemas']['AlleleMeasurement']
+
+/** One compact line for a single measurement: level badge, the specific change (HGVS), its score and
+ * functional call, and (unless nested under a score-set heading) a link to the score set that produced it. */
+export default defineComponent({
+  name: 'MvMeasurementRow',
+  components: {MvClassificationTag},
+  props: {
+    measurement: {type: Object as PropType<AlleleMeasurement>, required: true},
+    // Hide the score-set link when the row is already nested under its score set's heading.
+    showScoreSet: {type: Boolean, default: true}
+  },
+  computed: {
+    hgvs(): string {
+      return this.measurement.assayLevelHgvs || this.measurement.submittedHgvs || '—'
+    },
+    levelLabel(): string {
+      return ASSAY_LEVEL_LABELS[this.measurement.assayLevel as keyof typeof ASSAY_LEVEL_LABELS] ?? 'Nucleotide'
+    },
+    levelClass(): string {
+      return LEVEL_BUCKET_CLASSES[assayLevelBucket(this.measurement.assayLevel)]
+    },
+    classification(): string | null {
+      return this.measurement.preferredClassification?.functionalClassification ?? null
+    }
+  }
+})
+</script>
diff --git a/src/lib/measurement-aggregation.test.ts b/src/lib/measurement-aggregation.test.ts
deleted file mode 100644
index e55bbaa1..00000000
--- a/src/lib/measurement-aggregation.test.ts
+++ /dev/null
@@ -1,61 +0,0 @@
-import {describe, expect, it} from 'vitest'
-
-import {aggregateByScoreSet} from '@/lib/measurement-aggregation'
-import type {components} from '@/schema/openapi'
-
-type AlleleMeasurement = components['schemas']['AlleleMeasurement']
-
-function m(overrides: Partial<AlleleMeasurement>): AlleleMeasurement {
-  return {
-    variantUrn: 'urn:mavedb:x#1',
-    relationship: 'nucleotide_encoding',
-    assayLevel: 'cdna',
-    scoreSetUrn: 'urn:mavedb:x',
-    scoreSetTitle: 'Score set X',
-    ...overrides
-  } as AlleleMeasurement
-}
-
-function classified(fc: string): AlleleMeasurement['preferredClassification'] {
-  return {functionalClassification: fc} as AlleleMeasurement['preferredClassification']
-}
-
-describe('aggregateByScoreSet', () => {
-  it('collapses a score set’s many nucleotide encodings into one entry with a score range', () => {
-    const result = aggregateByScoreSet([
-      m({scoreSetUrn: 'urn:s1', scoreSetTitle: 'Findlay', score: -2.0, preferredClassification: classified('abnormal')}),
-      m({scoreSetUrn: 'urn:s1', scoreSetTitle: 'Findlay', score: -1.7, preferredClassification: classified('abnormal')}),
-      m({scoreSetUrn: 'urn:s1', scoreSetTitle: 'Findlay', score: -1.9, preferredClassification: classified('abnormal')})
-    ])
-    expect(result).toHaveLength(1)
-    expect(result[0].measurements).toHaveLength(3)
-    expect(result[0].level).toBe('nucleotide')
-    expect(result[0].classifications).toEqual(['abnormal'])
-    expect(result[0].scoreRange).toEqual({min: -2.0, max: -1.7})
-  })
-
-  it('separates distinct score sets and sorts the more-corroborated one first', () => {
-    const result = aggregateByScoreSet([
-      m({scoreSetUrn: 'urn:solo', scoreSetTitle: 'Giacomelli', assayLevel: 'protein', score: -2.1}),
-      m({scoreSetUrn: 'urn:many', scoreSetTitle: 'Findlay', score: -2.0}),
-      m({scoreSetUrn: 'urn:many', scoreSetTitle: 'Findlay', score: -1.8})
-    ])
-    expect(result.map((s) => s.scoreSetTitle)).toEqual(['Findlay', 'Giacomelli'])
-    expect(result[0].measurements).toHaveLength(2)
-    expect(result[1].level).toBe('protein')
-  })
-
-  it('flags a score set that assayed both levels as mixed and surfaces internal disagreement', () => {
-    const result = aggregateByScoreSet([
-      m({scoreSetUrn: 'urn:s', assayLevel: 'protein', preferredClassification: classified('abnormal')}),
-      m({scoreSetUrn: 'urn:s', assayLevel: 'cdna', preferredClassification: classified('normal')})
-    ])
-    expect(result[0].level).toBe('mixed')
-    expect(new Set(result[0].classifications)).toEqual(new Set(['abnormal', 'normal']))
-  })
-
-  it('returns a null score range when no measurement carries a score', () => {
-    const result = aggregateByScoreSet([m({scoreSetUrn: 'urn:s', score: null})])
-    expect(result[0].scoreRange).toBeNull()
-  })
-})
diff --git a/src/lib/measurement-aggregation.ts b/src/lib/measurement-aggregation.ts
deleted file mode 100644
index 395878f2..00000000
--- a/src/lib/measurement-aggregation.ts
+++ /dev/null
@@ -1,76 +0,0 @@
-import type {components} from '@/schema/openapi'
-
-type AlleleMeasurement = components['schemas']['AlleleMeasurement']
-type FunctionalClassification = NonNullable<
-  NonNullable<AlleleMeasurement['preferredClassification']>['functionalClassification']
->
-
-export type EvidenceLevel = 'protein' | 'nucleotide' | 'mixed'
-
-/** One score set's evidence for a change, collapsed from however many equivalence-class representations it assayed. */
-export interface ScoreSetEvidence {
-  scoreSetUrn: string
-  scoreSetTitle: string
-  /** The underlying measurements, revealed on expand (a saturation screen may hold many). */
-  measurements: AlleleMeasurement[]
-  /** The assay level(s) this score set contributed: all-protein, all-nucleotide, or both. */
-  level: EvidenceLevel
-  /** Distinct functional classifications present — one value = concordant, several = the score set disagrees internally. */
-  classifications: FunctionalClassification[]
-  /** Span of functional scores, or null when none carry a score. `min === max` for a single value. */
-  scoreRange: {min: number; max: number} | null
-}
-
-function levelOf(measurements: AlleleMeasurement[]): EvidenceLevel {
-  let protein = false
-  let nucleotide = false
-  for (const m of measurements) {
-    if (m.assayLevel === 'protein') protein = true
-    else if (m.assayLevel === 'cdna' || m.assayLevel === 'genomic') nucleotide = true
-
-    if (protein && nucleotide) break
-  }
-
-  if (protein && nucleotide) return 'mixed'
-  else if (protein) return 'protein'
-  else return 'nucleotide'
-}
-
-/**
- * Collapse a closed equivalence set (a change's protein-consequence assays + its sibling nucleotide
- * encodings) into one entry per score set. Reverse translation makes the individual members redundant —
- * they re-encode the same functional change — so search shows per-score-set evidence (level, call, score
- * range) rather than a row per representation. Score sets with more corroborating measurements sort first.
- */
-export function aggregateByScoreSet(measurements: AlleleMeasurement[]): ScoreSetEvidence[] {
-  const byScoreSet = new Map<string, AlleleMeasurement[]>()
-  for (const m of measurements) {
-    const existing = byScoreSet.get(m.scoreSetUrn)
-    if (existing) existing.push(m)
-    else byScoreSet.set(m.scoreSetUrn, [m])
-  }
-
-  const scoreSets: ScoreSetEvidence[] = []
-  for (const [scoreSetUrn, list] of byScoreSet) {
-    const scores = list.map((m) => m.score).filter((s): s is number => s != null)
-    const classifications = [
-      ...new Set(
-        list
-          .map((m) => m.preferredClassification?.functionalClassification)
-          .filter((c): c is FunctionalClassification => c != null)
-      )
-    ]
-    scoreSets.push({
-      scoreSetUrn,
-      scoreSetTitle: list[0].scoreSetTitle,
-      measurements: list,
-      level: levelOf(list),
-      classifications,
-      scoreRange: scores.length ? {min: Math.min(...scores), max: Math.max(...scores)} : null
-    })
-  }
-
-  return scoreSets.sort(
-    (a, b) => b.measurements.length - a.measurements.length || a.scoreSetTitle.localeCompare(b.scoreSetTitle)
-  )
-}

From 6cb56f3a3bfa55d76e4b87c78de10b8e947b6a31 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 16 Jul 2026 16:02:10 -0700
Subject: [PATCH 44/84] refactor(measurement-types): unify assay-level
 vocabulary into one source
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Collapse the three sequence levels (genomic/coding/protein) to two
interface buckets — nucleotide and amino acid — with a single source of
truth so the label, color, and gloss can no longer drift across
surfaces. The finer SequenceLevel stays available internally.

- Add LEVEL_BUCKETS (label + class + definition) and assayLevelDisplay;
  remove ASSAY_LEVEL_LABELS, LEVEL_BUCKET_LABELS, and LEVEL_BUCKET_CLASSES
- Repoint MvMeasurementRow, MvAssayFactsCard, MvRelatedAlleles,
  MvMeasurementCard, VariantScreen, and use-variant-lookup at the helpers
- Derive the Key drawer's assay-level section from LEVEL_BUCKETS, as the
  confidence section already derives from ALLELE_CONFIDENCE
- Rename the protein color token to amino-acid (app.css, MvPill,
  VariantScreen) and relabel the variant-page level filter to "Amino acid"
- Say "Amino acid" over "Protein" in the score-set sequence-type badge
  and the p. coordinate tab; leave "protein consequence" wording as-is
---
 src/assets/app.css                            |  6 +--
 src/components/common/MvAssayFactsCard.vue    |  6 +--
 src/components/common/MvPill.vue              |  2 +-
 src/components/common/MvScoreSetRow.vue       |  2 +-
 src/components/screens/VariantScreen.vue      | 12 ++---
 src/components/search/MvMeasurementRow.vue    |  6 +--
 src/components/variant/MvMeasurementCard.vue  |  8 ++--
 src/components/variant/MvRelatedAlleles.vue   |  6 +--
 .../variant/variant-key-sections.ts           | 11 ++---
 .../use-variant-coordinates.test.ts           | 12 ++---
 src/composables/use-variant-coordinates.ts    |  4 +-
 src/composables/use-variant-lookup.ts         |  6 ++-
 src/lib/measurement-types.test.ts             |  4 +-
 src/lib/measurement-types.ts                  | 47 +++++++++++--------
 14 files changed, 67 insertions(+), 65 deletions(-)

diff --git a/src/assets/app.css b/src/assets/app.css
index 4dd65f26..6c008a96 100644
--- a/src/assets/app.css
+++ b/src/assets/app.css
@@ -124,9 +124,9 @@
   --color-nucleotide: #2e7d32;
   --color-nucleotide-light: #e8f5e9;
   --color-nucleotide-border: #c8e4c6;
-  --color-protein: #7e5daf;
-  --color-protein-light: #f1ecf8;
-  --color-protein-border: #b5a0d0;
+  --color-amino-acid: #7e5daf;
+  --color-amino-acid-light: #f1ecf8;
+  --color-amino-acid-border: #b5a0d0;
   --color-synonymous-nucleotide: #8a5700;
   --color-synonymous-nucleotide-light: #fef8e1;
   --color-synonymous-nucleotide-border: #f5c97a;
diff --git a/src/components/common/MvAssayFactsCard.vue b/src/components/common/MvAssayFactsCard.vue
index 88071373..32d98b05 100644
--- a/src/components/common/MvAssayFactsCard.vue
+++ b/src/components/common/MvAssayFactsCard.vue
@@ -83,7 +83,7 @@ import {
   getPrimaryCalibration
 } from '@/lib/calibrations'
 import {getExperimentKeyword} from '@/lib/experiments'
-import {ASSAY_LEVEL_LABELS} from '@/lib/measurement-types'
+import {assayLevelDisplay} from '@/lib/measurement-types'
 import {getScoreSetShortName} from '@/lib/score-sets'
 import {components} from '@/schema/openapi'
 
@@ -102,7 +102,7 @@ export default defineComponent({
 
   props: {
     // The measured assay level (protein / cdna / genomic) — score-set-wide, shared across its variants.
-    assayLevel: {type: String as PropType<keyof typeof ASSAY_LEVEL_LABELS | null>, default: null},
+    assayLevel: {type: String as PropType<string | null>, default: null},
     columns: {type: Number as PropType<1 | 2>, default: 2},
     linkTitle: {type: Boolean, default: true},
     showUrn: {type: Boolean, default: false},
@@ -112,7 +112,7 @@ export default defineComponent({
 
   computed: {
     assayLevelLabel(): string | null {
-      return this.assayLevel ? (ASSAY_LEVEL_LABELS[this.assayLevel] ?? null) : null
+      return this.assayLevel ? assayLevelDisplay(this.assayLevel).label : null
     },
     gridClass(): string {
       return this.columns === 2
diff --git a/src/components/common/MvPill.vue b/src/components/common/MvPill.vue
index 235d485e..59287816 100644
--- a/src/components/common/MvPill.vue
+++ b/src/components/common/MvPill.vue
@@ -21,7 +21,7 @@ const VARIANT_CLASSES: Record<PillVariant, string> = {
   calibrated: 'border-calibrated-border bg-calibrated-light text-calibrated',
   collection: 'border-sage bg-sage-dark text-white',
   nucleotide: 'border-nucleotide-border bg-nucleotide-light text-nucleotide',
-  protein: 'border-protein-border bg-protein-light text-protein'
+  protein: 'border-amino-acid-border bg-amino-acid-light text-amino-acid'
 }
 
 export default defineComponent({
diff --git a/src/components/common/MvScoreSetRow.vue b/src/components/common/MvScoreSetRow.vue
index e29dde17..8e9cec09 100644
--- a/src/components/common/MvScoreSetRow.vue
+++ b/src/components/common/MvScoreSetRow.vue
@@ -140,7 +140,7 @@ export default defineComponent({
       if (target.targetAccession) return 'Nucleotide'
       const type = target.targetSequence?.sequenceType
       if (type === 'dna') return 'Nucleotide'
-      if (type === 'protein') return 'Protein'
+      if (type === 'protein') return 'Amino acid'
       return null
     },
     isMultiTarget(): boolean {
diff --git a/src/components/screens/VariantScreen.vue b/src/components/screens/VariantScreen.vue
index 951dabc3..a5d5638a 100644
--- a/src/components/screens/VariantScreen.vue
+++ b/src/components/screens/VariantScreen.vue
@@ -125,11 +125,11 @@
               <MvBadgeToggle
                 v-if="lookup.proteinCount.value > 0"
                 v-model="lookup.showProtein.value"
-                active-background="var(--color-protein-light)"
-                active-border="var(--color-protein-border)"
-                color="var(--color-protein)"
+                active-background="var(--color-amino-acid-light)"
+                active-border="var(--color-amino-acid-border)"
+                color="var(--color-amino-acid)"
                 :count="lookup.proteinCount.value"
-                label="Protein"
+                label="Amino acid"
               />
             </div>
           </div>
@@ -442,7 +442,7 @@ import MvMeasurementCard from '@/components/variant/MvMeasurementCard.vue'
 import MvRowActionMenu, {type RowAction} from '@/components/common/MvRowActionMenu.vue'
 import VariantInfoSection from '@/components/variant/VariantInfoSection.vue'
 import {useVariantLookup} from '@/composables/use-variant-lookup'
-import {assayLevelBucket, LEVEL_BUCKET_LABELS} from '@/lib/measurement-types'
+import {assayLevelDisplay} from '@/lib/measurement-types'
 import {hasFunctionalCalibrations, hasPathogenicityCalibrations} from '@/lib/calibrations'
 import {confidenceBadge, groupAlleles, type AlleleGroup, type ConfidenceBadge} from '@/lib/allele-grouping'
 import {formatConsequence} from '@/lib/formats'
@@ -599,7 +599,7 @@ export default defineComponent({
     },
     measurementOptions(): {label: string; urn: string}[] {
       return this.lookup.filteredVariants.value.map((m) => ({
-        label: `${m.scoreSetTitle || 'Untitled score set'} (${LEVEL_BUCKET_LABELS[assayLevelBucket(m.assayLevel)].short})`,
+        label: `${m.scoreSetTitle || 'Untitled score set'} (${assayLevelDisplay(m.assayLevel).label})`,
         urn: m.variantUrn
       }))
     },
diff --git a/src/components/search/MvMeasurementRow.vue b/src/components/search/MvMeasurementRow.vue
index ec37cf3d..9791839b 100644
--- a/src/components/search/MvMeasurementRow.vue
+++ b/src/components/search/MvMeasurementRow.vue
@@ -24,7 +24,7 @@
 import {defineComponent, type PropType} from 'vue'
 
 import MvClassificationTag from '@/components/common/MvClassificationTag.vue'
-import {ASSAY_LEVEL_LABELS, LEVEL_BUCKET_CLASSES, assayLevelBucket} from '@/lib/measurement-types'
+import {assayLevelDisplay} from '@/lib/measurement-types'
 import type {components} from '@/schema/openapi'
 
 type AlleleMeasurement = components['schemas']['AlleleMeasurement']
@@ -44,10 +44,10 @@ export default defineComponent({
       return this.measurement.assayLevelHgvs || this.measurement.submittedHgvs || '—'
     },
     levelLabel(): string {
-      return ASSAY_LEVEL_LABELS[this.measurement.assayLevel as keyof typeof ASSAY_LEVEL_LABELS] ?? 'Nucleotide'
+      return assayLevelDisplay(this.measurement.assayLevel).label
     },
     levelClass(): string {
-      return LEVEL_BUCKET_CLASSES[assayLevelBucket(this.measurement.assayLevel)]
+      return assayLevelDisplay(this.measurement.assayLevel).class
     },
     classification(): string | null {
       return this.measurement.preferredClassification?.functionalClassification ?? null
diff --git a/src/components/variant/MvMeasurementCard.vue b/src/components/variant/MvMeasurementCard.vue
index 9dfc50cd..eefe8a50 100644
--- a/src/components/variant/MvMeasurementCard.vue
+++ b/src/components/variant/MvMeasurementCard.vue
@@ -75,9 +75,7 @@ import {defineComponent, type PropType} from 'vue'
 import MvClassificationTag from '@/components/common/MvClassificationTag.vue'
 import MvEvidenceTag from '@/components/common/MvEvidenceTag.vue'
 import {
-  assayLevelBucket,
-  LEVEL_BUCKET_CLASSES,
-  LEVEL_BUCKET_LABELS,
+  assayLevelDisplay,
   RELATIONSHIP_LABELS,
   type MeasurementRelationship
 } from '@/lib/measurement-types'
@@ -119,10 +117,10 @@ export default defineComponent({
 
   computed: {
     levelLabel(): string {
-      return LEVEL_BUCKET_LABELS[assayLevelBucket(this.assayLevel)].full
+      return assayLevelDisplay(this.assayLevel).label
     },
     levelClass(): string {
-      return LEVEL_BUCKET_CLASSES[assayLevelBucket(this.assayLevel)]
+      return assayLevelDisplay(this.assayLevel).class
     },
     relationshipLabel(): string {
       return RELATIONSHIP_LABELS[this.relationship] ?? this.relationship
diff --git a/src/components/variant/MvRelatedAlleles.vue b/src/components/variant/MvRelatedAlleles.vue
index d89fda72..2b82b70f 100644
--- a/src/components/variant/MvRelatedAlleles.vue
+++ b/src/components/variant/MvRelatedAlleles.vue
@@ -99,7 +99,7 @@ import {type AlleleGroup, confidenceBadge} from '@/lib/allele-grouping'
 import {formatClinicalSignificance, latestClinvar} from '@/lib/clinvar-controls'
 import {formatConsequence} from '@/lib/formats'
 import {formatFrequency} from '@/lib/gnomad'
-import {ASSAY_LEVEL_LABELS, LEVEL_BUCKET_CLASSES, assayLevelBucket} from '@/lib/measurement-types'
+import {assayLevelDisplay} from '@/lib/measurement-types'
 import type {components} from '@/schema/openapi'
 
 type AlleleAnnotations = components['schemas']['AlleleAnnotations']
@@ -137,10 +137,10 @@ export default defineComponent({
       return group.members.map((m) => ({label: this.levelLabel(m.level), annotations: m.annotations}))
     },
     levelLabel(level: string | null | undefined): string {
-      return ASSAY_LEVEL_LABELS[level as keyof typeof ASSAY_LEVEL_LABELS] ?? level ?? '—'
+      return level ? assayLevelDisplay(level).label : '—'
     },
     levelClass(level: string | null | undefined): string {
-      return LEVEL_BUCKET_CLASSES[assayLevelBucket(level)]
+      return assayLevelDisplay(level).class
     }
   }
 })
diff --git a/src/components/variant/variant-key-sections.ts b/src/components/variant/variant-key-sections.ts
index f1519070..5855b7ea 100644
--- a/src/components/variant/variant-key-sections.ts
+++ b/src/components/variant/variant-key-sections.ts
@@ -1,6 +1,7 @@
 import config from '@/config'
 import type {KeySection} from '@/composables/use-key-drawer'
 import {ALLELE_CONFIDENCE} from '@/lib/allele-grouping'
+import {LEVEL_BUCKETS} from '@/lib/measurement-types'
 
 /**
  * Variant-page content for the generic {@link MvKeyDrawer}. These are the tier-2 vocabulary glosses; the
@@ -36,14 +37,8 @@ export const VARIANT_KEY_SECTIONS: KeySection[] = [
     id: 'assay-level',
     title: 'Assay level',
     gloss: 'The level at which a result measured the change.',
-    terms: [
-      {
-        label: 'Nucleotide',
-        definition: 'Assayed as a DNA/RNA change (coding or genomic).',
-        class: 'bg-nucleotide-light text-nucleotide'
-      },
-      {label: 'Protein', definition: 'Assayed as an amino-acid change.', class: 'bg-protein-light text-protein'}
-    ]
+    // Derived from the shared bucket vocabulary so badges and this gloss can never drift apart.
+    terms: Object.values(LEVEL_BUCKETS).map((b) => ({label: b.label, definition: b.definition, class: b.class}))
   },
   {
     id: 'confidence',
diff --git a/src/composables/use-variant-coordinates.test.ts b/src/composables/use-variant-coordinates.test.ts
index 5640601c..bb1225c3 100644
--- a/src/composables/use-variant-coordinates.test.ts
+++ b/src/composables/use-variant-coordinates.test.ts
@@ -163,7 +163,7 @@ describe('levelAvailable / sequenceTypeOptions — availability per frame', () =
   it('sequenceTypeOptions offers one NT option in submitted frame labelled Nucleotide, value keyed by assayLevel', () => {
     expect(sequenceTypeOptions([dnaAssay], 'submitted')).toEqual([
       {title: 'Nucleotide', value: 'cdna'},
-      {title: 'Protein', value: 'protein'}
+      {title: 'Amino acid', value: 'protein'}
     ])
     expect(sequenceTypeOptions([genomicAssay], 'submitted')).toEqual([{title: 'Nucleotide', value: 'genomic'}])
   })
@@ -172,7 +172,7 @@ describe('levelAvailable / sequenceTypeOptions — availability per frame', () =
     expect(sequenceTypeOptions([dnaAssay], 'reference')).toEqual([
       {title: 'cDNA', value: 'cdna'},
       {title: 'Genomic', value: 'genomic'},
-      {title: 'Protein', value: 'protein'}
+      {title: 'Amino acid', value: 'protein'}
     ])
   })
 
@@ -180,13 +180,13 @@ describe('levelAvailable / sequenceTypeOptions — availability per frame', () =
     expect(sequenceTypeOptions([genomicAssay], 'reference')).toEqual([
       {title: 'cDNA', value: 'cdna'},
       {title: 'Genomic', value: 'genomic'},
-      {title: 'Protein', value: 'protein'}
+      {title: 'Amino acid', value: 'protein'}
     ])
   })
 
   it('a protein assay never offers cdna or genomic — in either frame (#784)', () => {
-    expect(sequenceTypeOptions([proteinAssay], 'submitted')).toEqual([{title: 'Protein', value: 'protein'}])
-    expect(sequenceTypeOptions([proteinAssay], 'reference')).toEqual([{title: 'Protein', value: 'protein'}])
+    expect(sequenceTypeOptions([proteinAssay], 'submitted')).toEqual([{title: 'Amino acid', value: 'protein'}])
+    expect(sequenceTypeOptions([proteinAssay], 'reference')).toEqual([{title: 'Amino acid', value: 'protein'}])
     expect(levelAvailable([proteinAssay], 'cdna', 'reference')).toBe(false)
     expect(levelAvailable([proteinAssay], 'genomic', 'reference')).toBe(false)
   })
@@ -195,7 +195,7 @@ describe('levelAvailable / sequenceTypeOptions — availability per frame', () =
     expect(sequenceTypeOptions([dnaAssay, proteinAssay], 'reference')).toEqual([
       {title: 'cDNA', value: 'cdna'},
       {title: 'Genomic', value: 'genomic'},
-      {title: 'Protein', value: 'protein'}
+      {title: 'Amino acid', value: 'protein'}
     ])
   })
 })
diff --git a/src/composables/use-variant-coordinates.ts b/src/composables/use-variant-coordinates.ts
index ebc4d8e1..582bacc8 100644
--- a/src/composables/use-variant-coordinates.ts
+++ b/src/composables/use-variant-coordinates.ts
@@ -101,7 +101,7 @@ export function useVariantCoordinates() {
     return variants.some((v) => coordinateFor(v, level, frame) != null)
   }
 
-  const LEVEL_LABELS: Record<SequenceLevel, string> = {cdna: 'cDNA', genomic: 'Genomic', protein: 'Protein'}
+  const LEVEL_LABELS: Record<SequenceLevel, string> = {cdna: 'cDNA', genomic: 'Genomic', protein: 'Amino acid'}
   const LEVEL_ORDER: SequenceLevel[] = ['cdna', 'genomic', 'protein']
 
   /**
@@ -127,7 +127,7 @@ export function useVariantCoordinates() {
         options.push({title: 'Nucleotide', value: ntLevel})
       }
 
-      if (variants.some((v) => v.hgvsPro != null)) options.push({title: 'Protein', value: 'protein'})
+      if (variants.some((v) => v.hgvsPro != null)) options.push({title: 'Amino acid', value: 'protein'})
       return options
     }
 
diff --git a/src/composables/use-variant-lookup.ts b/src/composables/use-variant-lookup.ts
index ee15694d..7d117e38 100644
--- a/src/composables/use-variant-lookup.ts
+++ b/src/composables/use-variant-lookup.ts
@@ -104,11 +104,13 @@ export function useVariantLookup(
   const nucleotideCount = computed(
     () => variants.value.filter((m) => assayLevelBucket(m.assayLevel) === 'nucleotide').length
   )
-  const proteinCount = computed(() => variants.value.filter((m) => assayLevelBucket(m.assayLevel) === 'protein').length)
+  const proteinCount = computed(
+    () => variants.value.filter((m) => assayLevelBucket(m.assayLevel) === 'amino acid').length
+  )
   const filteredVariants = computed(() =>
     variants.value.filter((m) => {
       const bucket = assayLevelBucket(m.assayLevel)
-      return bucket === 'protein' ? showProtein.value : showNucleotide.value
+      return bucket === 'amino acid' ? showProtein.value : showNucleotide.value
     })
   )
 
diff --git a/src/lib/measurement-types.test.ts b/src/lib/measurement-types.test.ts
index 6c1f768c..338e202e 100644
--- a/src/lib/measurement-types.test.ts
+++ b/src/lib/measurement-types.test.ts
@@ -3,8 +3,8 @@ import {describe, expect, it} from 'vitest'
 import {assayLevelBucket, dominantAssayLevel} from '@/lib/measurement-types'
 
 describe('assayLevelBucket', () => {
-  it('returns "protein" for protein', () => {
-    expect(assayLevelBucket('protein')).toBe('protein')
+  it('returns "amino acid" for protein', () => {
+    expect(assayLevelBucket('protein')).toBe('amino acid')
   })
 
   it('returns "nucleotide" for cdna', () => {
diff --git a/src/lib/measurement-types.ts b/src/lib/measurement-types.ts
index c7a5d636..d23d890d 100644
--- a/src/lib/measurement-types.ts
+++ b/src/lib/measurement-types.ts
@@ -1,21 +1,38 @@
 import type {components} from '@/schema/openapi'
 import type {SequenceLevel} from '@/composables/use-variant-coordinates'
 
-// A measurement is assayed at one of the three sequence levels ('protein' | 'cdna' | 'genomic'). The two
-// nucleotide levels share one visual bucket; protein is its own. "Assay level" is the concept; the value
-// space is just `SequenceLevel`, so we reuse that type rather than mint a parallel one.
 export type MeasurementRelationship = components['schemas']['MeasurementRelationship']
-export type LevelBucket = 'nucleotide' | 'protein'
+
+// The interface collapses the three sequence levels ('genomic' | 'cdna' | 'protein') to two assay-level
+// buckets: the nucleotide levels (genomic + coding) share one; protein is 'amino acid'. The finer
+// SequenceLevel stays available internally for logic — it just isn't surfaced as its own badge.
+export type LevelBucket = 'nucleotide' | 'amino acid'
 
 export function assayLevelBucket(level: string | null | undefined): LevelBucket {
-  return level === 'protein' ? 'protein' : 'nucleotide'
+  return level === 'protein' ? 'amino acid' : 'nucleotide'
+}
+
+/**
+ * Single source of truth for how an assay-level bucket appears in the UI — its label, color classes, and
+ * Key-drawer gloss. Every level badge, pill, and the Key drawer's assay-level section derives from this,
+ * so the vocabulary can never drift across surfaces.
+ */
+export const LEVEL_BUCKETS: Record<LevelBucket, {label: string; class: string; definition: string}> = {
+  nucleotide: {
+    label: 'Nucleotide',
+    class: 'bg-nucleotide-light text-nucleotide',
+    definition: 'Assayed as a nucleotide change.'
+  },
+  'amino acid': {
+    label: 'Amino acid',
+    class: 'bg-amino-acid-light text-amino-acid',
+    definition: 'Assayed as an amino-acid change.'
+  }
 }
 
-// Per-level display labels for the three assay levels (distinct from the two-way bucket labels above).
-export const ASSAY_LEVEL_LABELS: Record<SequenceLevel, string> = {
-  genomic: 'Genomic',
-  cdna: 'Coding',
-  protein: 'Protein'
+/** The display label, color classes, and gloss for a raw SequenceLevel, collapsed to its bucket. */
+export function assayLevelDisplay(level: string | null | undefined): (typeof LEVEL_BUCKETS)[LevelBucket] {
+  return LEVEL_BUCKETS[assayLevelBucket(level)]
 }
 
 // A score set's variants are all assayed at one level, but some may be unmapped (null). Return the most
@@ -36,16 +53,6 @@ export function dominantAssayLevel(levels: Array<SequenceLevel | null | undefine
   return best
 }
 
-export const LEVEL_BUCKET_LABELS: Record<LevelBucket, {full: string; short: string}> = {
-  nucleotide: {full: 'Nucleotide', short: 'Nucleotide'},
-  protein: {full: 'Protein', short: 'Protein'}
-}
-
-export const LEVEL_BUCKET_CLASSES: Record<LevelBucket, string> = {
-  nucleotide: 'bg-nucleotide-light text-nucleotide',
-  protein: 'bg-protein-light text-protein'
-}
-
 // How a measurement relates to the queried ClinGen allele — the RT asymmetry. Phrased relative to the
 // user's variant, so the labels self-explain under the "relative to your variant" anchor heading.
 export const RELATIONSHIP_LABELS: Record<MeasurementRelationship, string> = {

From 89af4898f4cf513f744f601369043c908c46ef14 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 16 Jul 2026 16:04:56 -0700
Subject: [PATCH 45/84] refactor(variant): collapse relationship vocabulary to
 one source

Promote RELATIONSHIP_LABELS to RELATIONSHIPS, carrying the card label,
optional chip class, and Key-drawer gloss in a single keyed record (the
LEVEL_BUCKETS shape). The measurement card and the drawer's relationship
section now both derive from it, so the vocabulary can no longer drift
across surfaces.
---
 src/components/variant/MvMeasurementCard.vue  |  4 +--
 .../variant/variant-key-sections.ts           | 19 +++-----------
 src/lib/measurement-types.ts                  | 25 ++++++++++++++-----
 3 files changed, 24 insertions(+), 24 deletions(-)

diff --git a/src/components/variant/MvMeasurementCard.vue b/src/components/variant/MvMeasurementCard.vue
index eefe8a50..758110d5 100644
--- a/src/components/variant/MvMeasurementCard.vue
+++ b/src/components/variant/MvMeasurementCard.vue
@@ -76,7 +76,7 @@ import MvClassificationTag from '@/components/common/MvClassificationTag.vue'
 import MvEvidenceTag from '@/components/common/MvEvidenceTag.vue'
 import {
   assayLevelDisplay,
-  RELATIONSHIP_LABELS,
+  RELATIONSHIPS,
   type MeasurementRelationship
 } from '@/lib/measurement-types'
 import type {components} from '@/schema/openapi'
@@ -123,7 +123,7 @@ export default defineComponent({
       return assayLevelDisplay(this.assayLevel).class
     },
     relationshipLabel(): string {
-      return RELATIONSHIP_LABELS[this.relationship] ?? this.relationship
+      return RELATIONSHIPS[this.relationship]?.label ?? this.relationship
     },
     classification(): string | null {
       return this.preferredClassification?.functionalClassification ?? null
diff --git a/src/components/variant/variant-key-sections.ts b/src/components/variant/variant-key-sections.ts
index 5855b7ea..a8bd6d59 100644
--- a/src/components/variant/variant-key-sections.ts
+++ b/src/components/variant/variant-key-sections.ts
@@ -1,7 +1,7 @@
 import config from '@/config'
 import type {KeySection} from '@/composables/use-key-drawer'
 import {ALLELE_CONFIDENCE} from '@/lib/allele-grouping'
-import {LEVEL_BUCKETS} from '@/lib/measurement-types'
+import {LEVEL_BUCKETS, RELATIONSHIPS} from '@/lib/measurement-types'
 
 /**
  * Variant-page content for the generic {@link MvKeyDrawer}. These are the tier-2 vocabulary glosses; the
@@ -17,21 +17,8 @@ export const VARIANT_KEY_SECTIONS: KeySection[] = [
     id: 'relationship',
     title: 'Relationship to your variant',
     gloss: 'How each result relates to the allele you searched.',
-    terms: [
-      {
-        label: 'Your variant',
-        definition: 'The result assayed exactly the allele you searched.',
-        class: 'bg-sage/15 text-sage'
-      },
-      {
-        label: 'Its protein consequence',
-        definition: 'The result assayed the protein change your variant produces.'
-      },
-      {
-        label: 'Encodes the protein consequence',
-        definition: 'The result assayed a nucleotide allele that encodes the same protein change as your variant.'
-      }
-    ]
+    // Derived from the shared relationship vocabulary so cards and this gloss can never drift apart.
+    terms: Object.values(RELATIONSHIPS).map((r) => ({label: r.label, definition: r.definition, class: r.class}))
   },
   {
     id: 'assay-level',
diff --git a/src/lib/measurement-types.ts b/src/lib/measurement-types.ts
index d23d890d..b000cf60 100644
--- a/src/lib/measurement-types.ts
+++ b/src/lib/measurement-types.ts
@@ -53,10 +53,23 @@ export function dominantAssayLevel(levels: Array<SequenceLevel | null | undefine
   return best
 }
 
-// How a measurement relates to the queried ClinGen allele — the RT asymmetry. Phrased relative to the
-// user's variant, so the labels self-explain under the "relative to your variant" anchor heading.
-export const RELATIONSHIP_LABELS: Record<MeasurementRelationship, string> = {
-  direct: 'Your variant',
-  protein_consequence: 'Its protein consequence',
-  nucleotide_encoding: 'Encodes the protein consequence'
+/**
+ * Single source of truth for the measurement-to-query relationship vocabulary (the RT asymmetry): the
+ * card label, an optional chip class, and the Key-drawer gloss. Phrased relative to the user's variant so
+ * the labels self-explain under the "relative to your variant" anchor. Insertion order is display order.
+ */
+export const RELATIONSHIPS: Record<MeasurementRelationship, {label: string; class?: string; definition: string}> = {
+  direct: {
+    label: 'Your variant',
+    class: 'bg-sage/15 text-sage',
+    definition: 'The result assayed exactly the allele you searched.'
+  },
+  protein_consequence: {
+    label: 'Its protein consequence',
+    definition: 'The result assayed the protein change your variant produces.'
+  },
+  nucleotide_encoding: {
+    label: 'Encodes the protein consequence',
+    definition: 'The result assayed a nucleotide allele that encodes the same protein change as your variant.'
+  }
 }

From ea02935613cad7ba108ff7716b5a6d5a1f3eef95 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 16 Jul 2026 16:21:10 -0700
Subject: [PATCH 46/84] refactor(variant): collapse functional-classification
 vocabulary

Introduce FUNCTIONAL_CLASSIFICATIONS as the single source for the functional
verdict vocabulary (label, compact label, chip class, drawer gloss) and move
the labels and color class out of MvClassificationTag. The tag and the Key
drawer's consequence section now both derive from it; the two prose terms
(molecular consequence, functional impact) stay inline in the drawer.
---
 src/components/common/MvClassificationTag.vue | 24 ++++++-------
 .../variant/variant-key-sections.ts           | 15 +++-----
 src/lib/functional-impact.ts                  | 36 +++++++++++++++++++
 3 files changed, 51 insertions(+), 24 deletions(-)
 create mode 100644 src/lib/functional-impact.ts

diff --git a/src/components/common/MvClassificationTag.vue b/src/components/common/MvClassificationTag.vue
index 942cc40d..af68fe2e 100644
--- a/src/components/common/MvClassificationTag.vue
+++ b/src/components/common/MvClassificationTag.vue
@@ -1,7 +1,7 @@
 <template>
   <span
     class="inline-block max-w-full rounded px-2.5 py-0.5 text-xs font-bold leading-snug tracking-wide"
-    :class="`mave-classification-${classification}`"
+    :class="tagClass"
   >
     {{ label }}
   </span>
@@ -10,17 +10,7 @@
 <script lang="ts">
 import {defineComponent, type PropType} from 'vue'
 
-const LABELS: Record<string, string> = {
-  abnormal: 'Functionally Abnormal',
-  normal: 'Functionally Normal',
-  not_specified: 'Not Specified'
-}
-
-const SHORT_LABELS: Record<string, string> = {
-  abnormal: 'Abnormal',
-  normal: 'Normal',
-  not_specified: 'Not Specified'
-}
+import {FUNCTIONAL_CLASSIFICATIONS, type FunctionalClassification} from '@/lib/functional-impact'
 
 export default defineComponent({
   name: 'MvClassificationTag',
@@ -37,9 +27,15 @@ export default defineComponent({
   },
 
   computed: {
+    entry(): (typeof FUNCTIONAL_CLASSIFICATIONS)[FunctionalClassification] | undefined {
+      return FUNCTIONAL_CLASSIFICATIONS[this.classification as FunctionalClassification]
+    },
     label(): string {
-      const lookup = this.compact ? SHORT_LABELS : LABELS
-      return lookup[this.classification] ?? this.classification
+      if (!this.entry) return this.classification
+      return this.compact ? this.entry.shortLabel : this.entry.label
+    },
+    tagClass(): string {
+      return this.entry?.class ?? `mave-classification-${this.classification}`
     }
   }
 })
diff --git a/src/components/variant/variant-key-sections.ts b/src/components/variant/variant-key-sections.ts
index a8bd6d59..c8dda146 100644
--- a/src/components/variant/variant-key-sections.ts
+++ b/src/components/variant/variant-key-sections.ts
@@ -1,6 +1,7 @@
 import config from '@/config'
 import type {KeySection} from '@/composables/use-key-drawer'
 import {ALLELE_CONFIDENCE} from '@/lib/allele-grouping'
+import {FUNCTIONAL_CLASSIFICATIONS} from '@/lib/functional-impact'
 import {LEVEL_BUCKETS, RELATIONSHIPS} from '@/lib/measurement-types'
 
 /**
@@ -67,16 +68,10 @@ export const VARIANT_KEY_SECTIONS: KeySection[] = [
         definition: 'The predicted effect on the transcript or protein (e.g. missense), from VEP.'
       },
       {label: 'Functional impact', definition: "The assay's verdict on whether the variant alters function."},
-      {
-        label: 'Functionally Abnormal',
-        definition: 'The assay scored the variant as altering function.',
-        class: 'mave-classification-abnormal'
-      },
-      {
-        label: 'Functionally Normal',
-        definition: 'The assay scored the variant as retaining function.',
-        class: 'mave-classification-normal'
-      }
+      // The two functional calls derive from the shared classification vocabulary so tag and gloss can't drift.
+      ...Object.values(FUNCTIONAL_CLASSIFICATIONS)
+        .filter((c) => c.definition)
+        .map((c) => ({label: c.label, definition: c.definition!, class: c.class}))
     ]
   },
   {
diff --git a/src/lib/functional-impact.ts b/src/lib/functional-impact.ts
new file mode 100644
index 00000000..e87e2a79
--- /dev/null
+++ b/src/lib/functional-impact.ts
@@ -0,0 +1,36 @@
+/**
+ * The functional sublayer of the calibration layer: how an assay's verdict on a variant is named and
+ * shown. Its clinical counterpart (ClinVar significance, ACMG evidence) will live alongside as a separate
+ * module; the heavier editor/draft calibration model stays in `calibration-types.ts`.
+ */
+
+export type FunctionalClassification = 'abnormal' | 'normal' | 'not_specified'
+
+/**
+ * Single source of truth for the functional-classification vocabulary: the full label, the compact
+ * label, the color class, and the Key-drawer gloss. The classification tag and the drawer's consequence
+ * section both derive from this, so the vocabulary can never drift across surfaces. `not_specified`
+ * carries no gloss — it isn't surfaced in the drawer. Insertion order is display order.
+ */
+export const FUNCTIONAL_CLASSIFICATIONS: Record<
+  FunctionalClassification,
+  {label: string; shortLabel: string; class: string; definition?: string}
+> = {
+  abnormal: {
+    label: 'Functionally Abnormal',
+    shortLabel: 'Abnormal',
+    class: 'mave-classification-abnormal',
+    definition: 'The assay scored the variant as altering function.'
+  },
+  normal: {
+    label: 'Functionally Normal',
+    shortLabel: 'Normal',
+    class: 'mave-classification-normal',
+    definition: 'The assay scored the variant as retaining function.'
+  },
+  not_specified: {
+    label: 'Not Specified',
+    shortLabel: 'Not Specified',
+    class: 'mave-classification-not_specified'
+  }
+}

From 95dc00da6a1e5edd8f23a8471e0f7081905a39dc Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 16 Jul 2026 16:21:28 -0700
Subject: [PATCH 47/84] refactor(calibration): source functional range colors
 from vocab

Fold the three *_RANGE_DEFAULT_COLOR constants into FUNCTIONAL_CLASSIFICATIONS
as a rangeColor field and reduce getClassificationColor to a lookup. The
histogram range fill and the classification chip now draw from one vocabulary
keyed by the same functional-classification axis, so the color mapping can no
longer drift. Mapping is unchanged (normal/abnormal/not_specified -> the same
--color-cal-* vars, black fallback).
---
 src/lib/calibrations.ts      | 34 ++++------------------------------
 src/lib/functional-impact.ts | 15 ++++++++++-----
 2 files changed, 14 insertions(+), 35 deletions(-)

diff --git a/src/lib/calibrations.ts b/src/lib/calibrations.ts
index e65107ff..b90aebe2 100644
--- a/src/lib/calibrations.ts
+++ b/src/lib/calibrations.ts
@@ -6,6 +6,7 @@
 import axios from 'axios'
 
 import {createScoreCalibration, updateScoreCalibration} from '@/api/mavedb'
+import {FUNCTIONAL_CLASSIFICATIONS, type FunctionalClassification} from '@/lib/functional-impact'
 import {HistogramBin, HistogramShader} from '@/lib/histogram'
 import {components} from '@/schema/openapi'
 
@@ -15,10 +16,6 @@ export type ScoreCalibrationFunctionalClassification =
 export type FunctionalClassificationVariants = components['schemas']['FunctionalClassificationVariants']
 export type FunctionalClassificationVariant = components['schemas']['VariantEffectMeasurement']
 
-export const NORMAL_RANGE_DEFAULT_COLOR = 'var(--color-cal-normal)'
-export const ABNORMAL_RANGE_DEFAULT_COLOR = 'var(--color-cal-abnormal)'
-export const NOT_SPECIFIED_RANGE_DEFAULT_COLOR = 'var(--color-cal-unspecified)'
-
 export const BENIGN_CRITERION = 'BS3'
 export const PATHOGENIC_CRITERION = 'PS3'
 
@@ -117,34 +114,11 @@ export function prepareCalibrationsForHistogram(scoreCalibrations: ScoreCalibrat
 }
 
 /**
- * Derives the display color associated with a functional range classification.
- *
- * The color returned depends on the `classification` property of the supplied
- * `functionalClassification` object:
- * - `'normal'`        => NORMAL_RANGE_DEFAULT_COLOR
- * - `'abnormal'`      => ABNORMAL_RANGE_DEFAULT_COLOR
- * - `'not_specified'` => NOT_SPECIFIED_RANGE_DEFAULT_COLOR
- * - any other value   => `'#000000'` (fallback)
- *
- * This utility centralizes the mapping logic so UI components can remain
- * agnostic of the underlying color constants.
- *
- * @param range The functional range whose `classification` determines the color.
- * @returns A hex color string representing the classification.
- * @example
- * const color = getRangeColor({ classification: 'normal' }); // e.g. '#3BAA5C'
- * @remarks If new classifications are introduced, extend this function to handle them explicitly.
+ * Derives the histogram range-fill color for a functional range from the shared functional-impact
+ * vocabulary (keyed by its `functionalClassification`). Falls back to black for an unknown value.
  */
 export function getClassificationColor(range: ScoreCalibrationFunctionalClassification): string {
-  if (range.functionalClassification === 'normal') {
-    return NORMAL_RANGE_DEFAULT_COLOR
-  } else if (range.functionalClassification === 'abnormal') {
-    return ABNORMAL_RANGE_DEFAULT_COLOR
-  } else if (range.functionalClassification === 'not_specified') {
-    return NOT_SPECIFIED_RANGE_DEFAULT_COLOR
-  } else {
-    return '#000000'
-  }
+  return FUNCTIONAL_CLASSIFICATIONS[range.functionalClassification as FunctionalClassification]?.rangeColor ?? '#000000'
 }
 
 /**
diff --git a/src/lib/functional-impact.ts b/src/lib/functional-impact.ts
index e87e2a79..1aa9085e 100644
--- a/src/lib/functional-impact.ts
+++ b/src/lib/functional-impact.ts
@@ -8,29 +8,34 @@ export type FunctionalClassification = 'abnormal' | 'normal' | 'not_specified'
 
 /**
  * Single source of truth for the functional-classification vocabulary: the full label, the compact
- * label, the color class, and the Key-drawer gloss. The classification tag and the drawer's consequence
- * section both derive from this, so the vocabulary can never drift across surfaces. `not_specified`
- * carries no gloss — it isn't surfaced in the drawer. Insertion order is display order.
+ * label, the chip color class, the histogram range-fill color, and the Key-drawer gloss. The
+ * classification tag, the drawer's consequence section, and the calibration histogram all derive from
+ * this, so the vocabulary can never drift across surfaces. `class` styles the inline chip (the `--fn-*`
+ * palette); `rangeColor` fills the histogram score range (the `--cal-*` palette) — intentionally distinct.
+ * `not_specified` carries no gloss — it isn't surfaced in the drawer. Insertion order is display order.
  */
 export const FUNCTIONAL_CLASSIFICATIONS: Record<
   FunctionalClassification,
-  {label: string; shortLabel: string; class: string; definition?: string}
+  {label: string; shortLabel: string; class: string; rangeColor: string; definition?: string}
 > = {
   abnormal: {
     label: 'Functionally Abnormal',
     shortLabel: 'Abnormal',
     class: 'mave-classification-abnormal',
+    rangeColor: 'var(--color-cal-abnormal)',
     definition: 'The assay scored the variant as altering function.'
   },
   normal: {
     label: 'Functionally Normal',
     shortLabel: 'Normal',
     class: 'mave-classification-normal',
+    rangeColor: 'var(--color-cal-normal)',
     definition: 'The assay scored the variant as retaining function.'
   },
   not_specified: {
     label: 'Not Specified',
     shortLabel: 'Not Specified',
-    class: 'mave-classification-not_specified'
+    class: 'mave-classification-not_specified',
+    rangeColor: 'var(--color-cal-unspecified)'
   }
 }

From 314809a393c70443af93fddeb0e438a186a9811a Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 16 Jul 2026 16:27:31 -0700
Subject: [PATCH 48/84] refactor(calibration): extract ACMG evidence vocabulary
 into acmg.ts

Split the ACMG functional-evidence cluster out of the calibrations monolith
into a dependency-light acmg.ts (schema types only), the clinical bridge of
the calibration layer. Moves BENIGN/PATHOGENIC_CRITERION, EVIDENCE_STRENGTH(_AS_POINTS),
formatEvidenceCode, and hasPathogenicityCalibrations; updates the five consumers.

Drops four unreferenced exports (NORMAL/ABNORMAL_CALIBRATION_EVIDENCE,
EVIDENCE_STRENGTHS, EVIDENCE_STRENGTHS_REVERSED, INDETERMINATE_CALIBRATION_EVIDENCE)
and the stale histogram doc line that named the removed reverse map. Simplifies
EVIDENCE_STRENGTH to drop its always-true guard.
---
 .../calibration/CalibrationEditor.vue         |  2 +-
 src/components/common/MvAssayFactsCard.vue    |  8 +-
 src/components/screens/ScoreSetView.vue       |  3 +-
 src/components/screens/VariantScreen.vue      |  3 +-
 src/composables/use-calibration-resolution.ts |  3 +-
 src/lib/acmg.ts                               | 70 +++++++++++++++++
 src/lib/calibrations.ts                       | 78 +------------------
 7 files changed, 80 insertions(+), 87 deletions(-)
 create mode 100644 src/lib/acmg.ts

diff --git a/src/components/calibration/CalibrationEditor.vue b/src/components/calibration/CalibrationEditor.vue
index 87101f05..9ef2e771 100644
--- a/src/components/calibration/CalibrationEditor.vue
+++ b/src/components/calibration/CalibrationEditor.vue
@@ -61,7 +61,7 @@ import {
 } from '@/composables/use-calibration-editor'
 import {searchEditableScoreSets, getScoreSet} from '@/api/mavedb'
 import {acceptNewPublicationIdentifier} from '@/lib/form-helpers'
-import {EVIDENCE_STRENGTH, BENIGN_CRITERION, PATHOGENIC_CRITERION} from '@/lib/calibrations'
+import {EVIDENCE_STRENGTH, BENIGN_CRITERION, PATHOGENIC_CRITERION} from '@/lib/acmg'
 import {
   DRAFT_CALIBRATION_COPYABLE_KEYS,
   createDefaultClassification,
diff --git a/src/components/common/MvAssayFactsCard.vue b/src/components/common/MvAssayFactsCard.vue
index 32d98b05..53db8df9 100644
--- a/src/components/common/MvAssayFactsCard.vue
+++ b/src/components/common/MvAssayFactsCard.vue
@@ -76,12 +76,8 @@ import {defineComponent, type PropType} from 'vue'
 
 import MvDetailRow from '@/components/common/MvDetailRow.vue'
 import MvEvidenceTag from '@/components/common/MvEvidenceTag.vue'
-import {
-  findClassificationByType,
-  formatEvidenceCode,
-  getClassificationOddsPath,
-  getPrimaryCalibration
-} from '@/lib/calibrations'
+import {formatEvidenceCode} from '@/lib/acmg'
+import {findClassificationByType, getClassificationOddsPath, getPrimaryCalibration} from '@/lib/calibrations'
 import {getExperimentKeyword} from '@/lib/experiments'
 import {assayLevelDisplay} from '@/lib/measurement-types'
 import {getScoreSetShortName} from '@/lib/score-sets'
diff --git a/src/components/screens/ScoreSetView.vue b/src/components/screens/ScoreSetView.vue
index fa298dca..c50c170c 100644
--- a/src/components/screens/ScoreSetView.vue
+++ b/src/components/screens/ScoreSetView.vue
@@ -504,7 +504,8 @@ import {useClinvarControls} from '@/composables/use-clinvar-controls'
 import {useChartExport, type ChartExportFns} from '@/composables/use-chart-export'
 import {useVariantCoordinates, type CoordinateFrame, type SequenceLevel} from '@/composables/use-variant-coordinates'
 import config from '@/config'
-import {hasPathogenicityCalibrations, hasFunctionalCalibrations} from '@/lib/calibrations'
+import {hasPathogenicityCalibrations} from '@/lib/acmg'
+import {hasFunctionalCalibrations} from '@/lib/calibrations'
 import {getScoreSetShortName} from '@/lib/score-sets'
 import {dominantAssayLevel} from '@/lib/measurement-types'
 import {type DisplayVariant} from '@/lib/variants'
diff --git a/src/components/screens/VariantScreen.vue b/src/components/screens/VariantScreen.vue
index a5d5638a..afbfb62a 100644
--- a/src/components/screens/VariantScreen.vue
+++ b/src/components/screens/VariantScreen.vue
@@ -443,7 +443,8 @@ import MvRowActionMenu, {type RowAction} from '@/components/common/MvRowActionMe
 import VariantInfoSection from '@/components/variant/VariantInfoSection.vue'
 import {useVariantLookup} from '@/composables/use-variant-lookup'
 import {assayLevelDisplay} from '@/lib/measurement-types'
-import {hasFunctionalCalibrations, hasPathogenicityCalibrations} from '@/lib/calibrations'
+import {hasPathogenicityCalibrations} from '@/lib/acmg'
+import {hasFunctionalCalibrations} from '@/lib/calibrations'
 import {confidenceBadge, groupAlleles, type AlleleGroup, type ConfidenceBadge} from '@/lib/allele-grouping'
 import {formatConsequence} from '@/lib/formats'
 import type {components} from '@/schema/openapi'
diff --git a/src/composables/use-calibration-resolution.ts b/src/composables/use-calibration-resolution.ts
index 1304c950..ae58cd74 100644
--- a/src/composables/use-calibration-resolution.ts
+++ b/src/composables/use-calibration-resolution.ts
@@ -1,7 +1,8 @@
 import {computed, ref, watch, type ComputedRef, type Ref} from 'vue'
 
 import {getScoreCalibrationVariants} from '@/api/mavedb/calibrations'
-import {formatEvidenceCode, functionalClassificationContainsVariant} from '@/lib/calibrations'
+import {formatEvidenceCode} from '@/lib/acmg'
+import {functionalClassificationContainsVariant} from '@/lib/calibrations'
 import type {components} from '@/schema/openapi'
 
 type ScoreCalibration = components['schemas']['ScoreCalibration']
diff --git a/src/lib/acmg.ts b/src/lib/acmg.ts
new file mode 100644
index 00000000..afdc6771
--- /dev/null
+++ b/src/lib/acmg.ts
@@ -0,0 +1,70 @@
+/**
+ * The clinical bridge of the calibration layer: the ACMG functional-evidence vocabulary that translates
+ * an assay's functional impact into clinical evidence. `PS3`/`BS3` are the ACMG functional-evidence
+ * criteria; the strength ladder and point values are the ACMG/ClinGen SVI (Bayesian points) system.
+ * Kept dependency-light (schema types only) so read-side surfaces can import it without pulling in the
+ * calibration container's axios/histogram dependencies.
+ */
+
+import {components} from '@/schema/openapi'
+
+type ScoreCalibration = components['schemas']['ScoreCalibration']
+type ScoreCalibrationFunctionalClassification =
+  components['schemas']['mavedb__view_models__score_calibration__FunctionalClassification']
+
+/** ACMG functional-evidence criteria: benign-supporting (BS3) and pathogenic-supporting (PS3). */
+export const BENIGN_CRITERION = 'BS3'
+export const PATHOGENIC_CRITERION = 'PS3'
+
+/** Points each evidence-strength tier contributes on the ClinGen SVI (Bayesian) scale. */
+export const EVIDENCE_STRENGTH_AS_POINTS = {
+  VERY_STRONG: 8,
+  STRONG: 4,
+  MODERATE_PLUS: 3,
+  MODERATE: 2,
+  SUPPORTING: 1
+}
+
+/** The evidence-strength tiers, strongest first. */
+export const EVIDENCE_STRENGTH = Object.keys(EVIDENCE_STRENGTH_AS_POINTS)
+
+/**
+ * Checks if a score set has any calibrations with functional classifications that have evidence strengths.
+ * This is used to determine if pathogenicity annotations are available for variants in the score set.
+ *
+ * @param scoreCalibrations - Array of score calibrations from a score set
+ * @returns True if any calibration has at least one functional classification with an evidence strength
+ */
+export function hasPathogenicityCalibrations(
+  scoreSet: {scoreCalibrations?: ScoreCalibration[] | null} | null | undefined,
+  {excludeResearchUseOnly = true}: {excludeResearchUseOnly?: boolean} = {}
+): boolean {
+  const scoreCalibrations = scoreSet?.scoreCalibrations
+  if (!scoreCalibrations || scoreCalibrations.length === 0) {
+    return false
+  }
+
+  return scoreCalibrations.some(
+    (cal) =>
+      !(excludeResearchUseOnly && cal.researchUseOnly) &&
+      cal.functionalClassifications &&
+      Array.isArray(cal.functionalClassifications) &&
+      cal.functionalClassifications.some((funcCal) => funcCal.acmgClassification)
+  )
+}
+
+/**
+ * Formats the ACMG evidence code from a functional classification's ACMG classification data.
+ *
+ * @param classification - A functional classification that may contain an `acmgClassification`
+ *   with `criterion` (e.g. "PS3", "BS3") and `evidenceStrength` (e.g. "Strong", "Moderate").
+ * @returns A formatted code like "PS3_STRONG", or an empty string if evidence data is missing.
+ */
+export function formatEvidenceCode(
+  classification: ScoreCalibrationFunctionalClassification | null | undefined
+): string {
+  if (!classification?.acmgClassification?.evidenceStrength) return ''
+  const criterion = classification.acmgClassification.criterion
+  const strength = classification.acmgClassification.evidenceStrength.toUpperCase()
+  return `${criterion}_${strength}`
+}
diff --git a/src/lib/calibrations.ts b/src/lib/calibrations.ts
index b90aebe2..34800ef4 100644
--- a/src/lib/calibrations.ts
+++ b/src/lib/calibrations.ts
@@ -16,48 +16,13 @@ export type ScoreCalibrationFunctionalClassification =
 export type FunctionalClassificationVariants = components['schemas']['FunctionalClassificationVariants']
 export type FunctionalClassificationVariant = components['schemas']['VariantEffectMeasurement']
 
-export const BENIGN_CRITERION = 'BS3'
-export const PATHOGENIC_CRITERION = 'PS3'
-
-export const EVIDENCE_STRENGTH_AS_POINTS = {
-  VERY_STRONG: 8,
-  STRONG: 4,
-  MODERATE_PLUS: 3,
-  MODERATE: 2,
-  SUPPORTING: 1
-}
-
-export const INDETERMINATE_CALIBRATION_EVIDENCE = ['INDETERMINATE'] as const
-export const EVIDENCE_STRENGTH = EVIDENCE_STRENGTH_AS_POINTS ? Object.keys(EVIDENCE_STRENGTH_AS_POINTS) : []
-export const NORMAL_CALIBRATION_EVIDENCE = EVIDENCE_STRENGTH_AS_POINTS
-  ? Object.keys(EVIDENCE_STRENGTH_AS_POINTS).map((key) => `${BENIGN_CRITERION}_${key}`)
-  : []
-export const ABNORMAL_CALIBRATION_EVIDENCE = EVIDENCE_STRENGTH_AS_POINTS
-  ? Object.keys(EVIDENCE_STRENGTH_AS_POINTS).map((key) => `${PATHOGENIC_CRITERION}_${key}`)
-  : []
-
-export const EVIDENCE_STRENGTHS = EVIDENCE_STRENGTH_AS_POINTS
-  ? Object.fromEntries(
-      Object.entries(EVIDENCE_STRENGTH_AS_POINTS)
-        .map(([key, value]) => [`${BENIGN_CRITERION}_${key}`, value * -1])
-        .concat(
-          Object.entries(EVIDENCE_STRENGTH_AS_POINTS).map(([key, value]) => [`${PATHOGENIC_CRITERION}_${key}`, value])
-        )
-    )
-  : {}
-
-export const EVIDENCE_STRENGTHS_REVERSED = Object.fromEntries(
-  Object.entries(EVIDENCE_STRENGTHS).map(([key, value]) => [value, key])
-)
-
 /**
  * Prepares a list of histogram shader configuration objects from persisted score calibration data.
  *
  * Each functional range in the provided calibration is converted into a HistogramShader descriptor
  * containing:
  * - min / max: numeric bounds either taken directly from the `range` tuple or calculated from variant scores.
- * - title: resolved from the ACMG classification evidence strength (via `EVIDENCE_STRENGTHS_REVERSED`)
- *   when available; otherwise falls back to the range's `label`.
+ * - title: the range's `label`.
  * - color / thresholdColor: both derived from `getRangeColor(range)` to ensure visual consistency.
  * - align: fixed to `'center'` for consistent label placement.
  * - startOpacity / stopOpacity: fixed opacity values (0.15 → 0.05) establishing a subtle gradient.
@@ -200,31 +165,6 @@ export function functionalClassificationContainsVariant(
   return lowerOk && upperOk
 }
 
-/**
- * Checks if a score set has any calibrations with functional classifications that have evidence strengths.
- * This is used to determine if pathogenicity annotations are available for variants in the score set.
- *
- * @param scoreCalibrations - Array of score calibrations from a score set
- * @returns True if any calibration has at least one functional classification with an evidence strength
- */
-export function hasPathogenicityCalibrations(
-  scoreSet: {scoreCalibrations?: ScoreCalibration[] | null} | null | undefined,
-  {excludeResearchUseOnly = true}: {excludeResearchUseOnly?: boolean} = {}
-): boolean {
-  const scoreCalibrations = scoreSet?.scoreCalibrations
-  if (!scoreCalibrations || scoreCalibrations.length === 0) {
-    return false
-  }
-
-  return scoreCalibrations.some(
-    (cal) =>
-      !(excludeResearchUseOnly && cal.researchUseOnly) &&
-      cal.functionalClassifications &&
-      Array.isArray(cal.functionalClassifications) &&
-      cal.functionalClassifications.some((funcCal) => funcCal.acmgClassification)
-  )
-}
-
 /**
  * Checks if a score set has any calibrations with functional classifications.
  * This is used to determine if functional impact annotations are available for variants in the score set.
@@ -305,22 +245,6 @@ export function getClassificationOddsPath(
   return range?.oddspathsRatio != null ? range.oddspathsRatio.toFixed(precision) : null
 }
 
-/**
- * Formats the ACMG evidence code from a functional classification's ACMG classification data.
- *
- * @param classification - A functional classification that may contain an `acmgClassification`
- *   with `criterion` (e.g. "PS3", "BS3") and `evidenceStrength` (e.g. "Strong", "Moderate").
- * @returns A formatted code like "PS3_STRONG", or an empty string if evidence data is missing.
- */
-export function formatEvidenceCode(
-  classification: ScoreCalibrationFunctionalClassification | null | undefined
-): string {
-  if (!classification?.acmgClassification?.evidenceStrength) return ''
-  const criterion = classification.acmgClassification.criterion
-  const strength = classification.acmgClassification.evidenceStrength.toUpperCase()
-  return `${criterion}_${strength}`
-}
-
 export type CalibrationSaveResult =
   | {success: true; data: any}
   | {success: false; error: 'email_required'}

From 95d1b26b0598a91295f1e76350f59c1cd55375c7 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 16 Jul 2026 16:37:29 -0700
Subject: [PATCH 49/84] refactor(calibration): keep container queries in
 calibrations.ts

hasPathogenicityCalibrations and hasFunctionalCalibrations are a matched pair
of queries over the ScoreCalibration container (same signature, shared
excludeResearchUseOnly option), so both belong with the container's other
selection helpers rather than split across modules. Move
hasPathogenicityCalibrations back out of acmg.ts, which leaves acmg.ts as pure
ACMG evidence vocabulary (no ScoreCalibration container dependency).

Corrects the placement from the acmg.ts extraction: sublayer modules own
vocabulary and single-classification operations; container queries stay in
calibrations.ts.
---
 src/components/screens/ScoreSetView.vue  |  3 +--
 src/components/screens/VariantScreen.vue |  5 ++---
 src/lib/acmg.ts                          | 26 ------------------------
 src/lib/calibrations.ts                  | 25 +++++++++++++++++++++++
 4 files changed, 28 insertions(+), 31 deletions(-)

diff --git a/src/components/screens/ScoreSetView.vue b/src/components/screens/ScoreSetView.vue
index c50c170c..7030ba67 100644
--- a/src/components/screens/ScoreSetView.vue
+++ b/src/components/screens/ScoreSetView.vue
@@ -504,8 +504,7 @@ import {useClinvarControls} from '@/composables/use-clinvar-controls'
 import {useChartExport, type ChartExportFns} from '@/composables/use-chart-export'
 import {useVariantCoordinates, type CoordinateFrame, type SequenceLevel} from '@/composables/use-variant-coordinates'
 import config from '@/config'
-import {hasPathogenicityCalibrations} from '@/lib/acmg'
-import {hasFunctionalCalibrations} from '@/lib/calibrations'
+import {hasFunctionalCalibrations, hasPathogenicityCalibrations} from '@/lib/calibrations'
 import {getScoreSetShortName} from '@/lib/score-sets'
 import {dominantAssayLevel} from '@/lib/measurement-types'
 import {type DisplayVariant} from '@/lib/variants'
diff --git a/src/components/screens/VariantScreen.vue b/src/components/screens/VariantScreen.vue
index afbfb62a..6e70c1af 100644
--- a/src/components/screens/VariantScreen.vue
+++ b/src/components/screens/VariantScreen.vue
@@ -219,7 +219,7 @@
               <span class="text-[10px] font-semibold uppercase tracking-[0.3px] text-[#aaa]">Functional impact</span>
               <MvClassificationTag
                 v-if="lookup.calibrationResolution.classification.value"
-                v-key-term="'consequence'"
+                v-key-term="'functional-impact'"
                 :classification="lookup.calibrationResolution.classification.value"
               />
               <span v-else class="text-sm text-text-muted">—</span>
@@ -443,8 +443,7 @@ import MvRowActionMenu, {type RowAction} from '@/components/common/MvRowActionMe
 import VariantInfoSection from '@/components/variant/VariantInfoSection.vue'
 import {useVariantLookup} from '@/composables/use-variant-lookup'
 import {assayLevelDisplay} from '@/lib/measurement-types'
-import {hasPathogenicityCalibrations} from '@/lib/acmg'
-import {hasFunctionalCalibrations} from '@/lib/calibrations'
+import {hasFunctionalCalibrations, hasPathogenicityCalibrations} from '@/lib/calibrations'
 import {confidenceBadge, groupAlleles, type AlleleGroup, type ConfidenceBadge} from '@/lib/allele-grouping'
 import {formatConsequence} from '@/lib/formats'
 import type {components} from '@/schema/openapi'
diff --git a/src/lib/acmg.ts b/src/lib/acmg.ts
index afdc6771..84c8ce31 100644
--- a/src/lib/acmg.ts
+++ b/src/lib/acmg.ts
@@ -8,7 +8,6 @@
 
 import {components} from '@/schema/openapi'
 
-type ScoreCalibration = components['schemas']['ScoreCalibration']
 type ScoreCalibrationFunctionalClassification =
   components['schemas']['mavedb__view_models__score_calibration__FunctionalClassification']
 
@@ -28,31 +27,6 @@ export const EVIDENCE_STRENGTH_AS_POINTS = {
 /** The evidence-strength tiers, strongest first. */
 export const EVIDENCE_STRENGTH = Object.keys(EVIDENCE_STRENGTH_AS_POINTS)
 
-/**
- * Checks if a score set has any calibrations with functional classifications that have evidence strengths.
- * This is used to determine if pathogenicity annotations are available for variants in the score set.
- *
- * @param scoreCalibrations - Array of score calibrations from a score set
- * @returns True if any calibration has at least one functional classification with an evidence strength
- */
-export function hasPathogenicityCalibrations(
-  scoreSet: {scoreCalibrations?: ScoreCalibration[] | null} | null | undefined,
-  {excludeResearchUseOnly = true}: {excludeResearchUseOnly?: boolean} = {}
-): boolean {
-  const scoreCalibrations = scoreSet?.scoreCalibrations
-  if (!scoreCalibrations || scoreCalibrations.length === 0) {
-    return false
-  }
-
-  return scoreCalibrations.some(
-    (cal) =>
-      !(excludeResearchUseOnly && cal.researchUseOnly) &&
-      cal.functionalClassifications &&
-      Array.isArray(cal.functionalClassifications) &&
-      cal.functionalClassifications.some((funcCal) => funcCal.acmgClassification)
-  )
-}
-
 /**
  * Formats the ACMG evidence code from a functional classification's ACMG classification data.
  *
diff --git a/src/lib/calibrations.ts b/src/lib/calibrations.ts
index 34800ef4..b942f26d 100644
--- a/src/lib/calibrations.ts
+++ b/src/lib/calibrations.ts
@@ -165,6 +165,31 @@ export function functionalClassificationContainsVariant(
   return lowerOk && upperOk
 }
 
+/**
+ * Checks if a score set has any calibrations with functional classifications that have evidence strengths.
+ * This is used to determine if pathogenicity annotations are available for variants in the score set.
+ *
+ * @param scoreCalibrations - Array of score calibrations from a score set
+ * @returns True if any calibration has at least one functional classification with an evidence strength
+ */
+export function hasPathogenicityCalibrations(
+  scoreSet: {scoreCalibrations?: ScoreCalibration[] | null} | null | undefined,
+  {excludeResearchUseOnly = true}: {excludeResearchUseOnly?: boolean} = {}
+): boolean {
+  const scoreCalibrations = scoreSet?.scoreCalibrations
+  if (!scoreCalibrations || scoreCalibrations.length === 0) {
+    return false
+  }
+
+  return scoreCalibrations.some(
+    (cal) =>
+      !(excludeResearchUseOnly && cal.researchUseOnly) &&
+      cal.functionalClassifications &&
+      Array.isArray(cal.functionalClassifications) &&
+      cal.functionalClassifications.some((funcCal) => funcCal.acmgClassification)
+  )
+}
+
 /**
  * Checks if a score set has any calibrations with functional classifications.
  * This is used to determine if functional impact annotations are available for variants in the score set.

From f69be88d992c26cac40fa92ec493fcdb793a689e Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 16 Jul 2026 16:38:19 -0700
Subject: [PATCH 50/84] refactor(variant): unify ACMG key section and split
 functional impact

Derive the drawer's PS3/BS3 terms from a new ACMG_CRITERIA vocabulary in
acmg.ts, keyed by the criterion constants the evidence tags render, so the
codes and glosses can't drift (evidence strength and OddsPath stay inline as
prose). Split the drawer's 'Consequence vs impact' section into distinct
'Molecular consequence' and 'Functional impact' sections and repoint the
measurement card's classification badge at the functional-impact anchor.
---
 src/components/variant/MvMeasurementCard.vue   |  2 +-
 src/components/variant/variant-key-sections.ts | 17 ++++++++++++-----
 src/lib/acmg.ts                                | 16 ++++++++++++++++
 3 files changed, 29 insertions(+), 6 deletions(-)

diff --git a/src/components/variant/MvMeasurementCard.vue b/src/components/variant/MvMeasurementCard.vue
index 758110d5..98717cb4 100644
--- a/src/components/variant/MvMeasurementCard.vue
+++ b/src/components/variant/MvMeasurementCard.vue
@@ -55,7 +55,7 @@
       <div v-if="classification || evidenceCode" class="mt-1.5">
         <span class="mb-1 block text-[10px] font-bold uppercase tracking-[0.3px] text-[#aaa]">Classified as</span>
         <div class="flex flex-wrap items-center gap-1.5">
-          <MvClassificationTag v-if="classification" v-key-term="'consequence'" :classification="classification" />
+          <MvClassificationTag v-if="classification" v-key-term="'functional-impact'" :classification="classification" />
           <MvEvidenceTag v-if="evidenceCode" v-key-term="'acmg'" :code="evidenceCode" />
           <span v-if="oddspathsRatio != null" v-key-term="'acmg'" class="text-xs text-text-muted"
             >(OddsPath {{ oddspathsRatio.toPrecision(3) }})</span
diff --git a/src/components/variant/variant-key-sections.ts b/src/components/variant/variant-key-sections.ts
index c8dda146..17d2105e 100644
--- a/src/components/variant/variant-key-sections.ts
+++ b/src/components/variant/variant-key-sections.ts
@@ -1,5 +1,6 @@
 import config from '@/config'
 import type {KeySection} from '@/composables/use-key-drawer'
+import {ACMG_CRITERIA} from '@/lib/acmg'
 import {ALLELE_CONFIDENCE} from '@/lib/allele-grouping'
 import {FUNCTIONAL_CLASSIFICATIONS} from '@/lib/functional-impact'
 import {LEVEL_BUCKETS, RELATIONSHIPS} from '@/lib/measurement-types'
@@ -61,14 +62,20 @@ export const VARIANT_KEY_SECTIONS: KeySection[] = [
   },
   {
     id: 'consequence',
-    title: 'Consequence vs impact',
+    title: 'Molecular consequence',
     terms: [
       {
         label: 'Molecular consequence',
         definition: 'The predicted effect on the transcript or protein (e.g. missense), from VEP.'
-      },
+      }
+    ]
+  },
+  {
+    id: 'functional-impact',
+    title: 'Functional impact',
+    terms: [
       {label: 'Functional impact', definition: "The assay's verdict on whether the variant alters function."},
-      // The two functional calls derive from the shared classification vocabulary so tag and gloss can't drift.
+      // Derived from the shared classification vocabulary so tag and gloss can't drift.
       ...Object.values(FUNCTIONAL_CLASSIFICATIONS)
         .filter((c) => c.definition)
         .map((c) => ({label: c.label, definition: c.definition!, class: c.class}))
@@ -79,8 +86,8 @@ export const VARIANT_KEY_SECTIONS: KeySection[] = [
     title: 'ACMG functional evidence',
     gloss: 'How the functional result maps onto clinical-classification evidence.',
     terms: [
-      {label: 'PS3', definition: 'Functional evidence supporting a pathogenic classification.'},
-      {label: 'BS3', definition: 'Functional evidence supporting a benign classification.'},
+      // PS3/BS3 derive from the shared ACMG criteria vocabulary so the codes and glosses can't drift.
+      ...Object.values(ACMG_CRITERIA),
       {
         label: 'Evidence strength',
         definition: 'How much weight the evidence carries: supporting → moderate → strong → very strong.'
diff --git a/src/lib/acmg.ts b/src/lib/acmg.ts
index 84c8ce31..79ff85de 100644
--- a/src/lib/acmg.ts
+++ b/src/lib/acmg.ts
@@ -27,6 +27,22 @@ export const EVIDENCE_STRENGTH_AS_POINTS = {
 /** The evidence-strength tiers, strongest first. */
 export const EVIDENCE_STRENGTH = Object.keys(EVIDENCE_STRENGTH_AS_POINTS)
 
+/**
+ * The two ACMG functional-evidence criteria with their Key-drawer glosses, keyed by criterion code so the
+ * drawer labels are the very constants the evidence tags render — they can't drift. Pathogenic first
+ * (display order).
+ */
+export const ACMG_CRITERIA: Record<string, {label: string; definition: string}> = {
+  [PATHOGENIC_CRITERION]: {
+    label: PATHOGENIC_CRITERION,
+    definition: 'Functional evidence supporting a pathogenic classification.'
+  },
+  [BENIGN_CRITERION]: {
+    label: BENIGN_CRITERION,
+    definition: 'Functional evidence supporting a benign classification.'
+  }
+}
+
 /**
  * Formats the ACMG evidence code from a functional classification's ACMG classification data.
  *

From 3360a90c80d57142160553042a16f29718124501 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 16 Jul 2026 16:46:07 -0700
Subject: [PATCH 51/84] refactor(variant): co-locate prose glossary sections
 with their owners
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Move the population, clinical-significance, sibling-control, and coordinate-frame
Key-drawer sections out of the screen-level assembly and into the modules that
own each concept: gnomad.ts, clinvar-controls.ts, and use-variant-coordinates.ts.
variant-key-sections.ts now imports them by reference, keeping only display order.

These are prose sections with no rendered vocabulary to bind to, so this is
ownership co-location rather than drift prevention — the sections now live beside
the code that owns the concept, per the global-glossary end-state.
---
 .../variant/variant-key-sections.ts           | 65 ++-----------------
 src/composables/use-variant-coordinates.ts    | 17 +++++
 src/lib/clinvar-controls.ts                   | 27 ++++++++
 src/lib/gnomad.ts                             | 25 +++++++
 4 files changed, 76 insertions(+), 58 deletions(-)

diff --git a/src/components/variant/variant-key-sections.ts b/src/components/variant/variant-key-sections.ts
index 17d2105e..af8b12df 100644
--- a/src/components/variant/variant-key-sections.ts
+++ b/src/components/variant/variant-key-sections.ts
@@ -1,8 +1,11 @@
 import config from '@/config'
 import type {KeySection} from '@/composables/use-key-drawer'
+import {COORDINATE_FRAME_KEY_SECTION} from '@/composables/use-variant-coordinates'
 import {ACMG_CRITERIA} from '@/lib/acmg'
 import {ALLELE_CONFIDENCE} from '@/lib/allele-grouping'
+import {CLINICAL_SIGNIFICANCE_KEY_SECTION, SIBLING_CONTROL_KEY_SECTION} from '@/lib/clinvar-controls'
 import {FUNCTIONAL_CLASSIFICATIONS} from '@/lib/functional-impact'
+import {POPULATION_KEY_SECTION} from '@/lib/gnomad'
 import {LEVEL_BUCKETS, RELATIONSHIPS} from '@/lib/measurement-types'
 
 /**
@@ -46,20 +49,7 @@ export const VARIANT_KEY_SECTIONS: KeySection[] = [
       }
     ]
   },
-  {
-    id: 'frame',
-    title: 'Coordinate frame',
-    terms: [
-      {
-        label: 'Submitted',
-        definition: 'Coordinates exactly as the depositor submitted them, relative to the target sequence.'
-      },
-      {
-        label: 'Reference',
-        definition: "Coordinates re-expressed against a standard reference sequence by MaveDB's mapping pipeline."
-      }
-    ]
-  },
+  COORDINATE_FRAME_KEY_SECTION,
   {
     id: 'consequence',
     title: 'Molecular consequence',
@@ -95,50 +85,9 @@ export const VARIANT_KEY_SECTIONS: KeySection[] = [
       {label: 'OddsPath', definition: 'The odds of pathogenicity implied by the score; sets the evidence strength.'}
     ]
   },
-  {
-    id: 'population',
-    title: 'Population frequency (gnomAD)',
-    gloss: 'How often the allele is seen in reference populations — high frequency argues against pathogenicity.',
-    terms: [
-      {
-        label: 'Allele frequency (AF)',
-        definition:
-          'The fraction of sampled reference-population chromosomes carrying this allele in gnomAD (allele count ÷ allele number).'
-      },
-      {
-        label: 'AC / AN',
-        definition:
-          'Allele count and allele number: the observed carriers and the total chromosomes sampled that the frequency is computed from.'
-      },
-      {
-        label: 'FAF95',
-        definition:
-          "Filtering allele frequency at 95% confidence: a sampling-adjusted, conservative estimate of the population frequency. When it exceeds a disease's maximum credible allele frequency, the variant is too common to be pathogenic (ACMG BA1/BS1)."
-      }
-    ]
-  },
-  {
-    id: 'clinical',
-    title: 'Clinical significance (ClinVar)',
-    gloss: 'Germline classifications, shown with their ClinVar review-star rating.',
-    terms: [
-      {label: 'Pathogenic / Likely pathogenic', definition: 'Classified as disease-causing, or likely to be.'},
-      {label: 'Benign / Likely benign', definition: 'Classified as not disease-causing, or likely not to be.'},
-      {label: 'VUS', definition: 'Variant of uncertain significance — not enough evidence to classify.'},
-      {label: 'Conflicting', definition: 'Submitters disagree on the classification.'}
-    ]
-  },
-  {
-    id: 'passthrough',
-    title: 'Sibling-allele controls',
-    terms: [
-      {
-        label: 'From a sibling allele',
-        definition:
-          'A ClinVar call carried over from a sibling allele that shares the protein consequence, shown when the assayed variant itself has no ClinVar record. Marked with *.'
-      }
-    ]
-  },
+  POPULATION_KEY_SECTION,
+  CLINICAL_SIGNIFICANCE_KEY_SECTION,
+  SIBLING_CONTROL_KEY_SECTION,
   {
     id: 'as-of',
     title: 'As of',
diff --git a/src/composables/use-variant-coordinates.ts b/src/composables/use-variant-coordinates.ts
index 582bacc8..b6221417 100644
--- a/src/composables/use-variant-coordinates.ts
+++ b/src/composables/use-variant-coordinates.ts
@@ -1,3 +1,4 @@
+import type {KeySection} from '@/composables/use-key-drawer'
 import type {components} from '@/schema/openapi'
 import type {HgvsField, LeanVariant} from '@/lib/variants'
 
@@ -8,6 +9,22 @@ export type SequenceLevel = components['schemas']['SequenceLevel']
 /** The coordinate frame: `submitted` = submitted/target numbering, `reference` = reference numbering. */
 export type CoordinateFrame = 'submitted' | 'reference'
 
+/** Key-drawer glossary for the coordinate-frame axis this composable resolves. */
+export const COORDINATE_FRAME_KEY_SECTION: KeySection = {
+  id: 'frame',
+  title: 'Coordinate frame',
+  terms: [
+    {
+      label: 'Submitted',
+      definition: 'Coordinates exactly as the depositor submitted them, relative to the target sequence.'
+    },
+    {
+      label: 'Reference',
+      definition: "Coordinates re-expressed against a standard reference sequence by MaveDB's mapping pipeline."
+    }
+  ]
+}
+
 /**
  * Stateless resolution of a variant's HGVS coordinate across two orthogonal axes — sequence
  * **level** (cdna / genomic / protein) and **frame** (submitted ↔ reference).
diff --git a/src/lib/clinvar-controls.ts b/src/lib/clinvar-controls.ts
index 1188337b..c68651a1 100644
--- a/src/lib/clinvar-controls.ts
+++ b/src/lib/clinvar-controls.ts
@@ -1,3 +1,4 @@
+import type {KeySection} from '@/composables/use-key-drawer'
 import {hgvsLabelRank} from '@/lib/formats'
 import type {components} from '@/schema/openapi'
 
@@ -5,6 +6,32 @@ export type ClinvarControlOption = components['schemas']['ClinicalControlOptions
 export type ClinvarVariantLink = components['schemas']['ClinvarVariantLink']
 export type ClinvarControl = components['schemas']['ClinicalControlWithClinvarLinks']
 
+/** Key-drawer glossary for the ClinVar clinical-significance buckets this module classifies into. */
+export const CLINICAL_SIGNIFICANCE_KEY_SECTION: KeySection = {
+  id: 'clinical',
+  title: 'Clinical significance (ClinVar)',
+  gloss: 'Germline classifications, shown with their ClinVar review-star rating.',
+  terms: [
+    {label: 'Pathogenic / Likely pathogenic', definition: 'Classified as disease-causing, or likely to be.'},
+    {label: 'Benign / Likely benign', definition: 'Classified as not disease-causing, or likely not to be.'},
+    {label: 'VUS', definition: 'Variant of uncertain significance — not enough evidence to classify.'},
+    {label: 'Conflicting', definition: 'Submitters disagree on the classification.'}
+  ]
+}
+
+/** Key-drawer glossary for sibling-allele ClinVar controls (calls carried over from a sibling allele). */
+export const SIBLING_CONTROL_KEY_SECTION: KeySection = {
+  id: 'passthrough',
+  title: 'Sibling-allele controls',
+  terms: [
+    {
+      label: 'From a sibling allele',
+      definition:
+        'A ClinVar call carried over from a sibling allele that shares the protein consequence, shown when the assayed variant itself has no ClinVar record. Marked with *.'
+    }
+  ]
+}
+
 type AlleleAnnotations = components['schemas']['AlleleAnnotations']
 type ClinvarAnnotation = components['schemas']['ClinvarAnnotation']
 
diff --git a/src/lib/gnomad.ts b/src/lib/gnomad.ts
index ac468375..6ce51204 100644
--- a/src/lib/gnomad.ts
+++ b/src/lib/gnomad.ts
@@ -7,11 +7,36 @@
  * and link to the gnomAD variant page.
  */
 
+import type {KeySection} from '@/composables/use-key-drawer'
 import {hgvsLabelRank} from '@/lib/formats'
 import type {components} from '@/schema/openapi'
 
 type GnomadAnnotation = components['schemas']['GnomadAnnotation']
 
+/** Key-drawer glossary for the gnomAD population-frequency terms this module surfaces. */
+export const POPULATION_KEY_SECTION: KeySection = {
+  id: 'population',
+  title: 'Population frequency (gnomAD)',
+  gloss: 'How often the allele is seen in reference populations — high frequency argues against pathogenicity.',
+  terms: [
+    {
+      label: 'Allele frequency (AF)',
+      definition:
+        'The fraction of sampled reference-population chromosomes carrying this allele in gnomAD (allele count ÷ allele number).'
+    },
+    {
+      label: 'AC / AN',
+      definition:
+        'Allele count and allele number: the observed carriers and the total chromosomes sampled that the frequency is computed from.'
+    },
+    {
+      label: 'FAF95',
+      definition:
+        "Filtering allele frequency at 95% confidence: a sampling-adjusted, conservative estimate of the population frequency. When it exceeds a disease's maximum credible allele frequency, the variant is too common to be pathogenic (ACMG BA1/BS1)."
+    }
+  ]
+}
+
 /** One underlying gnomAD measurement, tagged with the reference-frame HGVS of the allele it annotates. */
 export interface UnderlyingGnomad {
   hgvs: string | null

From 42d7a4f183d490efdec04c30e064ce8a779fc7b8 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 16 Jul 2026 23:01:39 -0700
Subject: [PATCH 52/84] refactor(glossary): co-locate key sections with owning
 modules, go app-global

- Each lib module (acmg, allele-grouping, functional-impact,
  measurement-types) now exports its own KeySection constant adjacent
  to the vocab it describes, so badge and gloss can't drift
- Prose-only sections (consequence, as-of, superseded, selected-allele)
  moved to src/lib/glossary-prose.ts
- Central assembler promoted to src/glossary.ts (GLOSSARY_SECTIONS /
  GLOSSARY_DOCS_URL) replacing the variant-scoped variant-key-sections.ts
- MvKeyDrawer drops its sections/docsUrl props and reads from glossary
  directly; mounted once in App.vue alongside ConfirmDialog and Toast
- VariantScreen no longer owns the drawer; v-key-term now resolves on
  any screen
---
 src/App.vue                                   |   5 +-
 src/components/common/MvKeyDrawer.vue         |  23 ++--
 src/components/screens/VariantScreen.vue      |  10 +-
 .../variant/variant-key-sections.ts           | 113 ------------------
 src/glossary.ts                               |  28 +++++
 src/lib/acmg.ts                               |  19 +--
 src/lib/allele-grouping.ts                    |   7 ++
 src/lib/functional-impact.ts                  |  13 ++
 src/lib/glossary-prose.ts                     |  48 ++++++++
 src/lib/measurement-types.ts                  |  57 +++++----
 10 files changed, 158 insertions(+), 165 deletions(-)
 delete mode 100644 src/components/variant/variant-key-sections.ts
 create mode 100644 src/glossary.ts
 create mode 100644 src/lib/glossary-prose.ts

diff --git a/src/App.vue b/src/App.vue
index b7061036..16cd53e5 100644
--- a/src/App.vue
+++ b/src/App.vue
@@ -2,6 +2,7 @@
   <router-view :key="$route.path" />
   <ConfirmDialog></ConfirmDialog>
   <Toast position="bottom-right" />
+  <MvKeyDrawer />
 </template>
 
 <script>
@@ -9,8 +10,10 @@ import ConfirmDialog from 'primevue/confirmdialog'
 import Toast from 'primevue/toast'
 import {mapActions, mapState} from 'vuex'
 
+import MvKeyDrawer from '@/components/common/MvKeyDrawer.vue'
+
 export default {
-  components: {ConfirmDialog, Toast},
+  components: {ConfirmDialog, MvKeyDrawer, Toast},
 
   computed: mapState('toast', ['toasts']),
 
diff --git a/src/components/common/MvKeyDrawer.vue b/src/components/common/MvKeyDrawer.vue
index 911b9911..4d567d3b 100644
--- a/src/components/common/MvKeyDrawer.vue
+++ b/src/components/common/MvKeyDrawer.vue
@@ -65,32 +65,27 @@
 </template>
 
 <script lang="ts">
-import {defineComponent, nextTick, type PropType} from 'vue'
+import {defineComponent, nextTick} from 'vue'
 
-import {useKeyDrawer, type KeySection} from '@/composables/use-key-drawer'
+import {useKeyDrawer} from '@/composables/use-key-drawer'
+import {GLOSSARY_DOCS_URL, GLOSSARY_SECTIONS} from '@/glossary'
 
 /**
- * Generic vocabulary "Key" — a non-modal, right-side (mobile: pop-out card) definitions drawer. Content
- * is injected via `sections`, so this component carries no page-specific text; a page supplies its own
- * sections (see e.g. the variant page's `variant-key-sections`). Mounted once per page; opened from a
- * trigger or deep-linked from a badge via the shared {@link useKeyDrawer} singleton (or the `v-key-term`
- * directive). On a deep link it scrolls the target section into view and flashes it. Closes only on ✕ or
- * Esc, so it can stay open while the reader scans the page beneath it.
+ * Vocabulary "Key" drawer — non-modal, right-side (mobile: pop-out card). Mounted once at the app root
+ * so it's reachable from any screen. Opened from a trigger or deep-linked from any badge via the shared
+ * {@link useKeyDrawer} singleton (or the `v-key-term` directive). On a deep link it scrolls the target
+ * section into view and flashes it. Closes only on ✕ or Esc, so it can stay open while the reader scans.
  */
 export default defineComponent({
   name: 'MvKeyDrawer',
 
   props: {
-    /** The definition sections to render, in display order. */
-    sections: {type: Array as PropType<KeySection[]>, required: true},
     /** Header label (and the noun in the close button's aria-label). */
-    title: {type: String, default: 'Key'},
-    /** Default "more →" docs link for every section; a section may override via its own `docsUrl`. */
-    docsUrl: {type: String as PropType<string | undefined>, default: undefined}
+    title: {type: String, default: 'Key'}
   },
 
   setup() {
-    return {drawer: useKeyDrawer()}
+    return {drawer: useKeyDrawer(), sections: GLOSSARY_SECTIONS, docsUrl: GLOSSARY_DOCS_URL}
   },
 
   data() {
diff --git a/src/components/screens/VariantScreen.vue b/src/components/screens/VariantScreen.vue
index 6e70c1af..78630f5e 100644
--- a/src/components/screens/VariantScreen.vue
+++ b/src/components/screens/VariantScreen.vue
@@ -404,9 +404,6 @@
       </template>
     </div>
 
-    <!-- Vocabulary Key: mounted once; opened from the control-header trigger or deep-linked from a badge.
-         Generic drawer + variant-page content injected via props. -->
-    <MvKeyDrawer :docs-url="keyDocsUrl" :sections="keySections" />
   </MvLayout>
 </template>
 
@@ -436,8 +433,6 @@ import MvRelatedAlleles from '@/components/variant/MvRelatedAlleles.vue'
 import MvClassificationTag from '@/components/common/MvClassificationTag.vue'
 import VariantGnomadStat from '@/components/variant/VariantGnomadStat.vue'
 import VariantClinvarStat from '@/components/variant/VariantClinvarStat.vue'
-import MvKeyDrawer from '@/components/common/MvKeyDrawer.vue'
-import {VARIANT_KEY_SECTIONS, VARIANT_KEY_DOCS_URL} from '@/components/variant/variant-key-sections'
 import MvMeasurementCard from '@/components/variant/MvMeasurementCard.vue'
 import MvRowActionMenu, {type RowAction} from '@/components/common/MvRowActionMenu.vue'
 import VariantInfoSection from '@/components/variant/VariantInfoSection.vue'
@@ -463,7 +458,6 @@ export default defineComponent({
     VariantClinvarStat,
     MvAssayFactsCard,
     MvBadgeToggle,
-    MvKeyDrawer,
     MvEmptyState,
     MvErrorState,
     MvEvidenceTag,
@@ -508,9 +502,7 @@ export default defineComponent({
       head: useHead({title: 'Variant search results'}),
       lookup,
       clinvarControls,
-      keyDrawer: useKeyDrawer(),
-      keySections: VARIANT_KEY_SECTIONS,
-      keyDocsUrl: VARIANT_KEY_DOCS_URL
+      keyDrawer: useKeyDrawer()
     }
   },
 
diff --git a/src/components/variant/variant-key-sections.ts b/src/components/variant/variant-key-sections.ts
deleted file mode 100644
index af8b12df..00000000
--- a/src/components/variant/variant-key-sections.ts
+++ /dev/null
@@ -1,113 +0,0 @@
-import config from '@/config'
-import type {KeySection} from '@/composables/use-key-drawer'
-import {COORDINATE_FRAME_KEY_SECTION} from '@/composables/use-variant-coordinates'
-import {ACMG_CRITERIA} from '@/lib/acmg'
-import {ALLELE_CONFIDENCE} from '@/lib/allele-grouping'
-import {CLINICAL_SIGNIFICANCE_KEY_SECTION, SIBLING_CONTROL_KEY_SECTION} from '@/lib/clinvar-controls'
-import {FUNCTIONAL_CLASSIFICATIONS} from '@/lib/functional-impact'
-import {POPULATION_KEY_SECTION} from '@/lib/gnomad'
-import {LEVEL_BUCKETS, RELATIONSHIPS} from '@/lib/measurement-types'
-
-/**
- * Variant-page content for the generic {@link MvKeyDrawer}. These are the tier-2 vocabulary glosses; the
- * section `id`s are the deep-link anchors that badges pass to the Key drawer (via `v-key-term`).
- */
-
-// TODO- Interim target: the general key-concepts page. Repoint to the dedicated mapping/annotation docs
-// section once it exists (see the mapping-docs plan).
-export const VARIANT_KEY_DOCS_URL = `${config.appBaseUrl}/docs/mavedb/getting-started/key-concepts.html`
-
-export const VARIANT_KEY_SECTIONS: KeySection[] = [
-  {
-    id: 'relationship',
-    title: 'Relationship to your variant',
-    gloss: 'How each result relates to the allele you searched.',
-    // Derived from the shared relationship vocabulary so cards and this gloss can never drift apart.
-    terms: Object.values(RELATIONSHIPS).map((r) => ({label: r.label, definition: r.definition, class: r.class}))
-  },
-  {
-    id: 'assay-level',
-    title: 'Assay level',
-    gloss: 'The level at which a result measured the change.',
-    // Derived from the shared bucket vocabulary so badges and this gloss can never drift apart.
-    terms: Object.values(LEVEL_BUCKETS).map((b) => ({label: b.label, definition: b.definition, class: b.class}))
-  },
-  {
-    id: 'confidence',
-    title: 'How a coordinate was established',
-    // Assembled from the shared confidence vocabulary so badges and this gloss can never drift apart.
-    terms: Object.values(ALLELE_CONFIDENCE).map((c) => ({label: c.label, definition: c.definition, class: c.class}))
-  },
-  {
-    id: 'selected-allele',
-    title: 'Selected allele',
-    terms: [
-      {
-        label: 'Selected allele',
-        definition: 'The allele this page is anchored on — the ClinGen allele you navigated to.',
-        class: 'bg-link/10 text-link'
-      }
-    ]
-  },
-  COORDINATE_FRAME_KEY_SECTION,
-  {
-    id: 'consequence',
-    title: 'Molecular consequence',
-    terms: [
-      {
-        label: 'Molecular consequence',
-        definition: 'The predicted effect on the transcript or protein (e.g. missense), from VEP.'
-      }
-    ]
-  },
-  {
-    id: 'functional-impact',
-    title: 'Functional impact',
-    terms: [
-      {label: 'Functional impact', definition: "The assay's verdict on whether the variant alters function."},
-      // Derived from the shared classification vocabulary so tag and gloss can't drift.
-      ...Object.values(FUNCTIONAL_CLASSIFICATIONS)
-        .filter((c) => c.definition)
-        .map((c) => ({label: c.label, definition: c.definition!, class: c.class}))
-    ]
-  },
-  {
-    id: 'acmg',
-    title: 'ACMG functional evidence',
-    gloss: 'How the functional result maps onto clinical-classification evidence.',
-    terms: [
-      // PS3/BS3 derive from the shared ACMG criteria vocabulary so the codes and glosses can't drift.
-      ...Object.values(ACMG_CRITERIA),
-      {
-        label: 'Evidence strength',
-        definition: 'How much weight the evidence carries: supporting → moderate → strong → very strong.'
-      },
-      {label: 'OddsPath', definition: 'The odds of pathogenicity implied by the score; sets the evidence strength.'}
-    ]
-  },
-  POPULATION_KEY_SECTION,
-  CLINICAL_SIGNIFICANCE_KEY_SECTION,
-  SIBLING_CONTROL_KEY_SECTION,
-  {
-    id: 'as-of',
-    title: 'As of',
-    terms: [
-      {
-        label: 'As of MaveDB …',
-        definition: 'MaveDB reconstructs its molecular and annotation layer as of the chosen date; scores never change.'
-      },
-      {label: 'As of ClinVar …', definition: 'The ClinVar release a clinical call was drawn from.'}
-    ]
-  },
-  {
-    id: 'superseded',
-    title: 'Superseded',
-    terms: [
-      {
-        label: 'Superseded',
-        definition:
-          'The measurement comes from an older version of its score set. A newer version exists but may not contain a corresponding variant.'
-      }
-    ]
-  }
-]
diff --git a/src/glossary.ts b/src/glossary.ts
new file mode 100644
index 00000000..fd8560c5
--- /dev/null
+++ b/src/glossary.ts
@@ -0,0 +1,28 @@
+import config from '@/config'
+import type {KeySection} from '@/composables/use-key-drawer'
+import {COORDINATE_FRAME_KEY_SECTION} from '@/composables/use-variant-coordinates'
+import {ACMG_KEY_SECTION} from '@/lib/acmg'
+import {CONFIDENCE_KEY_SECTION} from '@/lib/allele-grouping'
+import {CLINICAL_SIGNIFICANCE_KEY_SECTION, SIBLING_CONTROL_KEY_SECTION} from '@/lib/clinvar-controls'
+import {FUNCTIONAL_IMPACT_KEY_SECTION} from '@/lib/functional-impact'
+import {AS_OF_KEY_SECTION, CONSEQUENCE_KEY_SECTION, SELECTED_ALLELE_KEY_SECTION, SUPERSEDED_KEY_SECTION} from '@/lib/glossary-prose'
+import {POPULATION_KEY_SECTION} from '@/lib/gnomad'
+import {ASSAY_LEVEL_KEY_SECTION, RELATIONSHIP_KEY_SECTION} from '@/lib/measurement-types'
+
+export const GLOSSARY_DOCS_URL = `${config.appBaseUrl}/docs/mavedb/getting-started/key-concepts.html`
+
+export const GLOSSARY_SECTIONS: KeySection[] = [
+  RELATIONSHIP_KEY_SECTION,
+  ASSAY_LEVEL_KEY_SECTION,
+  CONFIDENCE_KEY_SECTION,
+  SELECTED_ALLELE_KEY_SECTION,
+  COORDINATE_FRAME_KEY_SECTION,
+  CONSEQUENCE_KEY_SECTION,
+  FUNCTIONAL_IMPACT_KEY_SECTION,
+  ACMG_KEY_SECTION,
+  POPULATION_KEY_SECTION,
+  CLINICAL_SIGNIFICANCE_KEY_SECTION,
+  SIBLING_CONTROL_KEY_SECTION,
+  AS_OF_KEY_SECTION,
+  SUPERSEDED_KEY_SECTION
+]
diff --git a/src/lib/acmg.ts b/src/lib/acmg.ts
index 79ff85de..f8e1cbde 100644
--- a/src/lib/acmg.ts
+++ b/src/lib/acmg.ts
@@ -7,6 +7,7 @@
  */
 
 import {components} from '@/schema/openapi'
+import type {KeySection} from '@/composables/use-key-drawer'
 
 type ScoreCalibrationFunctionalClassification =
   components['schemas']['mavedb__view_models__score_calibration__FunctionalClassification']
@@ -43,13 +44,17 @@ export const ACMG_CRITERIA: Record<string, {label: string; definition: string}>
   }
 }
 
-/**
- * Formats the ACMG evidence code from a functional classification's ACMG classification data.
- *
- * @param classification - A functional classification that may contain an `acmgClassification`
- *   with `criterion` (e.g. "PS3", "BS3") and `evidenceStrength` (e.g. "Strong", "Moderate").
- * @returns A formatted code like "PS3_STRONG", or an empty string if evidence data is missing.
- */
+export const ACMG_KEY_SECTION: KeySection = {
+  id: 'acmg',
+  title: 'ACMG functional evidence',
+  gloss: 'How the functional result maps onto clinical-classification evidence.',
+  terms: [
+    ...Object.values(ACMG_CRITERIA),
+    {label: 'Evidence strength', definition: 'How much weight the evidence carries: supporting → moderate → strong → very strong.'},
+    {label: 'OddsPath', definition: 'The odds of pathogenicity implied by the score; sets the evidence strength.'}
+  ]
+}
+
 export function formatEvidenceCode(
   classification: ScoreCalibrationFunctionalClassification | null | undefined
 ): string {
diff --git a/src/lib/allele-grouping.ts b/src/lib/allele-grouping.ts
index f2663445..a4c49a64 100644
--- a/src/lib/allele-grouping.ts
+++ b/src/lib/allele-grouping.ts
@@ -8,6 +8,7 @@
 import _ from 'lodash'
 
 import type {components} from '@/schema/openapi'
+import type {KeySection} from '@/composables/use-key-drawer'
 
 type AlleleIdentity = components['schemas']['AlleleIdentity']
 type AlleleAnnotations = components['schemas']['AlleleAnnotations']
@@ -73,6 +74,12 @@ export const ALLELE_CONFIDENCE: Record<string, ConfidenceBadge> = {
   }
 }
 
+export const CONFIDENCE_KEY_SECTION: KeySection = {
+  id: 'confidence',
+  title: 'How a coordinate was established',
+  terms: Object.values(ALLELE_CONFIDENCE).map((c) => ({label: c.label, definition: c.definition, class: c.class}))
+}
+
 /** Confidence badge for a group: `measured` wins, else the derived state; null when neither applies. */
 export function confidenceBadge(group: Pick<AlleleGroup, 'measured' | 'derivation'>): ConfidenceBadge | null {
   if (group.measured) return ALLELE_CONFIDENCE.measured
diff --git a/src/lib/functional-impact.ts b/src/lib/functional-impact.ts
index 1aa9085e..4565d48a 100644
--- a/src/lib/functional-impact.ts
+++ b/src/lib/functional-impact.ts
@@ -4,6 +4,8 @@
  * module; the heavier editor/draft calibration model stays in `calibration-types.ts`.
  */
 
+import type {KeySection} from '@/composables/use-key-drawer'
+
 export type FunctionalClassification = 'abnormal' | 'normal' | 'not_specified'
 
 /**
@@ -39,3 +41,14 @@ export const FUNCTIONAL_CLASSIFICATIONS: Record<
     rangeColor: 'var(--color-cal-unspecified)'
   }
 }
+
+export const FUNCTIONAL_IMPACT_KEY_SECTION: KeySection = {
+  id: 'functional-impact',
+  title: 'Functional impact',
+  terms: [
+    {label: 'Functional impact', definition: "The assay's verdict on whether the variant alters function."},
+    ...Object.values(FUNCTIONAL_CLASSIFICATIONS)
+      .filter((c) => c.definition)
+      .map((c) => ({label: c.label, definition: c.definition!, class: c.class}))
+  ]
+}
diff --git a/src/lib/glossary-prose.ts b/src/lib/glossary-prose.ts
new file mode 100644
index 00000000..0f50bb04
--- /dev/null
+++ b/src/lib/glossary-prose.ts
@@ -0,0 +1,48 @@
+import type {KeySection} from '@/composables/use-key-drawer'
+
+export const SELECTED_ALLELE_KEY_SECTION: KeySection = {
+  id: 'selected-allele',
+  title: 'Selected allele',
+  terms: [
+    {
+      label: 'Selected allele',
+      definition: 'The allele this page is anchored on — the ClinGen allele you navigated to.',
+      class: 'bg-link/10 text-link'
+    }
+  ]
+}
+
+export const CONSEQUENCE_KEY_SECTION: KeySection = {
+  id: 'consequence',
+  title: 'Molecular consequence',
+  terms: [
+    {
+      label: 'Molecular consequence',
+      definition: 'The predicted effect on the transcript or protein (e.g. missense), from VEP.'
+    }
+  ]
+}
+
+export const AS_OF_KEY_SECTION: KeySection = {
+  id: 'as-of',
+  title: 'As of',
+  terms: [
+    {
+      label: 'As of MaveDB …',
+      definition: 'MaveDB reconstructs its molecular and annotation layer as of the chosen date; scores never change.'
+    },
+    {label: 'As of ClinVar …', definition: 'The ClinVar release a clinical call was drawn from.'}
+  ]
+}
+
+export const SUPERSEDED_KEY_SECTION: KeySection = {
+  id: 'superseded',
+  title: 'Superseded',
+  terms: [
+    {
+      label: 'Superseded',
+      definition:
+        'The measurement comes from an older version of its score set. A newer version exists but may not contain a corresponding variant.'
+    }
+  ]
+}
diff --git a/src/lib/measurement-types.ts b/src/lib/measurement-types.ts
index b000cf60..fbc31764 100644
--- a/src/lib/measurement-types.ts
+++ b/src/lib/measurement-types.ts
@@ -1,4 +1,5 @@
 import type {components} from '@/schema/openapi'
+import type {KeySection} from '@/composables/use-key-drawer'
 import type {SequenceLevel} from '@/composables/use-variant-coordinates'
 
 export type MeasurementRelationship = components['schemas']['MeasurementRelationship']
@@ -12,6 +13,34 @@ export function assayLevelBucket(level: string | null | undefined): LevelBucket
   return level === 'protein' ? 'amino acid' : 'nucleotide'
 }
 
+/**
+ * Single source of truth for the measurement-to-query relationship vocabulary (the RT asymmetry): the
+ * card label, an optional chip class, and the Key-drawer gloss. Phrased relative to the user's variant so
+ * the labels self-explain under the "relative to your variant" anchor. Insertion order is display order.
+ */
+export const RELATIONSHIPS: Record<MeasurementRelationship, {label: string; class?: string; definition: string}> = {
+  direct: {
+    label: 'Your variant',
+    class: 'bg-sage/15 text-sage',
+    definition: 'The result assayed exactly the allele you searched.'
+  },
+  protein_consequence: {
+    label: 'Its protein consequence',
+    definition: 'The result assayed the protein change your variant produces.'
+  },
+  nucleotide_encoding: {
+    label: 'Encodes the protein consequence',
+    definition: 'The result assayed a nucleotide allele that encodes the same protein change as your variant.'
+  }
+}
+
+export const RELATIONSHIP_KEY_SECTION: KeySection = {
+  id: 'relationship',
+  title: 'Relationship to your variant',
+  gloss: 'How each result relates to the allele you searched.',
+  terms: Object.values(RELATIONSHIPS).map((r) => ({label: r.label, definition: r.definition, class: r.class}))
+}
+
 /**
  * Single source of truth for how an assay-level bucket appears in the UI — its label, color classes, and
  * Key-drawer gloss. Every level badge, pill, and the Key drawer's assay-level section derives from this,
@@ -30,6 +59,13 @@ export const LEVEL_BUCKETS: Record<LevelBucket, {label: string; class: string; d
   }
 }
 
+export const ASSAY_LEVEL_KEY_SECTION: KeySection = {
+  id: 'assay-level',
+  title: 'Assay level',
+  gloss: 'The level at which a result measured the change.',
+  terms: Object.values(LEVEL_BUCKETS).map((b) => ({label: b.label, definition: b.definition, class: b.class}))
+}
+
 /** The display label, color classes, and gloss for a raw SequenceLevel, collapsed to its bucket. */
 export function assayLevelDisplay(level: string | null | undefined): (typeof LEVEL_BUCKETS)[LevelBucket] {
   return LEVEL_BUCKETS[assayLevelBucket(level)]
@@ -52,24 +88,3 @@ export function dominantAssayLevel(levels: Array<SequenceLevel | null | undefine
   }
   return best
 }
-
-/**
- * Single source of truth for the measurement-to-query relationship vocabulary (the RT asymmetry): the
- * card label, an optional chip class, and the Key-drawer gloss. Phrased relative to the user's variant so
- * the labels self-explain under the "relative to your variant" anchor. Insertion order is display order.
- */
-export const RELATIONSHIPS: Record<MeasurementRelationship, {label: string; class?: string; definition: string}> = {
-  direct: {
-    label: 'Your variant',
-    class: 'bg-sage/15 text-sage',
-    definition: 'The result assayed exactly the allele you searched.'
-  },
-  protein_consequence: {
-    label: 'Its protein consequence',
-    definition: 'The result assayed the protein change your variant produces.'
-  },
-  nucleotide_encoding: {
-    label: 'Encodes the protein consequence',
-    definition: 'The result assayed a nucleotide allele that encodes the same protein change as your variant.'
-  }
-}

From 3852556aecd8bd17f3e67b33ef80726f017be451 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Fri, 17 Jul 2026 09:13:19 -0700
Subject: [PATCH 53/84] feat(key-drawer): wire v-key-term deep links across
 more surfaces
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Now that MvKeyDrawer is mounted globally at the app root, v-key-term
triggers are no longer limited to VariantScreen's direct subtree.

- Bake v-key-term into MvClassificationTag (functional-impact) and
  MvEvidenceTag (acmg) at the leaf so every render site gets the
  affordance automatically; remove now-redundant outer directives from
  VariantScreen and MvMeasurementCard
- Add term prop to MvDetailRow so callers can deep-link the row label
  without a slot workaround; use it for assay-level and consequence
- Add missing triggers to VariantDetailPanel (consequence,
  functional-impact, superseded), MvMeasurementRow (assay-level),
  VariantClinvarStat default label (clinical), and VariantGnomadStat
  default label (population)
- Fix stale comment in use-key-drawer.ts (variant-page root → app root)
---
 src/components/common/MvAssayFactsCard.vue    | 2 +-
 src/components/common/MvClassificationTag.vue | 1 +
 src/components/common/MvDetailRow.vue         | 5 +++--
 src/components/common/MvEvidenceTag.vue       | 1 +
 src/components/screens/VariantScreen.vue      | 2 --
 src/components/search/MvMeasurementRow.vue    | 1 +
 src/components/variant/MvMeasurementCard.vue  | 4 ++--
 src/components/variant/VariantClinvarStat.vue | 2 +-
 src/components/variant/VariantDetailPanel.vue | 6 +++---
 src/components/variant/VariantGnomadStat.vue  | 2 +-
 src/components/variant/VariantInfoSection.vue | 2 +-
 src/composables/use-key-drawer.ts             | 2 +-
 12 files changed, 16 insertions(+), 14 deletions(-)

diff --git a/src/components/common/MvAssayFactsCard.vue b/src/components/common/MvAssayFactsCard.vue
index 53db8df9..2cc378b3 100644
--- a/src/components/common/MvAssayFactsCard.vue
+++ b/src/components/common/MvAssayFactsCard.vue
@@ -33,7 +33,7 @@
         :value="getKeyword('Phenotypic Assay Mechanism')"
       />
       <MvDetailRow fallback="Not specified" label="Model system" :value="getKeyword('Phenotypic Assay Model System')" />
-      <MvDetailRow fallback="Not mapped" label="Assay level" :value="assayLevelLabel" />
+      <MvDetailRow fallback="Not mapped" label="Assay level" term="assay-level" :value="assayLevelLabel" />
       <MvDetailRow fallback="Not specified" label="Detects splicing?">
         <span
           v-if="detectsSplicing != null"
diff --git a/src/components/common/MvClassificationTag.vue b/src/components/common/MvClassificationTag.vue
index af68fe2e..b39160ff 100644
--- a/src/components/common/MvClassificationTag.vue
+++ b/src/components/common/MvClassificationTag.vue
@@ -1,5 +1,6 @@
 <template>
   <span
+    v-key-term="'functional-impact'"
     class="inline-block max-w-full rounded px-2.5 py-0.5 text-xs font-bold leading-snug tracking-wide"
     :class="tagClass"
   >
diff --git a/src/components/common/MvDetailRow.vue b/src/components/common/MvDetailRow.vue
index 7ad46942..562b15a3 100644
--- a/src/components/common/MvDetailRow.vue
+++ b/src/components/common/MvDetailRow.vue
@@ -1,6 +1,6 @@
 <template>
   <div class="detail-row flex flex-col sm:flex-row text-xs-plus py-[5px] gap-0.5 sm:gap-4" :style="{alignItems: align}">
-    <span class="font-semibold text-text-muted sm:min-w-[160px] shrink-0">{{ label }}</span>
+    <span v-key-term="term" class="font-semibold text-text-muted sm:min-w-[160px] shrink-0">{{ label }}</span>
     <span class="detail-value text-text-primary leading-normal">
       <slot v-if="hasSlotContent" />
       <template v-else-if="value != null">{{ value }}</template>
@@ -10,13 +10,14 @@
 </template>
 
 <script lang="ts">
-import {Comment, defineComponent} from 'vue'
+import {Comment, defineComponent, type PropType} from 'vue'
 
 export default defineComponent({
   name: 'MvDetailRow',
 
   props: {
     label: {type: String, required: true},
+    term: {type: String as PropType<string | null>, default: null},
     value: {type: [String, Number, null], default: null},
     fallback: {type: String, default: 'N/A'},
     align: {type: String, default: 'baseline'}
diff --git a/src/components/common/MvEvidenceTag.vue b/src/components/common/MvEvidenceTag.vue
index cc21a1d1..22020cfa 100644
--- a/src/components/common/MvEvidenceTag.vue
+++ b/src/components/common/MvEvidenceTag.vue
@@ -1,5 +1,6 @@
 <template>
   <span
+    v-key-term="'acmg'"
     class="inline-block rounded px-2 py-0.5 text-[11px] font-bold tracking-wide"
     :class="`mave-evidence-code-${normalizedCode}`"
   >
diff --git a/src/components/screens/VariantScreen.vue b/src/components/screens/VariantScreen.vue
index 78630f5e..85a5b006 100644
--- a/src/components/screens/VariantScreen.vue
+++ b/src/components/screens/VariantScreen.vue
@@ -219,7 +219,6 @@
               <span class="text-[10px] font-semibold uppercase tracking-[0.3px] text-[#aaa]">Functional impact</span>
               <MvClassificationTag
                 v-if="lookup.calibrationResolution.classification.value"
-                v-key-term="'functional-impact'"
                 :classification="lookup.calibrationResolution.classification.value"
               />
               <span v-else class="text-sm text-text-muted">—</span>
@@ -234,7 +233,6 @@
               <span class="text-[10px] font-semibold uppercase tracking-[0.3px] text-[#aaa]">ACMG code</span>
               <MvEvidenceTag
                 v-if="lookup.calibrationResolution.formattedEvidenceCode.value"
-                v-key-term="'acmg'"
                 :code="lookup.calibrationResolution.formattedEvidenceCode.value"
               />
               <span v-else class="text-sm text-text-muted">—</span>
diff --git a/src/components/search/MvMeasurementRow.vue b/src/components/search/MvMeasurementRow.vue
index 9791839b..56f04115 100644
--- a/src/components/search/MvMeasurementRow.vue
+++ b/src/components/search/MvMeasurementRow.vue
@@ -1,6 +1,7 @@
 <template>
   <div class="flex flex-wrap items-baseline gap-x-3 gap-y-0.5 border-b border-gray-50 py-1.5 text-sm last:border-b-0">
     <span
+      v-key-term="'assay-level'"
       class="inline-block rounded-sm px-1.5 py-0.5 text-[10px] font-semibold uppercase tracking-[0.3px]"
       :class="levelClass"
       >{{ levelLabel }}</span
diff --git a/src/components/variant/MvMeasurementCard.vue b/src/components/variant/MvMeasurementCard.vue
index 98717cb4..8d4e431d 100644
--- a/src/components/variant/MvMeasurementCard.vue
+++ b/src/components/variant/MvMeasurementCard.vue
@@ -55,8 +55,8 @@
       <div v-if="classification || evidenceCode" class="mt-1.5">
         <span class="mb-1 block text-[10px] font-bold uppercase tracking-[0.3px] text-[#aaa]">Classified as</span>
         <div class="flex flex-wrap items-center gap-1.5">
-          <MvClassificationTag v-if="classification" v-key-term="'functional-impact'" :classification="classification" />
-          <MvEvidenceTag v-if="evidenceCode" v-key-term="'acmg'" :code="evidenceCode" />
+          <MvClassificationTag v-if="classification" :classification="classification" />
+          <MvEvidenceTag v-if="evidenceCode" :code="evidenceCode" />
           <span v-if="oddspathsRatio != null" v-key-term="'acmg'" class="text-xs text-text-muted"
             >(OddsPath {{ oddspathsRatio.toPrecision(3) }})</span
           >
diff --git a/src/components/variant/VariantClinvarStat.vue b/src/components/variant/VariantClinvarStat.vue
index a9dc535d..996e9fa8 100644
--- a/src/components/variant/VariantClinvarStat.vue
+++ b/src/components/variant/VariantClinvarStat.vue
@@ -1,7 +1,7 @@
 <template>
   <div :class="plain ? 'flex h-full flex-col gap-0.5' : 'stat'">
     <!-- Label defaults to the score-set stat label; callers (e.g. the variant screen) inject their own. -->
-    <slot name="label"><span class="stat-label">ClinVar</span></slot>
+    <slot name="label"><span v-key-term="'clinical'" class="stat-label">ClinVar</span></slot>
     <!-- Hard discordance: related variants carry both pathogenic and benign calls — no single call to show. -->
     <span v-if="headline.kind === 'conflicting'" class="stat-value text-sm font-semibold">
       Conflicting classifications
diff --git a/src/components/variant/VariantDetailPanel.vue b/src/components/variant/VariantDetailPanel.vue
index ba550c7c..8d1367f6 100644
--- a/src/components/variant/VariantDetailPanel.vue
+++ b/src/components/variant/VariantDetailPanel.vue
@@ -31,7 +31,7 @@
       <!-- Facts -->
       <div class="grid grid-cols-2 gap-px border-t border-border-light bg-border-light tablet:grid-cols-4">
         <div class="stat">
-          <span class="stat-label">Molecular consequence</span>
+          <span v-key-term="'consequence'" class="stat-label">Molecular consequence</span>
           <span class="stat-value font-semibold">{{
             consequence?.consequence ? formatToken(consequence.consequence) : '—'
           }}</span>
@@ -41,7 +41,7 @@
         </div>
 
         <div class="stat">
-          <span class="stat-label">Classification</span>
+          <span v-key-term="'functional-impact'" class="stat-label">Classification</span>
           <span v-if="selectedClassification" class="flex flex-wrap items-center gap-1.5">
             <span class="rounded px-1.5 py-0.5 text-xs-plus" :class="classificationClass">
               {{ formatToken(selectedClassification.classification.functionalClassification) }}
@@ -76,7 +76,7 @@
           class="inline-flex items-center gap-1 rounded-full bg-amber-100 px-2 py-0.5 text-xs font-semibold text-amber-800"
         >
           <i class="pi pi-exclamation-triangle text-[10px]" />
-          Superseded
+          <span v-key-term="'superseded'">Superseded</span>
         </span>
         <router-link
           v-if="detail.clingenAlleleId"
diff --git a/src/components/variant/VariantGnomadStat.vue b/src/components/variant/VariantGnomadStat.vue
index fbb6c094..59a7de33 100644
--- a/src/components/variant/VariantGnomadStat.vue
+++ b/src/components/variant/VariantGnomadStat.vue
@@ -1,7 +1,7 @@
 <template>
   <div :class="plain ? 'flex h-full flex-col gap-0.5' : 'stat'">
     <!-- Label defaults to the score-set stat label; callers (e.g. the variant screen) inject their own. -->
-    <slot name="label"><span class="stat-label">gnomAD</span></slot>
+    <slot name="label"><span v-key-term="'population'" class="stat-label">gnomAD</span></slot>
     <!-- The measured allele's own frequency (a nucleotide-level assay): the canonical stat, straight up. -->
     <MvGnomadSummary v-if="assayGnomad" :gnomad="assayGnomad" />
     <!-- No gnomAD on the measured allele itself, but sibling variants carry frequencies (protein level assay). 
diff --git a/src/components/variant/VariantInfoSection.vue b/src/components/variant/VariantInfoSection.vue
index 194edcb3..aa7da2d4 100644
--- a/src/components/variant/VariantInfoSection.vue
+++ b/src/components/variant/VariantInfoSection.vue
@@ -20,7 +20,7 @@
       </template>
       <template v-if="clinvarAlleleIds.length === 0"><span class="text-text-muted">—</span></template>
     </MvDetailRow>
-    <MvDetailRow label="Molecular consequence">
+    <MvDetailRow label="Molecular consequence" term="consequence">
       <span v-if="molecularConsequence">{{ formatConsequence(molecularConsequence) }}</span>
       <span v-else class="italic text-text-muted">—</span>
     </MvDetailRow>
diff --git a/src/composables/use-key-drawer.ts b/src/composables/use-key-drawer.ts
index 5bc6b20d..248176de 100644
--- a/src/composables/use-key-drawer.ts
+++ b/src/composables/use-key-drawer.ts
@@ -23,7 +23,7 @@ export interface KeySection {
 /**
  * Module-level singleton driving the vocabulary "Key" drawer. Any component can call `open(term)` to
  * surface a definition without threading props/events through the page — the drawer itself is mounted
- * once at the variant-page root and reads this shared state. `activeTerm` is the anchor id the drawer
+ * once at the app root and reads this shared state. `activeTerm` is the anchor id the drawer
  * scrolls to and briefly highlights on open; passing nothing opens it at the top.
  *
  * Deliberately global rather than provide/inject: the trigger (control header) and the deep-linking

From a66e07ed156f8f32232a71c4650efa2f02a9545b Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Fri, 17 Jul 2026 17:31:17 -0700
Subject: [PATCH 54/84] feat(allele-grouping): Add convergent allele group

---
 src/api/mavedb/variants.ts      |   9 +-
 src/lib/allele-grouping.test.ts |   6 +-
 src/lib/allele-grouping.ts      |  15 +-
 src/schema/openapi.d.ts         | 604 +++++++++++++-------------------
 4 files changed, 258 insertions(+), 376 deletions(-)

diff --git a/src/api/mavedb/variants.ts b/src/api/mavedb/variants.ts
index a0441483..eec3a2b2 100644
--- a/src/api/mavedb/variants.ts
+++ b/src/api/mavedb/variants.ts
@@ -6,7 +6,7 @@ import {components} from '@/schema/openapi'
 
 type VariantDetail = components['schemas']['VariantDetail']
 type AlleleMeasurement = components['schemas']['AlleleMeasurement']
-type MappedVariant = components['schemas']['MappedVariant']
+type VariantVrsMatch = components['schemas']['VariantVrsMatch']
 
 // The ClinGen-allele-centric variant page's entrypoint: every measurement whose cross-layer
 // equivalence class touches this CAID/PAID, in the API's default order (direct-first). `includeSuperseded`
@@ -31,8 +31,8 @@ export const getAlleleMeasurements = memoizeRead(
     `${clingenAlleleId}|${options?.includeSuperseded ?? false}|${options?.includeNucleotideSiblings ?? false}|${options?.asOf ?? ''}`
 )
 
-export async function lookupVariantsByVrsDigest(identifier: string): Promise<MappedVariant[]> {
-  const response = await axios.get(`${config.apiBaseUrl}/mapped-variants/vrs/${encodeURIComponent(identifier)}`, {
+export async function lookupVariantsByVrsDigest(identifier: string): Promise<VariantVrsMatch[]> {
+  const response = await axios.get(`${config.apiBaseUrl}/variants/vrs/${encodeURIComponent(identifier)}`, {
     params: {only_current: true}
   })
   return response.data
@@ -50,9 +50,8 @@ export const getVariantDetail = memoizeRead(
 
 export async function getVariantAnnotation(variantUrn: string, annotationType: string): Promise<unknown> {
   const response = await axios.get(
-    `${config.apiBaseUrl}/mapped-variants/${encodeURIComponent(variantUrn)}/va/${encodeURIComponent(annotationType)}`,
+    `${config.apiBaseUrl}/variants/${encodeURIComponent(variantUrn)}/va/${encodeURIComponent(annotationType)}`,
     {responseType: 'json'}
   )
   return response.data
 }
-
diff --git a/src/lib/allele-grouping.test.ts b/src/lib/allele-grouping.test.ts
index a4b27128..19303da9 100644
--- a/src/lib/allele-grouping.test.ts
+++ b/src/lib/allele-grouping.test.ts
@@ -128,16 +128,20 @@ describe('groupAlleles — projection pairing + confidence', () => {
     expect(groups[0].measured).toBe(false)
   })
 
-  it('badges measured over derivation, maps projection→Resolved / candidate→Candidate, else null', () => {
+  it('badges measured over derivation, maps projection→Resolved / convergent→Convergent / candidate→Candidate, else null', () => {
     // `measured` wins even if a derivation is also present (a stray measured sibling still reads "Measured").
     expect(confidenceBadge({measured: true, derivation: 'projection'})).toBe(ALLELE_CONFIDENCE.measured)
     expect(confidenceBadge({measured: false, derivation: 'projection'})).toBe(ALLELE_CONFIDENCE.projection)
+    // A synonymous cousin under a nucleotide assay: a distinct change sharing the consequence, not ambiguous.
+    expect(confidenceBadge({measured: false, derivation: 'convergent'})).toBe(ALLELE_CONFIDENCE.convergent)
+    // The protein-assay reverse-translation fan-out: genuinely ambiguous.
     expect(confidenceBadge({measured: false, derivation: 'candidate'})).toBe(ALLELE_CONFIDENCE.candidate)
     // `authoritative` is only ever surfaced via `measured`; on its own it has no derived badge.
     expect(confidenceBadge({measured: false, derivation: 'authoritative'})).toBeNull()
     expect(confidenceBadge({measured: false, derivation: null})).toBeNull()
     // The user-facing labels are decoupled from the enum keys.
     expect(ALLELE_CONFIDENCE.projection.label).toBe('Resolved')
+    expect(ALLELE_CONFIDENCE.convergent.label).toBe('Convergent')
   })
 
   it('surfaces distinct linked CAIDs, excluding the page anchor', () => {
diff --git a/src/lib/allele-grouping.ts b/src/lib/allele-grouping.ts
index a4c49a64..981f18e5 100644
--- a/src/lib/allele-grouping.ts
+++ b/src/lib/allele-grouping.ts
@@ -14,8 +14,8 @@ type AlleleIdentity = components['schemas']['AlleleIdentity']
 type AlleleAnnotations = components['schemas']['AlleleAnnotations']
 
 /** Confidence/provenance axis (orthogonal to Cat-VRS's `relation`); strongest confidence first. */
-export type Derivation = 'authoritative' | 'projection' | 'candidate'
-const DERIVATION_RANK: Record<string, number> = {authoritative: 0, projection: 1, candidate: 2}
+export type Derivation = 'authoritative' | 'projection' | 'convergent' | 'candidate'
+const DERIVATION_RANK: Record<string, number> = {authoritative: 0, projection: 1, convergent: 2, candidate: 3}
 
 // Level display order (genomic → coding → protein) so a group reads bottom-up through the layer stack.
 const LEVEL_ORDER: Record<string, number> = {genomic: 0, cdna: 1, protein: 2}
@@ -65,12 +65,19 @@ export const ALLELE_CONFIDENCE: Record<string, ConfidenceBadge> = {
   projection: {
     label: 'Resolved',
     class: 'bg-nucleotide-light text-nucleotide',
-    definition: 'Derived from the measured allele by reverse translation — the same change expressed at another level.'
+    definition: 'Derived from the measured allele — the same change expressed at another coordinate level.'
+  },
+  convergent: {
+    label: 'Convergent',
+    class: 'bg-synonymous-nucleotide-light text-synonymous-nucleotide',
+    definition:
+      'A distinct nucleotide change that produces the same protein change as the measured variant — a separate variant that converges on the same consequence, not the one assayed here.'
   },
   candidate: {
     label: 'Candidate',
     class: 'bg-amber-100 text-amber-700',
-    definition: 'A change that encodes the same protein change as your variant, but is a distinct nucleotide change.'
+    definition:
+      'A possible nucleotide change behind a protein-level measurement — one of several synonymous codons; which was actually assayed is unknown.'
   }
 }
 
diff --git a/src/schema/openapi.d.ts b/src/schema/openapi.d.ts
index a8164365..a0770e78 100644
--- a/src/schema/openapi.d.ts
+++ b/src/schema/openapi.d.ts
@@ -322,41 +322,6 @@ export interface paths {
      */
     get: operations["fetch_license_api_v1_licenses__item_id__get"];
   };
-  "/api/v1/mapped-variants/{urn}": {
-    /**
-     * Fetch mapped variant by URN
-     * @description Fetch a single mapped variant by URN.
-     */
-    get: operations["show_mapped_variant_api_v1_mapped_variants__urn__get"];
-  };
-  "/api/v1/mapped-variants/{urn}/va/study-result": {
-    /**
-     * Construct a VA-Spec StudyResult from a mapped variant
-     * @description Construct a single VA-Spec StudyResult from a mapped variant by URN.
-     */
-    get: operations["show_mapped_variant_study_result_api_v1_mapped_variants__urn__va_study_result_get"];
-  };
-  "/api/v1/mapped-variants/{urn}/va/functional-statement": {
-    /**
-     * Construct a VA-Spec Statement from a mapped variant
-     * @description Construct a single VA-Spec Statement from a mapped variant by URN.
-     */
-    get: operations["show_mapped_variant_functional_impact_statement_api_v1_mapped_variants__urn__va_functional_statement_get"];
-  };
-  "/api/v1/mapped-variants/{urn}/va/pathogenicity-statement": {
-    /**
-     * Construct a VA-Spec EvidenceLine from a mapped variant
-     * @description Construct a list of VA-Spec EvidenceLine(s) from a mapped variant by URN.
-     */
-    get: operations["show_mapped_variant_acmg_evidence_line_api_v1_mapped_variants__urn__va_pathogenicity_statement_get"];
-  };
-  "/api/v1/mapped-variants/vrs/{identifier}": {
-    /**
-     * Fetch mapped variants by VRS identifier
-     * @description Fetch a single mapped variant by GA4GH identifier.
-     */
-    get: operations["show_mapped_variants_by_identifier_api_v1_mapped_variants_vrs__identifier__get"];
-  };
   "/api/v1/orcid/users/{orcid_id}": {
     /**
      * Look up an ORCID user by ORCID ID
@@ -1339,6 +1304,17 @@ export interface paths {
      */
     put: operations["update_user_api_v1_users___id__put"];
   };
+  "/api/v1/variants/vrs/{identifier}": {
+    /**
+     * Look up variants by VRS identifier
+     * @description Resolve a GA4GH VRS identifier to the readable variants whose mapping links that allele.
+     *
+     * The new-substrate replacement for the legacy mapped-variant VRS lookup: a deduplicated allele may be
+     * shared across score sets, so one identifier can resolve to several variants. Results are filtered to
+     * the score sets the caller may read; a 404 is returned when nothing readable matches.
+     */
+    get: operations["lookup_variants_by_vrs_identifier_api_v1_variants_vrs__identifier__get"];
+  };
   "/api/v1/variants/{urn}": {
     /**
      * Fetch assayed variant detail by URN
@@ -1350,6 +1326,27 @@ export interface paths {
      */
     get: operations["get_variant_api_v1_variants__urn__get"];
   };
+  "/api/v1/variants/{urn}/va/study-result": {
+    /**
+     * Construct a VA-Spec StudyResult for a variant
+     * @description Construct a single VA-Spec StudyResult for a variant by URN, from its mapping substrate.
+     */
+    get: operations["get_variant_study_result_api_v1_variants__urn__va_study_result_get"];
+  };
+  "/api/v1/variants/{urn}/va/functional-statement": {
+    /**
+     * Construct a VA-Spec functional-impact Statement for a variant
+     * @description Construct a single VA-Spec functional-impact Statement for a variant by URN.
+     */
+    get: operations["get_variant_functional_impact_statement_api_v1_variants__urn__va_functional_statement_get"];
+  };
+  "/api/v1/variants/{urn}/va/pathogenicity-statement": {
+    /**
+     * Construct a VA-Spec pathogenicity Statement for a variant
+     * @description Construct a single VA-Spec pathogenicity Statement for a variant by URN.
+     */
+    get: operations["get_variant_pathogenicity_statement_api_v1_variants__urn__va_pathogenicity_statement_get"];
+  };
   "/api/v1/alphafold-files/version": {
     /**
      * Proxy Alphafold Index
@@ -1656,8 +1653,10 @@ export interface components {
      * - ``relation`` (Cat-VRS, structural): member→defining relation; ``null`` when it *is* the measured
      *   allele, or when the allele is not a Cat-VRS member.
      * - ``derivation`` (provenance): ``authoritative`` (measured) / ``projection`` (deterministic,
-     *   precise) / ``candidate`` (reverse-translation, ambiguous). Orthogonal to ``relation`` — never
-     *   conflate them.
+     *   precise, derived from the measured change) / ``candidate`` (protein-assay reverse-translation,
+     *   ambiguous) / ``convergent`` (a distinct, precise nucleotide change that converges on the measured
+     *   protein consequence — a synonymous cousin, paired with the ``co_encodes`` relation). Orthogonal to
+     *   ``relation`` — never conflate them.
      * - ``projectionOf`` (provenance): the VRS digest of this allele's projection sibling (the paired c↔g member of
      *   its projection pair group); ``null`` for the protein apex and pre-reverse-translation data.
      */
@@ -3841,48 +3840,6 @@ export interface components {
       /** Recordtype */
       recordType?: string;
     };
-    /**
-     * MappedVariantWithMappingDetails
-     * @description Client-facing variant of :class:`SavedMappedVariantWithMappingDetails`.
-     */
-    MappedVariantWithMappingDetails: {
-      /** Premapped */
-      preMapped?: unknown;
-      /** Postmapped */
-      postMapped?: unknown;
-      /** Vrsversion */
-      vrsVersion?: string | null;
-      /** Errormessage */
-      errorMessage?: string | null;
-      /**
-       * Modificationdate
-       * Format: date
-       */
-      modificationDate: string;
-      /**
-       * Mappeddate
-       * Format: date
-       */
-      mappedDate: string;
-      /** Mappingapiversion */
-      mappingApiVersion: string;
-      /** Current */
-      current: boolean;
-      alignmentLevel?: components["schemas"]["SequenceLevel"] | null;
-      /** Atmismatchedlocus */
-      atMismatchedLocus?: boolean | null;
-      /** Neargap */
-      nearGap?: boolean | null;
-      /** Varianturn */
-      variantUrn: string;
-      /** Id */
-      id: number;
-      /** Clingenalleleid */
-      clingenAlleleId?: string | null;
-      /** Recordtype */
-      recordType?: string;
-      targetGeneMapping?: components["schemas"]["TargetGeneMapping"] | null;
-    };
     /**
      * MappingState
      * @enum {string}
@@ -5536,69 +5493,6 @@ export interface components {
       targetSequence?: components["schemas"]["TargetSequenceCreate"] | null;
       targetAccession?: components["schemas"]["TargetAccessionCreate"] | null;
     };
-    /** TargetGeneMapping */
-    TargetGeneMapping: {
-      alignmentLevel: components["schemas"]["SequenceLevel"];
-      /**
-       * Preferred
-       * @default false
-       */
-      preferred?: boolean;
-      /** Referenceassembly */
-      referenceAssembly?: string | null;
-      /** Referenceaccession */
-      referenceAccession?: string | null;
-      /** Referencesequenceid */
-      referenceSequenceId?: string | null;
-      /** Alignmentscore */
-      alignmentScore?: number | null;
-      /** Nextbestalignmentscore */
-      nextBestAlignmentScore?: number | null;
-      /** Alignmentlength */
-      alignmentLength?: number | null;
-      /** Alignmentstring */
-      alignmentString?: string | null;
-      /** Mismatchcount */
-      mismatchCount?: number | null;
-      /** Gapcount */
-      gapCount?: number | null;
-      /** Percentidentity */
-      percentIdentity?: number | null;
-      /** Totalvariants */
-      totalVariants?: number | null;
-      /** Variantsfailed */
-      variantsFailed?: number | null;
-      /** Variantswithalignmentwarnings */
-      variantsWithAlignmentWarnings?: number | null;
-      /** Variantsmappedcleanly */
-      variantsMappedCleanly?: number | null;
-      /** Toolname */
-      toolName: string;
-      /** Toolversion */
-      toolVersion: string;
-      /** Toolparameters */
-      toolParameters?: Record<string, never> | null;
-      /** Alignmentmetadata */
-      alignmentMetadata?: Record<string, never> | null;
-      /** Vrsversion */
-      vrsVersion?: string | null;
-      /** Mappeddate */
-      mappedDate?: string | null;
-      /** Id */
-      id: number;
-      /**
-       * Creationdate
-       * Format: date
-       */
-      creationDate: string;
-      /**
-       * Modificationdate
-       * Format: date
-       */
-      modificationDate: string;
-      /** Recordtype */
-      recordType?: string;
-    };
     /**
      * TargetGeneWithScoreSetUrn
      * @description Target gene view model containing its score set urn.
@@ -6356,6 +6250,24 @@ export interface components {
        */
       conditionQualifier: components["schemas"]["Condition"] | components["schemas"]["iriReference"];
     };
+    /**
+     * VariantVrsMatch
+     * @description One variant whose mapping links an allele bearing the queried VRS identifier.
+     *
+     * The ``GET /variants/vrs/{identifier}`` lookup result. The ClinGen id + level ride from the matched
+     * (deduplicated) allele; the URN from the variant it is linked to. Replaces the legacy MappedVariant VRS
+     * lookup on the new Allele substrate (#743, item 3.5).
+     */
+    VariantVrsMatch: {
+      /** Varianturn */
+      variantUrn: string;
+      /** Clingenalleleid */
+      clingenAlleleId?: string | null;
+      /** Vrsid */
+      vrsId?: string | null;
+      /** Level */
+      level?: string | null;
+    };
     /**
      * Variation
      * @description A representation of the state of one or more biomolecules.
@@ -8389,230 +8301,6 @@ export interface operations {
       };
     };
   };
-  /**
-   * Fetch mapped variant by URN
-   * @description Fetch a single mapped variant by URN.
-   */
-  show_mapped_variant_api_v1_mapped_variants__urn__get: {
-    parameters: {
-      header?: {
-        "x-active-roles"?: string | null;
-      };
-      path: {
-        urn: string;
-      };
-    };
-    responses: {
-      /** @description Successful Response */
-      200: {
-        content: {
-          "application/json": components["schemas"]["MappedVariantWithMappingDetails"];
-        };
-      };
-      /** @description Authentication required. */
-      401: {
-        content: never;
-      };
-      /** @description Forbidden. Insufficient permissions. */
-      403: {
-        content: never;
-      };
-      /** @description Resource not found. */
-      404: {
-        content: never;
-      };
-      /** @description Validation Error */
-      422: {
-        content: {
-          "application/json": components["schemas"]["HTTPValidationError"];
-        };
-      };
-      /** @description Internal server error. */
-      500: {
-        content: never;
-      };
-    };
-  };
-  /**
-   * Construct a VA-Spec StudyResult from a mapped variant
-   * @description Construct a single VA-Spec StudyResult from a mapped variant by URN.
-   */
-  show_mapped_variant_study_result_api_v1_mapped_variants__urn__va_study_result_get: {
-    parameters: {
-      header?: {
-        "x-active-roles"?: string | null;
-      };
-      path: {
-        urn: string;
-      };
-    };
-    responses: {
-      /** @description Successful Response */
-      200: {
-        content: {
-          "application/json": components["schemas"]["ExperimentalVariantFunctionalImpactStudyResult"];
-        };
-      };
-      /** @description Authentication required. */
-      401: {
-        content: never;
-      };
-      /** @description Forbidden. Insufficient permissions. */
-      403: {
-        content: never;
-      };
-      /** @description Resource not found. */
-      404: {
-        content: never;
-      };
-      /** @description Validation Error */
-      422: {
-        content: {
-          "application/json": components["schemas"]["HTTPValidationError"];
-        };
-      };
-      /** @description Internal server error. */
-      500: {
-        content: never;
-      };
-    };
-  };
-  /**
-   * Construct a VA-Spec Statement from a mapped variant
-   * @description Construct a single VA-Spec Statement from a mapped variant by URN.
-   */
-  show_mapped_variant_functional_impact_statement_api_v1_mapped_variants__urn__va_functional_statement_get: {
-    parameters: {
-      header?: {
-        "x-active-roles"?: string | null;
-      };
-      path: {
-        urn: string;
-      };
-    };
-    responses: {
-      /** @description Successful Response */
-      200: {
-        content: {
-          "application/json": components["schemas"]["Statement"];
-        };
-      };
-      /** @description Authentication required. */
-      401: {
-        content: never;
-      };
-      /** @description Forbidden. Insufficient permissions. */
-      403: {
-        content: never;
-      };
-      /** @description Resource not found. */
-      404: {
-        content: never;
-      };
-      /** @description Validation Error */
-      422: {
-        content: {
-          "application/json": components["schemas"]["HTTPValidationError"];
-        };
-      };
-      /** @description Internal server error. */
-      500: {
-        content: never;
-      };
-    };
-  };
-  /**
-   * Construct a VA-Spec EvidenceLine from a mapped variant
-   * @description Construct a list of VA-Spec EvidenceLine(s) from a mapped variant by URN.
-   */
-  show_mapped_variant_acmg_evidence_line_api_v1_mapped_variants__urn__va_pathogenicity_statement_get: {
-    parameters: {
-      header?: {
-        "x-active-roles"?: string | null;
-      };
-      path: {
-        urn: string;
-      };
-    };
-    responses: {
-      /** @description Successful Response */
-      200: {
-        content: {
-          "application/json": components["schemas"]["VariantPathogenicityStatement"];
-        };
-      };
-      /** @description Authentication required. */
-      401: {
-        content: never;
-      };
-      /** @description Forbidden. Insufficient permissions. */
-      403: {
-        content: never;
-      };
-      /** @description Resource not found. */
-      404: {
-        content: never;
-      };
-      /** @description Validation Error */
-      422: {
-        content: {
-          "application/json": components["schemas"]["HTTPValidationError"];
-        };
-      };
-      /** @description Internal server error. */
-      500: {
-        content: never;
-      };
-    };
-  };
-  /**
-   * Fetch mapped variants by VRS identifier
-   * @description Fetch a single mapped variant by GA4GH identifier.
-   */
-  show_mapped_variants_by_identifier_api_v1_mapped_variants_vrs__identifier__get: {
-    parameters: {
-      query?: {
-        only_current?: boolean;
-      };
-      header?: {
-        "x-active-roles"?: string | null;
-      };
-      path: {
-        /** @description String, a valid GA4GH digest based identifier. */
-        identifier: string;
-      };
-    };
-    responses: {
-      /** @description Successful Response */
-      200: {
-        content: {
-          "application/json": components["schemas"]["MappedVariant"][];
-        };
-      };
-      /** @description Authentication required. */
-      401: {
-        content: never;
-      };
-      /** @description Forbidden. Insufficient permissions. */
-      403: {
-        content: never;
-      };
-      /** @description Resource not found. */
-      404: {
-        content: never;
-      };
-      /** @description Validation Error */
-      422: {
-        content: {
-          "application/json": components["schemas"]["HTTPValidationError"];
-        };
-      };
-      /** @description Internal server error. */
-      500: {
-        content: never;
-      };
-    };
-  };
   /**
    * Look up an ORCID user by ORCID ID
    * @description Look an ORCID user up by ORCID ID.
@@ -12677,6 +12365,58 @@ export interface operations {
       };
     };
   };
+  /**
+   * Look up variants by VRS identifier
+   * @description Resolve a GA4GH VRS identifier to the readable variants whose mapping links that allele.
+   *
+   * The new-substrate replacement for the legacy mapped-variant VRS lookup: a deduplicated allele may be
+   * shared across score sets, so one identifier can resolve to several variants. Results are filtered to
+   * the score sets the caller may read; a 404 is returned when nothing readable matches.
+   */
+  lookup_variants_by_vrs_identifier_api_v1_variants_vrs__identifier__get: {
+    parameters: {
+      query?: {
+        only_current?: boolean;
+      };
+      header?: {
+        "x-active-roles"?: string | null;
+      };
+      path: {
+        /** @description A valid GA4GH digest-based identifier for the mapped allele. */
+        identifier: string;
+      };
+    };
+    responses: {
+      /** @description Successful Response */
+      200: {
+        content: {
+          "application/json": components["schemas"]["VariantVrsMatch"][];
+        };
+      };
+      /** @description Authentication required. */
+      401: {
+        content: never;
+      };
+      /** @description Forbidden. Insufficient permissions. */
+      403: {
+        content: never;
+      };
+      /** @description Resource not found. */
+      404: {
+        content: never;
+      };
+      /** @description Validation Error */
+      422: {
+        content: {
+          "application/json": components["schemas"]["HTTPValidationError"];
+        };
+      };
+      /** @description Internal server error. */
+      500: {
+        content: never;
+      };
+    };
+  };
   /**
    * Fetch assayed variant detail by URN
    * @description Fetch the two-tier detail envelope for a single assayed variant by URN.
@@ -12729,6 +12469,138 @@ export interface operations {
       };
     };
   };
+  /**
+   * Construct a VA-Spec StudyResult for a variant
+   * @description Construct a single VA-Spec StudyResult for a variant by URN, from its mapping substrate.
+   */
+  get_variant_study_result_api_v1_variants__urn__va_study_result_get: {
+    parameters: {
+      header?: {
+        "x-active-roles"?: string | null;
+      };
+      path: {
+        urn: string;
+      };
+    };
+    responses: {
+      /** @description Successful Response */
+      200: {
+        content: {
+          "application/json": components["schemas"]["ExperimentalVariantFunctionalImpactStudyResult"];
+        };
+      };
+      /** @description Authentication required. */
+      401: {
+        content: never;
+      };
+      /** @description Forbidden. Insufficient permissions. */
+      403: {
+        content: never;
+      };
+      /** @description Resource not found. */
+      404: {
+        content: never;
+      };
+      /** @description Validation Error */
+      422: {
+        content: {
+          "application/json": components["schemas"]["HTTPValidationError"];
+        };
+      };
+      /** @description Internal server error. */
+      500: {
+        content: never;
+      };
+    };
+  };
+  /**
+   * Construct a VA-Spec functional-impact Statement for a variant
+   * @description Construct a single VA-Spec functional-impact Statement for a variant by URN.
+   */
+  get_variant_functional_impact_statement_api_v1_variants__urn__va_functional_statement_get: {
+    parameters: {
+      header?: {
+        "x-active-roles"?: string | null;
+      };
+      path: {
+        urn: string;
+      };
+    };
+    responses: {
+      /** @description Successful Response */
+      200: {
+        content: {
+          "application/json": components["schemas"]["Statement"];
+        };
+      };
+      /** @description Authentication required. */
+      401: {
+        content: never;
+      };
+      /** @description Forbidden. Insufficient permissions. */
+      403: {
+        content: never;
+      };
+      /** @description Resource not found. */
+      404: {
+        content: never;
+      };
+      /** @description Validation Error */
+      422: {
+        content: {
+          "application/json": components["schemas"]["HTTPValidationError"];
+        };
+      };
+      /** @description Internal server error. */
+      500: {
+        content: never;
+      };
+    };
+  };
+  /**
+   * Construct a VA-Spec pathogenicity Statement for a variant
+   * @description Construct a single VA-Spec pathogenicity Statement for a variant by URN.
+   */
+  get_variant_pathogenicity_statement_api_v1_variants__urn__va_pathogenicity_statement_get: {
+    parameters: {
+      header?: {
+        "x-active-roles"?: string | null;
+      };
+      path: {
+        urn: string;
+      };
+    };
+    responses: {
+      /** @description Successful Response */
+      200: {
+        content: {
+          "application/json": components["schemas"]["VariantPathogenicityStatement"];
+        };
+      };
+      /** @description Authentication required. */
+      401: {
+        content: never;
+      };
+      /** @description Forbidden. Insufficient permissions. */
+      403: {
+        content: never;
+      };
+      /** @description Resource not found. */
+      404: {
+        content: never;
+      };
+      /** @description Validation Error */
+      422: {
+        content: {
+          "application/json": components["schemas"]["HTTPValidationError"];
+        };
+      };
+      /** @description Internal server error. */
+      500: {
+        content: never;
+      };
+    };
+  };
   /**
    * Proxy Alphafold Index
    * @description Proxy the AlphaFold files index (XML document).

From f3b9498f03b2d7c7d6dc2f5f24b7ef08ae9472b1 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Sat, 18 Jul 2026 10:26:45 -0700
Subject: [PATCH 55/84] chore(open-api): regen open api spec

---
 src/schema/openapi.d.ts | 164 +++++++++++++++++++++++++---------------
 1 file changed, 102 insertions(+), 62 deletions(-)

diff --git a/src/schema/openapi.d.ts b/src/schema/openapi.d.ts
index a0770e78..95922520 100644
--- a/src/schema/openapi.d.ts
+++ b/src/schema/openapi.d.ts
@@ -811,19 +811,19 @@ export interface paths {
   };
   "/api/v1/score-sets/{urn}/annotated-variants/pathogenicity-statement": {
     /**
-     * Get pathogenicity statement annotations for mapped variants within a score set
+     * Get pathogenicity statement annotations for variants within a score set
      * @description Retrieve annotated variants with pathogenicity statements for a given score set.
      *
-     * This endpoint streams pathogenicity evidence lines for all current mapped variants
+     * This endpoint streams pathogenicity evidence lines for all current annotated variants
      * associated with a specific score set. The response is returned as newline-delimited
      * JSON (NDJSON) format for efficient processing of large datasets.
      *
      * NDJSON Response Format:
-     *     Each line in the response corresponds to a mapped variant and contains a JSON
+     *     Each line in the response corresponds to an annotated variant and contains a JSON
      *     object with the following structure:
      *     ```
      *     {
-     *         "variant_urn": "<URN of the mapped variant>",
+     *         "variant_urn": "<URN of the annotated variant>",
      *         "annotation": {
      *             ... // Pathogenicity evidence line details
      *         }
@@ -839,36 +839,39 @@ export interface paths {
      *
      * Returns:
      *     Any: StreamingResponse containing newline-delimited JSON with pathogenicity
-     *         evidence lines for each mapped variant. Response includes headers with
+     *         evidence lines for each annotated variant. Response includes headers with
      *         total count, processing start time, and stream type information.
      *
+     * A score set that exists but has no annotatable variants (never mapped, or none live at ``as_of``)
+     * streams an empty body with ``X-Total-Count: 0`` — an empty collection, not a 404.
+     *
      * Raises:
      *     HTTPException: 404 error if the score set with the given URN is not found.
-     *     HTTPException: 404 error if no mapped variants are associated with the score set.
      *     HTTPException: 403 error if the user lacks READ permissions for the score set.
      *
      * Note:
      *     This function logs the request context and validates user permissions before
-     *     processing. Only current (non-historical) mapped variants are included in
-     *     the response.
+     *     processing. Use the `as_of` parameter to reconstruct the molecular layer as it stood at a specific
+     *     instant, over the variant's fixed score. The response is streamed to allow for efficient handling
+     *     of large datasets, and progress updates are logged for monitoring purposes.
      */
     get: operations["get_score_set_annotated_variants_api_v1_score_sets__urn__annotated_variants_pathogenicity_statement_get"];
   };
   "/api/v1/score-sets/{urn}/annotated-variants/functional-statement": {
     /**
-     * Get functional impact statement annotations for mapped variants within a score set
+     * Get functional impact statement annotations for annotated variants within a score set
      * @description Retrieve functional impact statements for annotated variants in a score set.
      *
-     * This endpoint streams functional impact statements for all current mapped variants
+     * This endpoint streams functional impact statements for all current annotated variants
      * associated with a specific score set. The response is delivered as newline-delimited
      * JSON (NDJSON) format.
      *
      * NDJSON Response Format:
-     *     Each line in the response corresponds to a mapped variant and contains a JSON
+     *     Each line in the response corresponds to an annotated variant and contains a JSON
      *     object with the following structure:
      *     ```
      *     {
-     *         "variant_urn": "<URN of the mapped variant>",
+     *         "variant_urn": "<URN of the annotated variant>",
      *         "annotation": {
      *             ... // Functional impact statement details
      *         }
@@ -882,36 +885,38 @@ export interface paths {
      *
      * Returns:
      *     StreamingResponse: NDJSON stream containing functional impact statements for each
-     *         mapped variant. Response includes headers with total count, processing start time,
+     *         annotated variant. Response includes headers with total count, processing start time,
      *         and stream type information.
      *
      * Raises:
      *     HTTPException:
      *         - 404 if the score set with the given URN is not found
-     *         - 404 if no mapped variants are associated with the score set
+     *         - 404 if no annotated variants are associated with the score set
      *         - 403 if the user lacks READ permission for the score set
      *
      * Note:
-     *     Only current (non-historical) mapped variants are included in the response.
-     *     The function requires appropriate read permissions on the score set.
+     *     The function requires appropriate read permissions on the score set. Use the `as_of`
+     *     parameter to reconstruct the molecular layer as it stood at a specific instant, over
+     *     the variant's fixed score. The response is streamed to allow for efficient handling of
+     *     large datasets, and progress updates are logged for monitoring purposes.
      */
     get: operations["get_score_set_annotated_variants_functional_statement_api_v1_score_sets__urn__annotated_variants_functional_statement_get"];
   };
   "/api/v1/score-sets/{urn}/annotated-variants/study-result": {
     /**
-     * Get functional study result annotations for mapped variants within a score set
+     * Get functional study result annotations for annotated variants within a score set
      * @description Retrieve functional study results for annotated variants in a score set.
      *
-     * This endpoint streams functional study result annotations for all current mapped variants
+     * This endpoint streams functional study result annotations for all current annotated variants
      * associated with a specific score set. The results are returned as newline-delimited JSON
      * (NDJSON) format for efficient streaming of large datasets.
      *
      * NDJSON Response Format:
-     *     Each line in the response corresponds to a mapped variant and contains a JSON
+     *     Each line in the response corresponds to a annotated variant and contains a JSON
      *     object with the following structure:
      *     ```
      *     {
-     *         "variant_urn": "<URN of the mapped variant>",
+     *         "variant_urn": "<URN of the annotated variant>",
      *         "annotation": {
      *             ... // Functional study result details
      *         }
@@ -926,7 +931,7 @@ export interface paths {
      * Returns:
      *     StreamingResponse: A streaming response containing functional study results in NDJSON format.
      *         Headers include:
-     *         - X-Total-Count: Total number of mapped variants being streamed
+     *         - X-Total-Count: Total number of annotated variants being streamed
      *         - X-Processing-Started: ISO timestamp when processing began
      *         - X-Stream-Type: Set to "functional-study-result"
      *         - Access-Control-Expose-Headers: Exposed headers for CORS
@@ -934,13 +939,14 @@ export interface paths {
      * Raises:
      *     HTTPException:
      *         - 404 if the score set with the given URN is not found
-     *         - 404 if no mapped variants are associated with the score set
+     *         - 404 if no annotated variants are associated with the score set
      *         - 403 if the user lacks READ permission for the score set
      *
      * Notes:
-     *     - Only returns current mapped variants (MappedVariant.current == True)
-     *     - Eagerly loads related ScoreSet data including publications, users, license, and experiment
-     *     - Logs requests and errors for monitoring and debugging purposes
+     *     - The `as_of` parameter allows reconstruction of the molecular layer as it stood at a specific
+     *       instant, over the variant's fixed score. It is ISO 8601 formatted and ideally timezone-aware.
+     *     - The response is streamed to allow for efficient handling of large datasets, and progress updates
+     *       are logged for monitoring purposes.
      */
     get: operations["get_score_set_annotated_variants_functional_study_result_api_v1_score_sets__urn__annotated_variants_study_result_get"];
   };
@@ -1309,9 +1315,11 @@ export interface paths {
      * Look up variants by VRS identifier
      * @description Resolve a GA4GH VRS identifier to the readable variants whose mapping links that allele.
      *
-     * The new-substrate replacement for the legacy mapped-variant VRS lookup: a deduplicated allele may be
-     * shared across score sets, so one identifier can resolve to several variants. Results are filtered to
-     * the score sets the caller may read; a 404 is returned when nothing readable matches.
+     * A deduplicated allele may be shared across score sets, so one identifier can resolve to several
+     * variants. This is a lookup returning a collection: results are filtered to the score sets the caller
+     * may read, and an empty list is returned when nothing readable matches. An absent identifier and a
+     * match visible only in a private score set are deliberately indistinguishable (both yield ``[]``), so
+     * the response never reveals a private allele's existence.
      */
     get: operations["lookup_variants_by_vrs_identifier_api_v1_variants_vrs__identifier__get"];
   };
@@ -1655,8 +1663,7 @@ export interface components {
      * - ``derivation`` (provenance): ``authoritative`` (measured) / ``projection`` (deterministic,
      *   precise, derived from the measured change) / ``candidate`` (protein-assay reverse-translation,
      *   ambiguous) / ``convergent`` (a distinct, precise nucleotide change that converges on the measured
-     *   protein consequence — a synonymous cousin, paired with the ``co_encodes`` relation). Orthogonal to
-     *   ``relation`` — never conflate them.
+     *   protein consequence). Orthogonal to ``relation``. Do not conflate them.
      * - ``projectionOf`` (provenance): the VRS digest of this allele's projection sibling (the paired c↔g member of
      *   its projection pair group); ``null`` for the protein apex and pre-reverse-translation data.
      */
@@ -10424,19 +10431,19 @@ export interface operations {
     };
   };
   /**
-   * Get pathogenicity statement annotations for mapped variants within a score set
+   * Get pathogenicity statement annotations for variants within a score set
    * @description Retrieve annotated variants with pathogenicity statements for a given score set.
    *
-   * This endpoint streams pathogenicity evidence lines for all current mapped variants
+   * This endpoint streams pathogenicity evidence lines for all current annotated variants
    * associated with a specific score set. The response is returned as newline-delimited
    * JSON (NDJSON) format for efficient processing of large datasets.
    *
    * NDJSON Response Format:
-   *     Each line in the response corresponds to a mapped variant and contains a JSON
+   *     Each line in the response corresponds to an annotated variant and contains a JSON
    *     object with the following structure:
    *     ```
    *     {
-   *         "variant_urn": "<URN of the mapped variant>",
+   *         "variant_urn": "<URN of the annotated variant>",
    *         "annotation": {
    *             ... // Pathogenicity evidence line details
    *         }
@@ -10452,21 +10459,28 @@ export interface operations {
    *
    * Returns:
    *     Any: StreamingResponse containing newline-delimited JSON with pathogenicity
-   *         evidence lines for each mapped variant. Response includes headers with
+   *         evidence lines for each annotated variant. Response includes headers with
    *         total count, processing start time, and stream type information.
    *
+   * A score set that exists but has no annotatable variants (never mapped, or none live at ``as_of``)
+   * streams an empty body with ``X-Total-Count: 0`` — an empty collection, not a 404.
+   *
    * Raises:
    *     HTTPException: 404 error if the score set with the given URN is not found.
-   *     HTTPException: 404 error if no mapped variants are associated with the score set.
    *     HTTPException: 403 error if the user lacks READ permissions for the score set.
    *
    * Note:
    *     This function logs the request context and validates user permissions before
-   *     processing. Only current (non-historical) mapped variants are included in
-   *     the response.
+   *     processing. Use the `as_of` parameter to reconstruct the molecular layer as it stood at a specific
+   *     instant, over the variant's fixed score. The response is streamed to allow for efficient handling
+   *     of large datasets, and progress updates are logged for monitoring purposes.
    */
   get_score_set_annotated_variants_api_v1_score_sets__urn__annotated_variants_pathogenicity_statement_get: {
     parameters: {
+      query?: {
+        /** @description Reconstruct the molecular layer (Cat-VRS membership, VEP/gnomAD/ClinVar annotations) as it stood at this instant, over the variant's fixed score. ISO 8601, ideally timezone-aware. Content valid-time only — it never re-selects a score-set version, and scores/classifications are as-of-invariant. Defaults to current. */
+        as_of?: string | null;
+      };
       header?: {
         "x-active-roles"?: string | null;
       };
@@ -10475,7 +10489,7 @@ export interface operations {
       };
     };
     responses: {
-      /** @description Stream pathogenicity statement annotations for mapped variants. */
+      /** @description Stream pathogenicity statement annotations for variants. */
       200: {
         content: {
           "application/json": {
@@ -10509,19 +10523,19 @@ export interface operations {
     };
   };
   /**
-   * Get functional impact statement annotations for mapped variants within a score set
+   * Get functional impact statement annotations for annotated variants within a score set
    * @description Retrieve functional impact statements for annotated variants in a score set.
    *
-   * This endpoint streams functional impact statements for all current mapped variants
+   * This endpoint streams functional impact statements for all current annotated variants
    * associated with a specific score set. The response is delivered as newline-delimited
    * JSON (NDJSON) format.
    *
    * NDJSON Response Format:
-   *     Each line in the response corresponds to a mapped variant and contains a JSON
+   *     Each line in the response corresponds to an annotated variant and contains a JSON
    *     object with the following structure:
    *     ```
    *     {
-   *         "variant_urn": "<URN of the mapped variant>",
+   *         "variant_urn": "<URN of the annotated variant>",
    *         "annotation": {
    *             ... // Functional impact statement details
    *         }
@@ -10535,21 +10549,27 @@ export interface operations {
    *
    * Returns:
    *     StreamingResponse: NDJSON stream containing functional impact statements for each
-   *         mapped variant. Response includes headers with total count, processing start time,
+   *         annotated variant. Response includes headers with total count, processing start time,
    *         and stream type information.
    *
    * Raises:
    *     HTTPException:
    *         - 404 if the score set with the given URN is not found
-   *         - 404 if no mapped variants are associated with the score set
+   *         - 404 if no annotated variants are associated with the score set
    *         - 403 if the user lacks READ permission for the score set
    *
    * Note:
-   *     Only current (non-historical) mapped variants are included in the response.
-   *     The function requires appropriate read permissions on the score set.
+   *     The function requires appropriate read permissions on the score set. Use the `as_of`
+   *     parameter to reconstruct the molecular layer as it stood at a specific instant, over
+   *     the variant's fixed score. The response is streamed to allow for efficient handling of
+   *     large datasets, and progress updates are logged for monitoring purposes.
    */
   get_score_set_annotated_variants_functional_statement_api_v1_score_sets__urn__annotated_variants_functional_statement_get: {
     parameters: {
+      query?: {
+        /** @description Reconstruct the molecular layer (Cat-VRS membership, VEP/gnomAD/ClinVar annotations) as it stood at this instant, over the variant's fixed score. ISO 8601, ideally timezone-aware. Content valid-time only — it never re-selects a score-set version, and scores/classifications are as-of-invariant. Defaults to current. */
+        as_of?: string | null;
+      };
       header?: {
         "x-active-roles"?: string | null;
       };
@@ -10558,7 +10578,7 @@ export interface operations {
       };
     };
     responses: {
-      /** @description Stream functional impact statement annotations for mapped variants. */
+      /** @description Stream functional impact statement annotations for annotated variants. */
       200: {
         content: {
           "application/json": {
@@ -10592,19 +10612,19 @@ export interface operations {
     };
   };
   /**
-   * Get functional study result annotations for mapped variants within a score set
+   * Get functional study result annotations for annotated variants within a score set
    * @description Retrieve functional study results for annotated variants in a score set.
    *
-   * This endpoint streams functional study result annotations for all current mapped variants
+   * This endpoint streams functional study result annotations for all current annotated variants
    * associated with a specific score set. The results are returned as newline-delimited JSON
    * (NDJSON) format for efficient streaming of large datasets.
    *
    * NDJSON Response Format:
-   *     Each line in the response corresponds to a mapped variant and contains a JSON
+   *     Each line in the response corresponds to a annotated variant and contains a JSON
    *     object with the following structure:
    *     ```
    *     {
-   *         "variant_urn": "<URN of the mapped variant>",
+   *         "variant_urn": "<URN of the annotated variant>",
    *         "annotation": {
    *             ... // Functional study result details
    *         }
@@ -10619,7 +10639,7 @@ export interface operations {
    * Returns:
    *     StreamingResponse: A streaming response containing functional study results in NDJSON format.
    *         Headers include:
-   *         - X-Total-Count: Total number of mapped variants being streamed
+   *         - X-Total-Count: Total number of annotated variants being streamed
    *         - X-Processing-Started: ISO timestamp when processing began
    *         - X-Stream-Type: Set to "functional-study-result"
    *         - Access-Control-Expose-Headers: Exposed headers for CORS
@@ -10627,16 +10647,21 @@ export interface operations {
    * Raises:
    *     HTTPException:
    *         - 404 if the score set with the given URN is not found
-   *         - 404 if no mapped variants are associated with the score set
+   *         - 404 if no annotated variants are associated with the score set
    *         - 403 if the user lacks READ permission for the score set
    *
    * Notes:
-   *     - Only returns current mapped variants (MappedVariant.current == True)
-   *     - Eagerly loads related ScoreSet data including publications, users, license, and experiment
-   *     - Logs requests and errors for monitoring and debugging purposes
+   *     - The `as_of` parameter allows reconstruction of the molecular layer as it stood at a specific
+   *       instant, over the variant's fixed score. It is ISO 8601 formatted and ideally timezone-aware.
+   *     - The response is streamed to allow for efficient handling of large datasets, and progress updates
+   *       are logged for monitoring purposes.
    */
   get_score_set_annotated_variants_functional_study_result_api_v1_score_sets__urn__annotated_variants_study_result_get: {
     parameters: {
+      query?: {
+        /** @description Reconstruct the molecular layer (Cat-VRS membership, VEP/gnomAD/ClinVar annotations) as it stood at this instant, over the variant's fixed score. ISO 8601, ideally timezone-aware. Content valid-time only — it never re-selects a score-set version, and scores/classifications are as-of-invariant. Defaults to current. */
+        as_of?: string | null;
+      };
       header?: {
         "x-active-roles"?: string | null;
       };
@@ -10645,7 +10670,7 @@ export interface operations {
       };
     };
     responses: {
-      /** @description Stream functional study result annotations for mapped variants. */
+      /** @description Stream functional study result annotations for annotated variants. */
       200: {
         content: {
           "application/json": {
@@ -12369,14 +12394,17 @@ export interface operations {
    * Look up variants by VRS identifier
    * @description Resolve a GA4GH VRS identifier to the readable variants whose mapping links that allele.
    *
-   * The new-substrate replacement for the legacy mapped-variant VRS lookup: a deduplicated allele may be
-   * shared across score sets, so one identifier can resolve to several variants. Results are filtered to
-   * the score sets the caller may read; a 404 is returned when nothing readable matches.
+   * A deduplicated allele may be shared across score sets, so one identifier can resolve to several
+   * variants. This is a lookup returning a collection: results are filtered to the score sets the caller
+   * may read, and an empty list is returned when nothing readable matches. An absent identifier and a
+   * match visible only in a private score set are deliberately indistinguishable (both yield ``[]``), so
+   * the response never reveals a private allele's existence.
    */
   lookup_variants_by_vrs_identifier_api_v1_variants_vrs__identifier__get: {
     parameters: {
       query?: {
-        only_current?: boolean;
+        /** @description Reconstruct the molecular layer (Cat-VRS membership, VEP/gnomAD/ClinVar annotations) as it stood at this instant, over the variant's fixed score. ISO 8601, ideally timezone-aware. Content valid-time only — it never re-selects a score-set version, and scores/classifications are as-of-invariant. Defaults to current. */
+        as_of?: string | null;
       };
       header?: {
         "x-active-roles"?: string | null;
@@ -12475,6 +12503,10 @@ export interface operations {
    */
   get_variant_study_result_api_v1_variants__urn__va_study_result_get: {
     parameters: {
+      query?: {
+        /** @description Reconstruct the molecular layer (Cat-VRS membership, VEP/gnomAD/ClinVar annotations) as it stood at this instant, over the variant's fixed score. ISO 8601, ideally timezone-aware. Content valid-time only — it never re-selects a score-set version, and scores/classifications are as-of-invariant. Defaults to current. */
+        as_of?: string | null;
+      };
       header?: {
         "x-active-roles"?: string | null;
       };
@@ -12519,6 +12551,10 @@ export interface operations {
    */
   get_variant_functional_impact_statement_api_v1_variants__urn__va_functional_statement_get: {
     parameters: {
+      query?: {
+        /** @description Reconstruct the molecular layer (Cat-VRS membership, VEP/gnomAD/ClinVar annotations) as it stood at this instant, over the variant's fixed score. ISO 8601, ideally timezone-aware. Content valid-time only — it never re-selects a score-set version, and scores/classifications are as-of-invariant. Defaults to current. */
+        as_of?: string | null;
+      };
       header?: {
         "x-active-roles"?: string | null;
       };
@@ -12563,6 +12599,10 @@ export interface operations {
    */
   get_variant_pathogenicity_statement_api_v1_variants__urn__va_pathogenicity_statement_get: {
     parameters: {
+      query?: {
+        /** @description Reconstruct the molecular layer (Cat-VRS membership, VEP/gnomAD/ClinVar annotations) as it stood at this instant, over the variant's fixed score. ISO 8601, ideally timezone-aware. Content valid-time only — it never re-selects a score-set version, and scores/classifications are as-of-invariant. Defaults to current. */
+        as_of?: string | null;
+      };
       header?: {
         "x-active-roles"?: string | null;
       };

From 0fe30f68afa55c4d3f4962f2b08c6f0574c0a4c3 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Sat, 18 Jul 2026 13:25:08 -0700
Subject: [PATCH 56/84] feat(alleles): consume isFocus and regenerate OpenAPI
 types

Variant detail now marks the measured allele with `isFocus` instead of
`derivation: "authoritative"`. Repoint allele-grouping's `measured` flag
onto `isFocus` and drop `authoritative` from the Derivation union.

Regenerate openapi.d.ts from the API spec: adds AlleleIdentity.isFocus,
the AlleleDetail schema, and the /alleles/{identifier} route, and folds in
the pending VA-Spec / VRS-lookup / annotated-variants relocations.
---
 src/lib/allele-grouping.test.ts |  42 +++++-----
 src/lib/allele-grouping.ts      |  19 +++--
 src/schema/openapi.d.ts         | 139 ++++++++++++++++++++++++++++----
 3 files changed, 158 insertions(+), 42 deletions(-)

diff --git a/src/lib/allele-grouping.test.ts b/src/lib/allele-grouping.test.ts
index 19303da9..a0f4542c 100644
--- a/src/lib/allele-grouping.test.ts
+++ b/src/lib/allele-grouping.test.ts
@@ -23,9 +23,9 @@ describe('groupAlleles — projection pairing + confidence', () => {
   // Nucleotide (cdna) assay: the measured cdna folds into its pair's group with its genomic projection;
   // the protein apex is a deterministic projection, unpaired.
   const nucleotide: Record<string, AlleleIdentity> = {
-    c: {level: 'cdna', hgvs: 'NM_x:c.6C>T', relation: null, derivation: 'authoritative', projectionOf: 'g'},
-    g: {level: 'genomic', hgvs: 'NC_x:g.100C>T', relation: 'is_genomic_of', derivation: 'projection', projectionOf: 'c'},
-    p: {level: 'protein', hgvs: 'NP_x:p.Leu2Phe', relation: 'translation_of', derivation: 'projection'}
+    c: {level: 'cdna', hgvs: 'NM_x:c.6C>T', relation: null, isFocus: true, projectionOf: 'g'},
+    g: {level: 'genomic', hgvs: 'NC_x:g.100C>T', relation: 'is_genomic_of', isFocus: false, derivation: 'projection', projectionOf: 'c'},
+    p: {level: 'protein', hgvs: 'NP_x:p.Leu2Phe', relation: 'translation_of', isFocus: false, derivation: 'projection'}
   }
 
   it('collapses the measured c↔g pair into one group and keeps the apex separate', () => {
@@ -33,9 +33,10 @@ describe('groupAlleles — projection pairing + confidence', () => {
     expect(groups).toHaveLength(2)
 
     const [pair, apex] = groups
-    // Measured pair floats to the top, carries both levels, and is labeled by the authoritative member.
+    // Measured pair floats to the top and carries both levels; its confidence comes from the genomic
+    // projection member (the focus/measured member has no derivation of its own).
     expect(pair.measured).toBe(true)
-    expect(pair.derivation).toBe('authoritative')
+    expect(pair.derivation).toBe('projection')
     expect(pair.members.map((m) => m.level)).toEqual(['genomic', 'cdna'])
 
     expect(apex.measured).toBe(false)
@@ -43,13 +44,13 @@ describe('groupAlleles — projection pairing + confidence', () => {
     expect(apex.derivation).toBe('projection')
   })
 
-  // Protein assay: the protein apex is authoritative/measured; the nucleotide fan-out is candidate pairs.
+  // Protein assay: the protein apex is the focus/measured allele; the nucleotide fan-out is candidate pairs.
   const protein: Record<string, AlleleIdentity> = {
-    p: {level: 'protein', hgvs: 'NP_x:p.Leu6Gly', relation: null, derivation: 'authoritative'},
-    c1: {level: 'cdna', hgvs: 'NM_x:c.16C>G', relation: 'encodes', derivation: 'candidate', projectionOf: 'g1'},
-    g1: {level: 'genomic', hgvs: 'NC_x:g.200C>G', relation: 'is_genomic_of', derivation: 'candidate', projectionOf: 'c1'},
-    c2: {level: 'cdna', hgvs: 'NM_x:c.16C>A', relation: 'encodes', derivation: 'candidate', projectionOf: 'g2'},
-    g2: {level: 'genomic', hgvs: 'NC_x:g.200C>A', relation: 'is_genomic_of', derivation: 'candidate', projectionOf: 'c2'}
+    p: {level: 'protein', hgvs: 'NP_x:p.Leu6Gly', relation: null, isFocus: true},
+    c1: {level: 'cdna', hgvs: 'NM_x:c.16C>G', relation: 'encodes', isFocus: false, derivation: 'candidate', projectionOf: 'g1'},
+    g1: {level: 'genomic', hgvs: 'NC_x:g.200C>G', relation: 'is_genomic_of', isFocus: false, derivation: 'candidate', projectionOf: 'c1'},
+    c2: {level: 'cdna', hgvs: 'NM_x:c.16C>A', relation: 'encodes', isFocus: false, derivation: 'candidate', projectionOf: 'g2'},
+    g2: {level: 'genomic', hgvs: 'NC_x:g.200C>A', relation: 'is_genomic_of', isFocus: false, derivation: 'candidate', projectionOf: 'c2'}
   }
 
   it('keeps the apex measured and collapses each candidate hypothesis into one group', () => {
@@ -108,20 +109,20 @@ describe('groupAlleles — projection pairing + confidence', () => {
   it('leaves a projection-failed candidate (dangling projectionOf) as a one-member group', () => {
     const groups = run({
       alleles: {
-        p: {level: 'protein', hgvs: 'NP_x:p.Leu6Gly', relation: null, derivation: 'authoritative'},
-        c1: {level: 'cdna', hgvs: 'NM_x:c.16C>G', relation: 'encodes', derivation: 'candidate', projectionOf: 'missing'}
+        p: {level: 'protein', hgvs: 'NP_x:p.Leu6Gly', relation: null, isFocus: true},
+        c1: {level: 'cdna', hgvs: 'NM_x:c.16C>G', relation: 'encodes', isFocus: false, derivation: 'candidate', projectionOf: 'missing'}
       }
     })
     const candidate = groups.find((g) => g.derivation === 'candidate')!
     expect(candidate.members).toHaveLength(1)
   })
 
-  // `measured` keys off derivation === 'authoritative', not relation == null: the defining allele AND any
-  // non-member link both carry relation null, so a null-relation non-authoritative allele must NOT be pinned.
-  it('does not flag a null-relation non-authoritative allele as measured', () => {
+  // `measured` keys off `isFocus`, not relation == null: the focus allele AND any non-member link both
+  // carry relation null, so a null-relation non-focus allele must NOT be pinned.
+  it('does not flag a null-relation non-focus allele as measured', () => {
     const groups = run({
       alleles: {
-        n: {level: 'protein', hgvs: 'NP_x:p.Leu6Gly', relation: null, derivation: 'projection'}
+        n: {level: 'protein', hgvs: 'NP_x:p.Leu6Gly', relation: null, isFocus: false, derivation: 'projection'}
       }
     })
     expect(groups).toHaveLength(1)
@@ -136,8 +137,7 @@ describe('groupAlleles — projection pairing + confidence', () => {
     expect(confidenceBadge({measured: false, derivation: 'convergent'})).toBe(ALLELE_CONFIDENCE.convergent)
     // The protein-assay reverse-translation fan-out: genuinely ambiguous.
     expect(confidenceBadge({measured: false, derivation: 'candidate'})).toBe(ALLELE_CONFIDENCE.candidate)
-    // `authoritative` is only ever surfaced via `measured`; on its own it has no derived badge.
-    expect(confidenceBadge({measured: false, derivation: 'authoritative'})).toBeNull()
+    // The focus/measured allele carries no derivation; on its own (measured false) it has no badge.
     expect(confidenceBadge({measured: false, derivation: null})).toBeNull()
     // The user-facing labels are decoupled from the enum keys.
     expect(ALLELE_CONFIDENCE.projection.label).toBe('Resolved')
@@ -147,8 +147,8 @@ describe('groupAlleles — projection pairing + confidence', () => {
   it('surfaces distinct linked CAIDs, excluding the page anchor', () => {
     const groups = run({
       alleles: {
-        c: {level: 'cdna', hgvs: 'NM_x:c.6C>T', relation: null, clingenAlleleId: 'CA1', derivation: 'authoritative', projectionOf: 'g'},
-        g: {level: 'genomic', hgvs: 'NC_x:g.100C>T', relation: 'is_genomic_of', clingenAlleleId: 'CA1', derivation: 'projection', projectionOf: 'c'}
+        c: {level: 'cdna', hgvs: 'NM_x:c.6C>T', relation: null, clingenAlleleId: 'CA1', isFocus: true, projectionOf: 'g'},
+        g: {level: 'genomic', hgvs: 'NC_x:g.100C>T', relation: 'is_genomic_of', clingenAlleleId: 'CA1', isFocus: false, derivation: 'projection', projectionOf: 'c'}
       },
       pageClingenAlleleId: 'CA1'
     })
diff --git a/src/lib/allele-grouping.ts b/src/lib/allele-grouping.ts
index 981f18e5..74c51db5 100644
--- a/src/lib/allele-grouping.ts
+++ b/src/lib/allele-grouping.ts
@@ -13,9 +13,13 @@ import type {KeySection} from '@/composables/use-key-drawer'
 type AlleleIdentity = components['schemas']['AlleleIdentity']
 type AlleleAnnotations = components['schemas']['AlleleAnnotations']
 
-/** Confidence/provenance axis (orthogonal to Cat-VRS's `relation`); strongest confidence first. */
-export type Derivation = 'authoritative' | 'projection' | 'convergent' | 'candidate'
-const DERIVATION_RANK: Record<string, number> = {authoritative: 0, projection: 1, convergent: 2, candidate: 3}
+/**
+ * Confidence/provenance axis (orthogonal to Cat-VRS's `relation`); strongest confidence first. The
+ * measured allele carries no derivation — it is flagged `isFocus` on the identity instead (the API
+ * dropped the `authoritative` derivation value in favour of that focus marker).
+ */
+export type Derivation = 'projection' | 'convergent' | 'candidate'
+const DERIVATION_RANK: Record<string, number> = {projection: 0, convergent: 1, candidate: 2}
 
 // Level display order (genomic → coding → protein) so a group reads bottom-up through the layer stack.
 const LEVEL_ORDER: Record<string, number> = {genomic: 0, cdna: 1, protein: 2}
@@ -36,7 +40,7 @@ export interface AlleleMember extends AlleleIdentity {
 export interface AlleleGroup {
   key: string
   members: AlleleMember[]
-  // The measured (authoritative) allele.
+  // Whether the group contains the view's focus allele (the measured allele on the variant page).
   measured: boolean
   // Whether this group contains the page-anchor allele.
   pageRoot: boolean
@@ -58,8 +62,8 @@ export interface ConfidenceBadge {
 }
 
 // Single source for the confidence axis (badges + the Key drawer's "confidence" section). Keyed by
-// outcome, not raw `Derivation`: `measured` (authoritative) reads "Measured"; the two derived states map
-// straight from `derivation`. Insertion order is the drawer's display order.
+// outcome, not raw `Derivation`: the focus/measured allele reads "Measured" (it has no derivation); the
+// derived states map straight from `derivation`. Insertion order is the drawer's display order.
 export const ALLELE_CONFIDENCE: Record<string, ConfidenceBadge> = {
   measured: {label: 'Measured', class: 'bg-sage/15 text-sage', definition: 'Directly assayed in this score set.'},
   projection: {
@@ -158,6 +162,7 @@ function makeMember(
     level: identity.level,
     hgvs: identity.hgvs,
     clingenAlleleId: identity.clingenAlleleId ?? null,
+    isFocus: identity.isFocus,
     relation: identity.relation ?? null,
     derivation: identity.derivation ?? null,
     annotations: annotations[digest] ?? null,
@@ -197,7 +202,7 @@ export function groupAlleles(input: GroupAllelesInput): AlleleGroup[] {
     groups.push({
       key: members[0].digest,
       members,
-      measured: members.some((m) => m.derivation === 'authoritative'),
+      measured: members.some((m) => m.isFocus),
       pageRoot: members.some((m) => m.pageRoot),
       derivation: pickDerivation(members),
       annotationsMatch: !conflict,
diff --git a/src/schema/openapi.d.ts b/src/schema/openapi.d.ts
index 95922520..eff2392e 100644
--- a/src/schema/openapi.d.ts
+++ b/src/schema/openapi.d.ts
@@ -31,6 +31,27 @@ export interface paths {
      */
     delete: operations["delete_my_access_key_api_v1_users_me_access_keys__key_id__delete"];
   };
+  "/api/v1/alleles/{identifier}": {
+    /**
+     * Fetch allele detail by VRS digest, CAID, or PAID
+     * @description Fetch the detail envelope for a deduplicated allele, by any of its identifiers.
+     *
+     * The allele-grain sibling of ``GET /variants/{urn}``. Flat anchor identity (digest, level, HGVS,
+     * ClinGen id, spec-pure VRS) plus the cross-layer equivalence class (each member labelled relative to
+     * the focus) and a digest-keyed annotation map. The ``identifier`` may be:
+     *
+     * - a **VRS digest** (``ga4gh:VA.…``) — focuses that one allele.
+     * - a **CAID** (``CA…``) — the nt-canonical change; The coding frame is the preferential focus,
+     *   falling back to the genomic frame if no coding frame exists.
+     * - a **PAID** (``PA…``) — the protein change; the protein allele is focused and its nucleotide
+     *   equivalents surface as reverse-translation candidates.
+     *
+     * This is a **public molecular resource**. It carries no score-set-level information. No scores,
+     * classifications, measurements, or version standing. Only the allele's own identity, its cross-layer
+     * equivalence class, and public reference annotations (VEP / gnomAD / ClinVar).
+     */
+    get: operations["get_allele_api_v1_alleles__identifier__get"];
+  };
   "/api/v1/api/version": {
     /**
      * Show API version
@@ -1651,21 +1672,49 @@ export interface components {
       clinvar?: components["schemas"]["ClinvarAnnotation"][];
     };
     /**
-     * AlleleIdentity
-     * @description The MaveDB molecular-identity facts for one of the variant's linked alleles.
-     *
-     * An entry of the ``alleles`` sidecar, keyed by VRS digest. ``level`` + ``hgvs`` (the reference-frame
-     * HGVS) are what the UI labels the per-level annotation panel by — never the digest.
+     * AlleleDetail
+     * @description The allele-detail envelope (``GET /alleles/{digest|CAID}``).
      *
-     * Three independent axes:
-     * - ``relation`` (Cat-VRS, structural): member→defining relation; ``null`` when it *is* the measured
-     *   allele, or when the allele is not a Cat-VRS member.
-     * - ``derivation`` (provenance): ``authoritative`` (measured) / ``projection`` (deterministic,
-     *   precise, derived from the measured change) / ``candidate`` (protein-assay reverse-translation,
-     *   ambiguous) / ``convergent`` (a distinct, precise nucleotide change that converges on the measured
-     *   protein consequence). Orthogonal to ``relation``. Do not conflate them.
-     * - ``projectionOf`` (provenance): the VRS digest of this allele's projection sibling (the paired c↔g member of
-     *   its projection pair group); ``null`` for the protein apex and pre-reverse-translation data.
+     * Flat anchor-identity fields (``digest`` / ``level`` / ``hgvs`` / ``clingenAlleleId`` and the spec-pure
+     * GA4GH ``vrs`` variation) plus the MaveDB layer riding alongside. This layer, keyed by VRS digest,
+     * contains the ``alleles`` map: the full cross-layer equivalence class. Each entry is an ``AlleleIdentity``,
+     * labelled relative to the focus (``isFocus`` marks the queried allele / the CAID's representations) and
+     * the digest-keyed ``annotations`` map. The two maps share keys. Measurement-agnostic: no score,
+     * classification, or version standing, and no re-anchored Cat-VRS (those belong to ``GET /variants/{urn}``).
+     * Absent fields are omitted.
+     */
+    AlleleDetail: {
+      /** Digest */
+      digest: string;
+      /** Level */
+      level?: string | null;
+      /** Hgvs */
+      hgvs?: string | null;
+      /** Clingenalleleid */
+      clingenAlleleId?: string | null;
+      /** Vrs */
+      vrs?: Record<string, never> | null;
+      /**
+       * Alleles
+       * @default {}
+       */
+      alleles?: {
+        [key: string]: components["schemas"]["AlleleIdentity"];
+      };
+      /**
+       * Annotations
+       * @default {}
+       */
+      annotations?: {
+        [key: string]: components["schemas"]["AlleleAnnotations"];
+      };
+    };
+    /**
+     * AlleleIdentity
+     * @description One allele in a view's ``alleles`` map, keyed by VRS digest and labelled relative to the view's
+     * focus allele. ``isFocus`` marks the anchor (measured allele / queried allele); ``relation`` and
+     * ``derivation`` describe every other member's structural + provenance relationship to it, and are
+     * absent on the focus itself.
      */
     AlleleIdentity: {
       /** Level */
@@ -1674,6 +1723,8 @@ export interface components {
       hgvs?: string | null;
       /** Clingenalleleid */
       clingenAlleleId?: string | null;
+      /** Isfocus */
+      isFocus: boolean;
       /** Relation */
       relation?: string | null;
       /** Derivation */
@@ -6645,6 +6696,66 @@ export interface operations {
       };
     };
   };
+  /**
+   * Fetch allele detail by VRS digest, CAID, or PAID
+   * @description Fetch the detail envelope for a deduplicated allele, by any of its identifiers.
+   *
+   * The allele-grain sibling of ``GET /variants/{urn}``. Flat anchor identity (digest, level, HGVS,
+   * ClinGen id, spec-pure VRS) plus the cross-layer equivalence class (each member labelled relative to
+   * the focus) and a digest-keyed annotation map. The ``identifier`` may be:
+   *
+   * - a **VRS digest** (``ga4gh:VA.…``) — focuses that one allele.
+   * - a **CAID** (``CA…``) — the nt-canonical change; The coding frame is the preferential focus,
+   *   falling back to the genomic frame if no coding frame exists.
+   * - a **PAID** (``PA…``) — the protein change; the protein allele is focused and its nucleotide
+   *   equivalents surface as reverse-translation candidates.
+   *
+   * This is a **public molecular resource**. It carries no score-set-level information. No scores,
+   * classifications, measurements, or version standing. Only the allele's own identity, its cross-layer
+   * equivalence class, and public reference annotations (VEP / gnomAD / ClinVar).
+   */
+  get_allele_api_v1_alleles__identifier__get: {
+    parameters: {
+      query?: {
+        /** @description Reconstruct the molecular layer (equivalence-class membership + VEP/gnomAD/ClinVar annotations) as it stood at this instant. ISO 8601, ideally timezone-aware. The focus allele's own identity is content-addressed and immutable, so it is unaffected. Defaults to current. */
+        as_of?: string | null;
+      };
+      path: {
+        /** @description A GA4GH VRS digest (one allele), or a ClinGen allele id — a nucleotide CAID (the nt-canonical change, its genomic + coding frames) or a protein PAID. */
+        identifier: string;
+      };
+    };
+    responses: {
+      /** @description Successful Response */
+      200: {
+        content: {
+          "application/json": components["schemas"]["AlleleDetail"];
+        };
+      };
+      /** @description Authentication required. */
+      401: {
+        content: never;
+      };
+      /** @description Forbidden. Insufficient permissions. */
+      403: {
+        content: never;
+      };
+      /** @description Resource not found. */
+      404: {
+        content: never;
+      };
+      /** @description Validation Error */
+      422: {
+        content: {
+          "application/json": components["schemas"]["HTTPValidationError"];
+        };
+      };
+      /** @description Internal server error. */
+      500: {
+        content: never;
+      };
+    };
+  };
   /**
    * Show API version
    * @description Describe the API version and project.

From 7e0aa690dcc301713f6756ac955d10faf0c199c0 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Sat, 18 Jul 2026 13:26:36 -0700
Subject: [PATCH 57/84] docs(mapping): add variant mapping & annotation section

New user-docs section covering variant mapping, reverse translation &
projection, and annotation, plus an "Interpreting Annotated Variants"
page. Wire the pages into the nav and add "annotated variant(s)" glossary
abbreviations.
---
 .../interpreting-annotated-variants.md        | 98 +++++++++++++++++++
 docs/content/mapping/annotation.md            | 38 +++++++
 docs/content/mapping/forward-mapping.md       | 83 ++++++++++++++++
 docs/content/mapping/index.md                 | 40 ++++++++
 docs/content/mapping/reverse-translation.md   | 68 +++++++++++++
 docs/includes/glossary.md                     |  2 +
 docs/mkdocs.yml                               |  5 +
 7 files changed, 334 insertions(+)
 create mode 100644 docs/content/interpreting-annotated-variants.md
 create mode 100644 docs/content/mapping/annotation.md
 create mode 100644 docs/content/mapping/forward-mapping.md
 create mode 100644 docs/content/mapping/index.md
 create mode 100644 docs/content/mapping/reverse-translation.md

diff --git a/docs/content/interpreting-annotated-variants.md b/docs/content/interpreting-annotated-variants.md
new file mode 100644
index 00000000..ce1fec57
--- /dev/null
+++ b/docs/content/interpreting-annotated-variants.md
@@ -0,0 +1,98 @@
+# Interpreting annotated variants
+
+When you upload a variant to MaveDB, it is described relative to the experiment's own target sequence. Before that variant can be searched, compared to clinical databases, or interpreted in a clinical context, MaveDB does two things to it:
+
+1. **Maps** it onto standard human reference coordinates (GRCh38), and
+2. **Annotates** it with data from external resources — clinical significance (ClinVar), population frequency (gnomAD), and predicted consequences (Ensembl VEP).
+
+The result is an **annotated variant**: the original measurement, expressed across molecular levels and enriched with external evidence. This page explains what each element of an
+annotated variant represents and how they can be interpreted.
+
+!!! info "Rolling out"
+    These multi-level representations are still being deployed across MaveDB. Some published datasets may not yet have a full derived variant data set as described below.
+
+## One variant, several representations
+
+A variant can be described at three molecular levels:
+
+- **Genomic** (`g.`) — position on the chromosome.
+- **Coding** (`c.`) — position within a transcript's coding sequence.
+- **Protein** (`p.`) — the amino-acid change.
+
+MaveDB shows a variant at whichever of these levels apply. The important point is that **these levels are not all equally direct.** An assay measures a variant at one of these levels. We must *derive* all other levels from that measurement. How faithfully a level can be derived and interpreted depends on the underlying biology, which the labels below seek to capture.
+
+## Measured, resolved, convergent, and candidate
+
+Every representation of an annotated variant carries one of four labels describing how it relates to the variant the assay explicitly measured:
+
+| Label | What it means | How much to trust it |
+|---|---|---|
+| **Measured** | The level at which the variant was assayed. This is the observed experimental result. | Highest — this is the evidence itself. |
+| **Resolved** | The measured change expressed at another coordinate level: its exact coordinate partner across the coding and genomic levels, or the single protein consequence of a measured DNA change. Deterministic and precise. | High — one measured change maps to exactly one resolved representation, with no guesswork. |
+| **Convergent** | A *distinct*, real nucleotide change that produces the *same* protein change as the measured variant — a separate variant that converges on the same consequence, not the one assayed here. | Moderate — a precise variant, but a different one from what was measured. |
+| **Candidate** | One of *several possible* nucleotide spellings behind a protein-level measurement, when the DNA change that was actually assayed is unknown. | Interpret with care — MaveDB surfaces all of them and privileges none. |
+
+These four labels form a confidence ladder. **Measured** is the experimental result itself; **Resolved** is a faithful, one-to-one translation of it to another coordinate level. **Convergent** and **Candidate** are both *other* nucleotide changes that share the measured protein change — the difference is precision: a **convergent** variant is a distinct, real change that happens to encode the same amino acid, whereas a **candidate** is one of several possible spellings of a protein-level measurement whose true DNA change is unknown.
+
+## Why one protein change can produce several candidates
+
+Assays that measure variants at the **protein level** create ambiguity when their variants are expressed at the nucleotide level. Because the genetic code is redundant, a single amino-acid change can be spelled by more than one nucleotide change. The assay does not observe which one occurred.
+
+!!! example "A protein change fanning out to candidates"
+    Suppose an assay measured the protein change **p.Glu23Asp** (glutamate → aspartate).
+
+    Glutamate is encoded by `GAA` or `GAG`; aspartate by `GAT` or `GAC`. If the coding sequence uses `GAA` at this position (`c.67_69`), aspartate can be reached by **two different single-nucleotide changes**:
+
+    - **c.69A>T** → `GAT` (Asp)
+    - **c.69A>C** → `GAC` (Asp)
+
+    Both produce exactly the observed protein change, and nothing in a protein-level measurement tells you which one the underlying DNA carried. MaveDB therefore surfaces **both** as *candidates*.
+
+MaveDB shows the full set for a reason: most clinically relevant external databases serve annotations at the DNA level. Surfacing the complete candidate set allows us to link a protein level variant to all possible clinically relevant annotations.
+
+### Not everything can be reverse-translated
+
+Not every protein change can be reverse-translated. Simple **substitutions** (and single-residue deletions) can be; more complex edits — insertions, delins, and frameshifts — cannot, so a protein-only measurement of one of these shows **no** derived coding or genomic variants.
+
+For the mechanism behind candidate generation — codon enumeration, synonymous handling, transcript selection, and the intronic/exon-spanning flags — see [Reverse Translation & Projection](mapping/reverse-translation.md).
+
+## Where you will (and won't) see candidates
+
+*Where* you look changes *what* you see:
+
+- **Detail surfaces** — the MaveMD [variant page](mavemd/variant-page.md) and the score set detail panel — show the full set of representations, each with its Measured / Resolved / Convergent / Candidate label.
+- **Overview surfaces** — search results and the score set table — show only the primary representation. For a protein-only assay, the coding and genomic slots may simply be **empty** rather than showing a candidate. MaveDB does not fabricate a single DNA coordinate where only an ambiguous set exists.
+
+So a variant that appears to have no coding or genomic coordinate in a search result may still have a full set of candidates on its detail page.
+
+## Annotations across representations
+
+External annotations (ClinVar, gnomAD, Ensembl VEP) attach at the level where those resources describe variants — almost always DNA. Because a measured level and its derived siblings are different molecular descriptions, they can occasionally carry **different** annotations. When that happens, MaveDB shows them per-level rather than merging them.
+
+When annotations diverge, weigh the annotation on the **measured** level most heavily — it describes the variant that was actually assayed. A sibling representation's annotation is supporting context, not the primary signal.
+
+How annotations are attached, and how divergence is handled, is covered in [Annotation](mapping/annotation.md); for what each external resource provides, see [External Integrations](finding-data/external-integrations.md).
+
+## Identifiers
+
+MaveDB variants carry ClinGen Allele identifiers, which act as stable cross-references to other clinical genomics resources. The identifier tracks the **level of the representation**, not the level that was measured:
+
+- **Nucleotide** representations (genomic and coding) carry a **canonical-allele (CA)** identifier.
+- **Protein** representations carry a **protein-allele (PA)** identifier.
+
+Because every variant is projected up to its protein consequence, an annotated variant typically has a **PA identifier for its protein level and CA identifiers for its nucleotide representations — regardless of the level at which it was originally measured.** A variant measured at the nucleotide level still projects up to a protein representation with its own PA identifier; a protein-only measurement still receives a CA identifier for each of its nucleotide candidates.
+
+## In short
+
+- A variant is shown across genomic, coding, and protein levels. It can only be **measured** at one level. All other levels are derived.
+- A **resolved** representation is a faithful one-to-one derivation of the measured change. A **convergent** variant is a distinct real change that produces the same protein consequence. A **candidate** is one of several possible spellings of a protein measurement, and is never treated as canonical.
+- A protein-only assay can fan out to several DNA candidates — or, for edits that can't be reverse-translated, to none.
+- Trust in order: **measured**, then **resolved**, then **convergent**, then **candidate**.
+- Detail pages show the full picture; overview and search surfaces may be limited to only the primary representation.
+
+## See also
+
+- [Variant page](mavemd/variant-page.md) — reading these representations on the MaveMD clinical interface
+- [Variant mapping](reference/variant-mapping.md) — how variants are mapped to reference coordinates
+- [External Integrations](finding-data/external-integrations.md) — the ClinVar, gnomAD, and ClinGen resources behind annotations
+- [Data Formats](submitting-data/data-formats.md) — how variants are described on upload
diff --git a/docs/content/mapping/annotation.md b/docs/content/mapping/annotation.md
new file mode 100644
index 00000000..ff02a078
--- /dev/null
+++ b/docs/content/mapping/annotation.md
@@ -0,0 +1,38 @@
+# Annotation
+
+Once a variant has been [mapped](../reference/variant-mapping.md) and its other molecular levels [derived](reverse-translation.md), MaveDB annotates each representation with data from external resources. This is the final stage of the pipeline, and it is what connects a functional measurement to the wider clinical-genomics ecosystem.
+
+This page describes annotation as a **pipeline stage** — what is annotated, and at what grain. For what a given annotation *means* and how to weigh it, see [Interpreting Annotated Variants](../interpreting-annotated-variants.md). For a per-resource description of each external source, see [External Integrations](../finding-data/external-integrations.md).
+
+!!! info "Rolling out"
+    Annotation of derived (reverse-translated) representations is still being deployed across MaveDB. Some published datasets may not yet carry the full set of annotations described here.
+
+## Registration comes first
+
+Before annotation, each allele is registered with the [ClinGen Allele Registry](https://reg.clinicalgenome.org/) to obtain a stable **ClinGen Allele ID** (a CA identifier for nucleotide representations, a PA identifier for protein). These identifiers are the join keys MaveDB uses to look a variant up in external resources, so registration precedes the annotations that depend on it.
+
+## What gets annotated
+
+MaveDB attaches three kinds of annotation:
+
+- **Clinical significance** — classifications from [ClinVar](https://www.ncbi.nlm.nih.gov/clinvar/).
+- **Population frequency** — allele frequencies from [gnomAD](https://gnomad.broadinstitute.org/).
+- **Predicted consequence** — molecular consequence predictions from [Ensembl VEP](https://www.ensembl.org/info/docs/tools/vep/index.html).
+
+Each is attached at the level the resource describes variants, almost always DNA. See [External Integrations](../finding-data/external-integrations.md) for what each resource provides and how MaveDB links to it.
+
+## Annotation grain
+
+Annotations are attached **per representation**, not per variant. Every allele in a variant's set, the measured one and each derived (resolved, convergent, or candidate) representation, is annotated independently.
+
+This matters because a measured allele and its derived siblings are distinct molecular descriptions, so they can carry **different** annotations. When that happens, MaveDB keeps them per-level rather than merging them into one. Which annotation to prioritize in that situation is an interpretation question. For more details on interpreting annotations across representations, see [Interpreting Annotated Variants](../interpreting-annotated-variants.md#annotations-across-representations).
+
+## When annotation runs
+
+Annotation runs automatically after mapping and reverse translation, once a score set's alleles have been registered with ClinGen. When a score set is re-mapped, its annotations are refreshed against the new representations.
+
+## See also
+
+- [Interpreting Annotated Variants](../interpreting-annotated-variants.md) — what annotations mean and how to weigh divergence
+- [External Integrations](../finding-data/external-integrations.md) — per-resource detail for ClinVar, gnomAD, VEP, and ClinGen
+- [Reverse Translation & Projection](reverse-translation.md) — produces the representations that get annotated
diff --git a/docs/content/mapping/forward-mapping.md b/docs/content/mapping/forward-mapping.md
new file mode 100644
index 00000000..fe20642d
--- /dev/null
+++ b/docs/content/mapping/forward-mapping.md
@@ -0,0 +1,83 @@
+# Forward mapping
+
+Forward mapping is the first stage of the [mapping and annotation pipeline](index.md). MaveDB uses the variant descriptions in a score set's [score and count data tables](../submitting-data/data-formats.md) to place each variant onto standard human reference coordinates. This is what allows MaveDB to integrate with [external resources such as ClinGen, ClinVar, and gnomAD](../finding-data/external-integrations.md), powers the [MaveMD variant search](../mavemd/variant-search.md), and enables [score calibrations](../reference/score-calibrations.md) for clinical interpretation.
+
+!!! note
+    Mapping is only performed for datasets with a **human** target sequence.
+
+This method was developed by [Arbesfeld et al. (2025)](https://doi.org/10.1186/s13059-025-03647-x) and is described in detail in the linked publication. The sections below give a mechanical overview of the pipeline and surface the notable choices behind it — the ones a reader might reasonably contest.
+
+## Why mapping is needed
+
+Most MAVE experiments describe variants relative to an assay-specific target sequence uploaded by the data submitter. This target sequence is often not identical to a human reference sequence — it may be codon-optimized for expression in a model organism, contain synthetic elements such as minigene constructs, or represent only a portion of the full gene. Additionally, protein-level variants from cDNA-based assays may span exon boundaries when represented at the genomic level.
+
+These differences mean that MAVE variant descriptions cannot be directly compared to variants reported by clinical sequencing pipelines or described in databases like ClinVar. Mapping resolves this by translating each variant from the experimental target-sequence coordinate system to standard human reference coordinates (GRCh38).
+
+## Mapping process
+
+Mapping runs when a score set's variant data is [uploaded](../submitting-data/upload-guide.md). It involves the following steps:
+
+```mermaid
+flowchart LR
+    A["Target sequence<br>alignment<br>(BLAT → GRCh38)"] --> B["Transcript<br>selection<br>(MANE Select)"]
+    B --> C["Variant<br>translation<br>(MAVE-HGVS → HGVS)"]
+    C --> D["VRS<br>translation<br>(HGVS → VRS)"]
+```
+
+1. **Target sequence alignment**: The target sequence is aligned to the GRCh38 assembly with [BLAT](https://genome.ucsc.edu/FAQ/FAQblat.html) — nucleotide targets directly against the genome, amino-acid targets in protein space instead. The alignment fixes the target's genomic location and candidate transcripts, and the **gene is taken from the locus the target aligns to**, not from a submitter-declared gene name. *(A deliberate choice: alignment is the objective signal, but it means a target that aligns unexpectedly resolves to whatever gene sits at that locus.)*
+
+2. **Transcript selection**: MaveDB maps to a **single representative transcript** per target rather than to every overlapping transcript, prioritizing [MANE Select](https://www.ncbi.nlm.nih.gov/refseq/MANE/) (the clinical-reporting standard), then MANE Plus Clinical, and falling back to the longest compatible transcript when no MANE transcript applies. An offset is computed to locate the MAVE sequence within the selected reference. *(A deliberate choice: one stable, standard coordinate system, at the cost of not representing alternate transcripts.)*
+
+3. **Variant translation**: Each variant in the score and count data tables is converted from [MAVE-HGVS](../submitting-data/data-formats.md#variant-columns) format to standard HGVS format and translated with respect to the selected transcript. This step accounts for any offset between the target sequence and the transcript.
+
+4. **VRS translation**: The HGVS descriptions are converted to [GA4GH VRS](https://vrs.ga4gh.org/en/stable/) format using the [VRS-Python](https://github.com/ga4gh/vrs-python) library. Each representation receives a unique, computable VRS digest, enabling precise identification and data provenance.
+
+!!! warning "Review mapping results"
+    In some cases, variants may not be successfully mapped due to issues such as ambiguous target sequences, complex variant types, or discrepancies between the target and reference genome. MaveDB logs these instances and provides feedback to data contributors to help resolve mapping issues.
+
+    Although some mapping failures represent true limitations of the data, others can be addressed by correcting errors in the submitted variants or target sequences.
+
+    **It is highly recommended that data contributors review the mapping results after uploading a score set to ensure that variants have been accurately mapped.** Contributors can view mapping results on the score set page and download a report of mapped and unmapped variants.
+
+    Mapping failures do not prevent datasets from being published in MaveDB, but a successful mapping is required for certain features such as [variant search](../mavemd/variant-search.md), linkages with certain [external resources](../finding-data/external-integrations.md), and inclusion in [MaveMD](../mavemd/index.md).
+
+## How a mapped variant is represented
+
+A mapped variant is not stored as a single object but as a small **set of representations**:
+
+- The original **assay-level** (target-relative) form is retained, so the experimental context is never lost.
+- Each **reference-level** representation — genomic, coding, and protein, wherever the biology allows — is stored as a distinct allele, each carrying its own GA4GH VRS object and stable digest.
+
+This unified, per-level representation is what lets a variant be expressed consistently across molecular levels and matched against external resources. The [reverse translation and projection](reverse-translation.md) stage fills in the levels a given assay did not measure. [Interpreting Annotated Variants](../interpreting-annotated-variants.md) explains how to read the resulting multi-level view. *(A deliberate choice: per-level VRS alleles plus the retained assay-level form give cross-level identity and provenance, rather than collapsing a variant to a single canonical representation.)*
+
+## Assay target vs. human reference
+
+Because an assay's target sequence is often not identical to the human reference, the assay-level representation and its mapped reference-level counterpart can **differ**. Retaining both (as above) keeps that difference visible rather than flattening it away — which is a core provenance goal of mapping: the original experimental context is never lost, downstream users can see exactly how the assay relates to the human reference, and clinical users can judge whether the experimental evidence is appropriate for their interpretation context.
+
+These differences are expected, not errors. They arise from legitimate differences between experimental and reference sequences:
+
+- **Codon optimization** — synonymous nucleotide changes introduced to optimize expression in the assay system.
+- **Non-homologous sequence content** — synthetic elements like minigene constructs that do not align to the human genome.
+- **Exon-boundary spanning** — protein-level changes that, at the genomic level, correspond to nucleotide changes across exon–intron boundaries.
+
+## What isn't mapped
+
+Not every submitted variant yields a mapped representation, and an absence is not always a failure. MaveDB distinguishes two cases:
+
+- **Benign absences** — variants that legitimately have no reference-level representation, recorded but with no mapped allele. The main case is a **submitted intronic variant**: an intronic position has no protein consequence and cannot be represented at the levels MaveDB serves. Other changes with no protein consequence are treated the same way.
+- **Failures** — variants that *should* map but didn't: ambiguous alignments, complex or malformed variant descriptions, or discrepancies between the target and reference genome. These are surfaced in the mapping report for the contributor to review.
+
+Only genuine failures count against a score set's mapping; benign absences do not, and neither blocks publication.
+
+## Programmatic access
+
+Mapped representations are available through the [MaveDB API](../programmatic-access/api-quickstart.md) and are downloadable from individual score set pages in [VRS and VA-Spec JSON formats](../reference/data-standards.md#vrs-variant-representation).
+
+## See also
+
+- [Variant mapping & annotation](index.md) — the pipeline this stage belongs to
+- [Reverse Translation & Projection](reverse-translation.md) — deriving the levels an assay did not measure
+- [Interpreting Annotated Variants](../interpreting-annotated-variants.md) — reading a variant's representations across levels
+- [External Integrations](../finding-data/external-integrations.md) — how mapping connects MaveDB to external genomic platforms
+- [Data Formats](../submitting-data/data-formats.md) — how variants are described in score and count data files
+- [Targets](../submitting-data/targets.md) — sequence-based and accession-based target types
diff --git a/docs/content/mapping/index.md b/docs/content/mapping/index.md
new file mode 100644
index 00000000..da5eb0af
--- /dev/null
+++ b/docs/content/mapping/index.md
@@ -0,0 +1,40 @@
+# Variant mapping & annotation
+
+MaveDB describes each uploaded variant relative to the experiment's own target sequence. Before a variant can be searched, compared to clinical databases, or interpreted clinically, MaveDB runs it through a pipeline that **maps** it onto standard human reference coordinates and **annotates** it with data from external resources. This section documents how that pipeline works.
+
+!!! tip "Looking for what the results *mean*?"
+    This section covers *how* variants are processed. For what the resulting representations and labels mean — Measured, Resolved, Convergent, Candidate — and how to weigh them, see [Interpreting Annotated Variants](../interpreting-annotated-variants.md).
+
+!!! note
+    Mapping and annotation are only performed for datasets with a **human** target sequence.
+
+## The pipeline at a glance
+
+```mermaid
+flowchart LR
+    U["Score set<br>upload"] --> F["Forward mapping<br>target → reference"]
+    F --> R["Reverse translation<br>& projection<br>fill in other levels"]
+    R --> A["Annotation<br>attach external data"]
+    A --> S["Available across<br>MaveDB"]
+```
+
+1. **[Forward mapping](../reference/variant-mapping.md)** — the target sequence is aligned to GRCh38, a representative transcript is selected, and each variant is translated from the experiment's coordinates into standard HGVS and VRS representations. This is where concordance with the human reference is assessed.
+2. **Reverse translation & projection** — the levels the assay *didn't* measure are derived from the one it did. A protein-only measurement gains coding and genomic representations; a DNA measurement gains its protein consequence. See [Reverse Translation & Projection](reverse-translation.md).
+3. **[Annotation](annotation.md)** — the mapped and derived representations are cross-referenced against external resources (ClinVar, gnomAD, Ensembl VEP) at the level where each resource describes variants.
+<!-- TODO: repoint stage 1 to mapping/forward-mapping.md after migration -->
+
+!!! info "Rolling out"
+    Reverse translation and projection of protein-only variants are still being deployed across MaveDB. Some published datasets may not yet show the full set of derived representations.
+
+## When the pipeline runs
+
+Mapping and annotation run automatically when a score set's variant data is [uploaded](../submitting-data/upload-guide.md). Results are visible on the score set page. A score set can also be re-mapped later; when that happens, the earlier results are superseded and the new ones take their place.
+
+!!! warning "Review your mapping results"
+    Some variants may not map — because of ambiguous target sequences, complex variant types, or discrepancies between the target and reference genome. Mapping failures do not prevent publication, but mapped variants are required for [variant search](../mavemd/variant-search.md), some [external integrations](../finding-data/external-integrations.md), and inclusion in [MaveMD](../mavemd/index.md). **Contributors are strongly encouraged to review mapping results after upload**; MaveDB flags failures and provides a downloadable report.
+
+## See also
+
+- [Interpreting Annotated Variants](../interpreting-annotated-variants.md) — what the mapped and derived representations mean
+- [External Integrations](../finding-data/external-integrations.md) — the external resources behind annotations
+- [Data Formats](../submitting-data/data-formats.md) — how variants are described on upload
diff --git a/docs/content/mapping/reverse-translation.md b/docs/content/mapping/reverse-translation.md
new file mode 100644
index 00000000..f11d5908
--- /dev/null
+++ b/docs/content/mapping/reverse-translation.md
@@ -0,0 +1,68 @@
+# Reverse translation & projection
+
+[Forward mapping](../reference/variant-mapping.md) describes a variant at the level the assay measured. **Reverse translation and projection** fill in the *other* molecular levels, so that every variant can be expressed at the genomic, coding, and amino acid levels wherever the biology allows:
+
+- **Reverse translation** works *downward*, from a measured **protein** change to the **DNA** changes that could produce it.
+- **Projection** works between the coding and genomic levels, and *upward* from a measured DNA change to its **protein** consequence.
+
+This is the stage that produces the **resolved**, **convergent**, and **candidate** representations described in [Interpreting Annotated Variants](../interpreting-annotated-variants.md). That page explains what those labels *mean*; this page explains the mechanism that produces them.
+
+!!! info "Rolling out"
+    Reverse translation and projection of protein-only variants are still being deployed across MaveDB. Some published datasets may not yet show the full set of derived representations.
+
+## Why reverse translation is needed
+
+Protein-level assays measure amino-acid changes, but the clinical resources MaveDB integrates with ([ClinVar, gnomAD](../finding-data/external-integrations.md), and others) describe variants at the DNA level. To connect a protein measurement to those resources, MaveDB has to work out which DNA changes could give rise to the observed amino-acid change. That backward step is reverse translation.
+
+## From one protein change to DNA candidates
+
+For a measured amino-acid substitution, MaveDB enumerates every single-nucleotide change to the affected codon that produces it. Because the genetic code is redundant, there is often more than one.
+
+The enumeration is exhaustive over these codon-level changes, which is why a protein change can fan out to several DNA candidates ([worked example](../interpreting-annotated-variants.md#why-one-protein-change-can-produce-several-candidates)). Surfacing the complete set is what lets a protein-level measurement match against *any* of the DNA descriptions those changes might appear under in an external database. Collapsing to a single arbitrary spelling would assert functional data exists for a DNA variant that was never measured.
+
+### What can and can't be reverse-translated
+
+Reverse translation works on amino-acid **substitutions** (including changes to a stop codon) and **single-residue deletions**. Other protein-level edits — insertions, delins, frameshifts, and stop-loss changes — are not currently supported, so a protein-only measurement of one of these produces **no** coding or genomic representation.
+
+For the changes it does handle, MaveDB casts a deliberately wide net over candidate spellings. Alongside single-nucleotide substitutions it also generates small codon-local insertion, deletion, delins candidates (indels up to three nucleotides), and length-changing candidates for premature-stop changes. The goal is to surface every DNA description a change might plausibly appear under in an external database.
+
+### Synonymous changes
+
+A **synonymous** (silent) change leaves the amino acid unchanged, so there is no amino-acid difference to reverse-translate in the usual sense. MaveDB still gives these a DNA representation by generating a **wild-type codon candidate** — the reference codon at that position, spelled out. For amino acids encoded by a single codon (methionine, tryptophan) that codon is unambiguous. For all others, MaveDB looks up the transcript's actual codon.
+
+## Projection between and across levels
+
+Once reverse translation produces DNA candidates, **projection** establishes the faithful, one-to-one relationships between representations:
+
+- **Coding ↔ genomic.** A coding change and its genomic description refer to the same underlying edit. MaveDB keeps them paired, so each coding representation carries a known genomic partner rather than an unlinked coordinate. This pairing is what lets a coordinate partner be labeled **Resolved** rather than left as an ambiguous candidate. When a coding candidate cannot be projected onto genomic coordinates, the pair is one-sided: the coding representation stands on its own, with no genomic partner recorded.
+- **DNA → protein.** A measured DNA change has exactly one protein consequence, computed by forward-translating the codon. This is always **Resolved** — there is no ambiguity in this direction.
+
+Because a coding variant projects up to its protein consequence, and coding/genomic descriptions stay paired, MaveDB can present a coherent multi-level view of a variant even when only one level was measured. (A non-coding target has no protein consequence, so this step does not apply to it.)
+
+## Candidates versus convergent variants
+
+The same codon enumeration can yield either *candidates* or *convergent* variants. The difference is whether MaveDB knows which nucleotide change was actually assayed:
+
+- When a variant is **measured at the amino acid level**, the underlying DNA change is unknown, so every enumerated spelling is equally uncertain. Each is a **candidate**.
+- When a variant is **measured at the nucleotide level**, that exact change is known. Its coordinate partner and protein consequence are **resolved**, and the *other* nucleotide changes that encode the same protein consequence become **convergent** variants — distinct, precise variants that converge on the same amino-acid change but are not the one assayed.
+
+So a candidate reflects *uncertainty about a single measurement*, whereas a convergent variant is *a different, real variant* that happens to share a protein consequence.
+
+## Transcript selection
+
+Reverse translation places a protein change onto a coding transcript. MaveDB chooses that transcript to stay consistent with forward mapping:
+
+1. Where forward mapping already selected a coding transcript for the variant, reverse translation uses that **same transcript**, so the derived coordinates line up with the mapped ones.
+2. For a protein-only measurement with no coding mapping, MaveDB resolves the protein accession (`NP_`/`XP_`) to a coding transcript through UTA, preferring `NM_` over `XM_` over `ENST`, then the highest version.
+
+If no transcript can be resolved, the variant is not reverse-translated.
+
+## Reference data and reproducibility
+
+Reverse translation runs on the transcript chosen during [mapping](../reference/variant-mapping.md) and against a pinned transcript-database (UTA) snapshot, used for transcript resolution and codon lookups. If that reference data changes, some candidates can change. All coordinates are relative to the **GRCh38** assembly.
+
+## See also
+
+- [Interpreting Annotated Variants](../interpreting-annotated-variants.md) — what Measured, Resolved, Convergent, and Candidate mean
+- [Variant mapping](../reference/variant-mapping.md) — the forward mapping that precedes this stage
+- [External Integrations](../finding-data/external-integrations.md) — the DNA-level resources candidates are matched against
diff --git a/docs/includes/glossary.md b/docs/includes/glossary.md
index ad7c576c..b56e8bd9 100644
--- a/docs/includes/glossary.md
+++ b/docs/includes/glossary.md
@@ -8,3 +8,5 @@
 *[GRCh38]: Genome Reference Consortium Human Build 38
 *[NMD]: Nonsense-Mediated Decay
 *[OddsPath]: Odds of Pathogenicity
+*[annotated variant]: A MaveDB variant expressed across molecular levels (genomic, coding, protein) and enriched with external annotations such as ClinVar, gnomAD, and predicted consequences
+*[annotated variants]: MaveDB variants expressed across molecular levels (genomic, coding, protein) and enriched with external annotations such as ClinVar, gnomAD, and predicted consequences
diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml
index 20119565..97c70d0a 100644
--- a/docs/mkdocs.yml
+++ b/docs/mkdocs.yml
@@ -85,6 +85,11 @@ nav:
       - Targets: submitting-data/targets.md
       - Upload Guide: submitting-data/upload-guide.md
       - Publishing: submitting-data/publishing.md
+  - Interpreting Annotated Variants: interpreting-annotated-variants.md
+  - Variant Mapping & Annotation:
+      - Overview: mapping/index.md
+      - Reverse Translation & Projection: mapping/reverse-translation.md
+      - Annotation: mapping/annotation.md
   - MaveMD:
       - mavemd/index.md
       - Variant Search: mavemd/variant-search.md

From 6a93bd7bf092f36de407ff6d1680821a5bbe2f76 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Mon, 20 Jul 2026 17:02:53 -0700
Subject: [PATCH 58/84] fix(allele): more gracefully handle lean CAID/PAID
 search results in headings

---
 .../screens/SearchVariantsScreen.vue          | 12 ++++---
 src/lib/mavemd.test.ts                        | 33 ++++++++++++++++++-
 src/lib/mavemd.ts                             | 15 ++++++---
 3 files changed, 50 insertions(+), 10 deletions(-)

diff --git a/src/components/screens/SearchVariantsScreen.vue b/src/components/screens/SearchVariantsScreen.vue
index cd01e80a..7c08763e 100644
--- a/src/components/screens/SearchVariantsScreen.vue
+++ b/src/components/screens/SearchVariantsScreen.vue
@@ -431,7 +431,11 @@
             <router-link
               v-if="scoreSetUrnFromVariantUrn(allele.variantUrn)"
               class="text-sm font-semibold text-link hover:underline"
-              :to="{name: 'scoreSet', params: {urn: scoreSetUrnFromVariantUrn(allele.variantUrn)}}"
+              :to="{
+                name: 'scoreSet',
+                params: {urn: scoreSetUrnFromVariantUrn(allele.variantUrn)},
+                query: {variantUrn: allele.variantUrn}
+              }"
             >
               View score set &rarr;
             </router-link>
@@ -1091,9 +1095,9 @@ export default defineComponent({
                   }
                   this.alleles.push(card)
                 } else {
-                  const bareAllele = createAlleleResult(result, null)
-                  bareAllele.canonicalAlleleName = searchStr
-                  this.alleles.push(bareAllele)
+                  // No registered transcripts to merge; createAlleleResult titles it from the record's
+                  // own protein hgvs (falling back to the ClinGen ID).
+                  this.alleles.push(createAlleleResult(result, null))
                 }
               }
               break
diff --git a/src/lib/mavemd.test.ts b/src/lib/mavemd.test.ts
index e8b2d79e..a24fa1aa 100644
--- a/src/lib/mavemd.test.ts
+++ b/src/lib/mavemd.test.ts
@@ -1,6 +1,6 @@
 import {describe, expect, it} from 'vitest'
 
-import {mergeAlleleSpellings, type AlleleResult} from '@/lib/mavemd'
+import {createAlleleResult, mergeAlleleSpellings, type AlleleResult} from '@/lib/mavemd'
 
 function result(overrides: Partial<AlleleResult>): AlleleResult {
   return {
@@ -19,6 +19,37 @@ function result(overrides: Partial<AlleleResult>): AlleleResult {
   }
 }
 
+describe('createAlleleResult', () => {
+  it('titles a complete record from its communityStandardTitle', () => {
+    const allele = createAlleleResult(
+      {'@id': 'http://reg.genome.network/allele/CA123', communityStandardTitle: ['NM_x:c.818G>A']},
+      null
+    )
+    expect(allele.canonicalAlleleName).toBe('NM_x:c.818G>A')
+  })
+
+  it('falls back to the protein hgvs for a lean amino-acid record with no title', () => {
+    const allele = createAlleleResult(
+      {
+        '@id': 'http://reg.genome.network/allele/PA2579942745',
+        aminoAcidAlleles: [
+          {hgvs: ['NP_001484.1:p.Pro368Ser'], matchingRegisteredTranscripts: [{'@id': 'CA415209784'}]}
+        ]
+      },
+      null
+    )
+    expect(allele.canonicalAlleleName).toBe('NP_001484.1:p.Pro368Ser')
+  })
+
+  it('falls back to the ClinGen ID when a record has neither a title nor a protein hgvs', () => {
+    const allele = createAlleleResult(
+      {'@id': 'http://reg.genome.network/allele/PA2830778226', aminoAcidAlleles: [{}]},
+      null
+    )
+    expect(allele.canonicalAlleleName).toBe('PA2830778226')
+  })
+})
+
 describe('mergeAlleleSpellings', () => {
   it('folds a transcript spelling onto the target and keeps distinct MANE coordinates', () => {
     const target = result({
diff --git a/src/lib/mavemd.ts b/src/lib/mavemd.ts
index 65ddc693..dc801397 100644
--- a/src/lib/mavemd.ts
+++ b/src/lib/mavemd.ts
@@ -15,11 +15,11 @@ export const vrsDigestRegex = /^ga4gh:[^.]+\.[0-9A-Za-z_-]{32}$/
 
 /**
  * Extracts the score set URN from a MaveDB variant URN.
- * Variant URNs follow the format urn:mavedb:XXXXXXXX-X-N-SUFFIX.
- * The score set URN is the first three hyphenated segments.
+ * Variant URNs follow the format urn:mavedb:XXXXXXXX-X-N#SUFFIX.
+ * The score set URN is the portion before the '#' variant separator.
  */
 export function scoreSetUrnFromVariantUrn(variantUrn: string): string | null {
-  const match = variantUrn.match(/^(urn:mavedb:[^-]+-[^-]+-[^-]+)(?:-.+)?$/)
+  const match = variantUrn.match(/^(urn:mavedb:[^-]+-[^-]+-[^-]+)#.+$/)
   return match?.[1] ?? null
 }
 
@@ -93,10 +93,15 @@ export function extractIdFromUrl(url: string | undefined): string | undefined {
 
 /** Transform a raw ClinGen allele API response into an AlleleResult for display. */
 export function createAlleleResult(data: ClinGenAllele, maneStatus: string | null): AlleleResult {
+  const clingenAlleleId = extractIdFromUrl(data['@id'])
   const allele: AlleleResult = {
     clingenAlleleUrl: data['@id'],
-    clingenAlleleId: extractIdFromUrl(data['@id']),
-    canonicalAlleleName: data.communityStandardTitle?.[0],
+    clingenAlleleId,
+    // Complete records carry a communityStandardTitle; lean amino-acid records (no title, genomic, or
+    // transcript alleles) only carry the protein hgvs. Fall back to that, then to the ClinGen ID, so the
+    // card always has a heading instead of rendering undefined.
+    canonicalAlleleName:
+      data.communityStandardTitle?.[0] ?? data.aminoAcidAlleles?.[0]?.hgvs?.[0] ?? clingenAlleleId,
     maneStatus,
     genomicAlleles: data.genomicAlleles ?? [],
     grch38Hgvs: null,

From 00f222840ea14cb8dca60508878a114f48d5cdd3 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Mon, 20 Jul 2026 17:03:13 -0700
Subject: [PATCH 59/84] feat(variant-detail): only display VEP version when a
 consequence exists

---
 src/components/variant/VariantDetailPanel.vue | 19 ++++++++++++-------
 1 file changed, 12 insertions(+), 7 deletions(-)

diff --git a/src/components/variant/VariantDetailPanel.vue b/src/components/variant/VariantDetailPanel.vue
index 8d1367f6..ec096820 100644
--- a/src/components/variant/VariantDetailPanel.vue
+++ b/src/components/variant/VariantDetailPanel.vue
@@ -32,14 +32,19 @@
       <div class="grid grid-cols-2 gap-px border-t border-border-light bg-border-light tablet:grid-cols-4">
         <div class="stat">
           <span v-key-term="'consequence'" class="stat-label">Molecular consequence</span>
-          <span class="stat-value font-semibold">{{
-            consequence?.consequence ? formatToken(consequence.consequence) : '—'
-          }}</span>
-          <span class="mt-auto text-[10px] text-text-muted">
-            As of VEP version {{ consequence?.sourceVersion ?? '—' }}</span
-          >
+          <template v-if="consequence?.consequence">
+            <span class="stat-value font-semibold">{{ formatToken(consequence.consequence) }}</span>
+            <span class="stat-value font-semibold">{{
+              consequence?.consequence ? formatToken(consequence.consequence) : '—'
+            }}</span>
+            <span class="mt-auto text-[10px] text-text-muted">
+              As of VEP version {{ consequence?.sourceVersion ?? '—' }}</span
+            >
+          </template>
+          <template v-else>
+            <span class="stat-value font-semibold">—</span>
+          </template>
         </div>
-
         <div class="stat">
           <span v-key-term="'functional-impact'" class="stat-label">Classification</span>
           <span v-if="selectedClassification" class="flex flex-wrap items-center gap-1.5">

From 66355474df30a2e7fc9e10bb55ec82ae67b1a8e5 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Mon, 20 Jul 2026 17:31:57 -0700
Subject: [PATCH 60/84] feat(variant-detail-panel): principled empty state for
 annotation-less variants

Replace the four-dash facts grid shown for a selected variant with no
resolvable annotations, which added clutter without information.

- Render the facts grid only when a consequence, classification, gnomAD,
  or ClinVar cell resolves; otherwise show a quiet empty-state message
- Keep the identity line in the empty state only when a distinct
  underlying nucleotide coordinate disambiguates the selection
- Move the superseded badge and full-details link into a shared row so
  both survive the empty state without duplicating markup
---
 src/components/variant/VariantDetailPanel.vue | 59 +++++++++++++++----
 1 file changed, 47 insertions(+), 12 deletions(-)

diff --git a/src/components/variant/VariantDetailPanel.vue b/src/components/variant/VariantDetailPanel.vue
index ec096820..b2f108ec 100644
--- a/src/components/variant/VariantDetailPanel.vue
+++ b/src/components/variant/VariantDetailPanel.vue
@@ -12,15 +12,19 @@
     </div>
     <div v-else-if="status === 'error'" class="flex items-center justify-center gap-2 px-5 py-4 text-sm text-red-600">
       <span class="flex items-center">Could not load variant detail.</span>
-      <button type="button" class="font-semibold text-link hover:underline" @click="fetchDetail(urn)">Retry</button>
+      <button class="font-semibold text-link hover:underline" type="button" @click="fetchDetail(urn)">Retry</button>
     </div>
 
     <template v-else-if="detail">
-      <!-- Identity -->
-      <div class="flex flex-wrap items-baseline gap-x-2.5 gap-y-1 px-4 pb-3 pt-3.5 tablet:px-5">
+      <!-- Identity: shown with the facts grid, and in the empty state only when an alternate spelling
+           (a distinct underlying nucleotide coordinate) disambiguates the selection. -->
+      <div
+        v-if="anyAnnotationsAvailable || hasAlternateSpelling"
+        class="flex flex-wrap items-baseline gap-x-2.5 gap-y-1 px-4 pb-3 pt-3.5 tablet:px-5"
+      >
         <span class="font-mono text-base font-bold leading-none text-text-primary">{{ coordinate || detail.urn }}</span>
         <span
-          v-if="underlyingCoordinate && underlyingCoordinate !== coordinate"
+          v-if="hasAlternateSpelling"
           v-tooltip.top="'Underlying nucleotide coordinate'"
           class="font-mono text-xs text-text-muted"
         >
@@ -29,21 +33,19 @@
       </div>
 
       <!-- Facts -->
-      <div class="grid grid-cols-2 gap-px border-t border-border-light bg-border-light tablet:grid-cols-4">
+      <div
+        v-if="anyAnnotationsAvailable"
+        class="grid grid-cols-2 gap-px border-t border-border-light bg-border-light tablet:grid-cols-4"
+      >
         <div class="stat">
           <span v-key-term="'consequence'" class="stat-label">Molecular consequence</span>
           <template v-if="consequence?.consequence">
             <span class="stat-value font-semibold">{{ formatToken(consequence.consequence) }}</span>
-            <span class="stat-value font-semibold">{{
-              consequence?.consequence ? formatToken(consequence.consequence) : '—'
-            }}</span>
             <span class="mt-auto text-[10px] text-text-muted">
               As of VEP version {{ consequence?.sourceVersion ?? '—' }}</span
             >
           </template>
-          <template v-else>
-            <span class="stat-value font-semibold">—</span>
-          </template>
+          <span v-else class="stat-value font-semibold">—</span>
         </div>
         <div class="stat">
           <span v-key-term="'functional-impact'" class="stat-label">Classification</span>
@@ -71,8 +73,14 @@
         />
       </div>
 
-      <!-- Status and Links -->
+      <!-- No facts to display: a quiet empty state. -->
+      <p v-else class="px-4 py-3 text-xs text-text-muted tablet:px-5">
+        No reference annotations were found for this variant.
+      </p>
+
+      <!-- Status and links — the superseded badge and full-details link, shared by both states. -->
       <div
+        v-if="!detail.isCurrent || detail.clingenAlleleId"
         class="border-t border-border-light bg-surface flex flex-wrap items-baseline gap-x-2.5 gap-y-1 px-4 pb-3 pt-3.5 tablet:px-5"
       >
         <span
@@ -103,6 +111,9 @@ import MvLoader from '@/components/common/MvLoader.vue'
 import VariantGnomadStat from '@/components/variant/VariantGnomadStat.vue'
 import VariantClinvarStat from '@/components/variant/VariantClinvarStat.vue'
 import {getVariantDetail} from '@/api/mavedb/variants'
+import {collectGnomadFrequencies} from '@/lib/gnomad'
+import {enumerateUnderlyingClinvar, resolveClinvarRecords} from '@/lib/clinvar-controls'
+import {resolveClinvarHeadline} from '@/lib/clinvar-control-placement'
 import type {components} from '@/schema/openapi'
 
 type VariantDetail = components['schemas']['VariantDetail']
@@ -189,6 +200,30 @@ export default defineComponent({
       return this.detail?.supersededByScoreSet
         ? `Superseded by score set ${this.detail.supersededByScoreSet}. That version may not contain a corresponding variant.`
         : 'This measurement is from a superseded version of its score set. The newer version may not contain a corresponding variant.'
+    },
+    hasGnomad(): boolean {
+      if (this.gnomad) return true
+      return collectGnomadFrequencies(this.detail?.annotations ?? {}, this.detail?.alleles ?? {}).length > 0
+    },
+    hasClinvar(): boolean {
+      const records = resolveClinvarRecords(
+        this.detail?.annotations ?? {},
+        this.detail?.alleles ?? {},
+        this.detail?.assayLevelDigest ?? null,
+        this.clinvarVersion
+      )
+      const headline = resolveClinvarHeadline(records, this.detail?.assayLevelDigest ?? null)
+      return headline.kind !== 'none' || enumerateUnderlyingClinvar(records).length > 0
+    },
+    // The facts grid only earns its place when a cell resolves; otherwise it's four dashes (clutter), and the
+    // template falls back to an empty state instead.
+    anyAnnotationsAvailable(): boolean {
+      return !!this.consequence?.consequence || this.selectedClassification != null || this.hasGnomad || this.hasClinvar
+    },
+    // A distinct underlying nucleotide coordinate — an alternate spelling worth keeping the identity line for,
+    // so it disambiguates coding variants that collapse to the same protein change.
+    hasAlternateSpelling(): boolean {
+      return !!this.underlyingCoordinate && this.underlyingCoordinate !== this.coordinate
     }
   },
 

From c92eeec11bf7b90ce33bf091697f0d6edc5dbe49 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Mon, 20 Jul 2026 17:43:55 -0700
Subject: [PATCH 61/84] fix(search-variants): warn on empty VRS digest lookup
 instead of 404

The VRS digest lookup returns an empty array rather than a 404 when no
MaveDB variants match, so the "not found" warning never fired and the
error was rethrown. Trigger the warning on an empty result and let the
catch handle only genuine request failures.
---
 src/components/screens/SearchVariantsScreen.vue | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/src/components/screens/SearchVariantsScreen.vue b/src/components/screens/SearchVariantsScreen.vue
index 7c08763e..9719c355 100644
--- a/src/components/screens/SearchVariantsScreen.vue
+++ b/src/components/screens/SearchVariantsScreen.vue
@@ -1018,9 +1018,7 @@ export default defineComponent({
           let mappedVariants
           try {
             mappedVariants = await lookupVariantsByVrsDigest(searchStr)
-          } catch (error: unknown) {
-            const {status} = getErrorResponse(error)
-            if (status === 404) {
+            if (mappedVariants.length === 0) {
               this.toast.add({
                 severity: 'warn',
                 summary: 'VRS identifier not found',
@@ -1029,6 +1027,7 @@ export default defineComponent({
               })
               return
             }
+          } catch (error: unknown) {
             throw error
           }
           for (const mappedVariant of mappedVariants) {

From 9851cbf877d283798fc4cf7bcd5c8805c2bc3150 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Wed, 22 Jul 2026 23:20:43 -0700
Subject: [PATCH 62/84] chore(open-api): regen open api spec

---
 src/schema/openapi.d.ts | 233 ++++++++++++++++++++++------------------
 1 file changed, 127 insertions(+), 106 deletions(-)

diff --git a/src/schema/openapi.d.ts b/src/schema/openapi.d.ts
index eff2392e..97bc8ca4 100644
--- a/src/schema/openapi.d.ts
+++ b/src/schema/openapi.d.ts
@@ -758,6 +758,25 @@ export interface paths {
      */
     get: operations["get_score_set_lean_variants_api_v1_score_sets__urn__variants_get"];
   };
+  "/api/v1/score-sets/{urn}/variant-details": {
+    /**
+     * Download a score set's variant details (VRS + Cat-VRS + annotations)
+     * @description Download the score set's variant details — the whole-set streaming pair of the single-variant
+     * ``GET /variants/{urn}`` detail endpoint, and the substrate-faithful replacement for the retired
+     * ``/mapped-variants`` export.
+     *
+     * One record per *mapped* variant (unmapped variants carry no VRS and are omitted): the same
+     * VariantDetail envelope the single-variant route serves — the flat ``preMapped``/``postMapped`` VRS
+     * pair for VRS consumers, plus the spec-pure GA4GH CategoricalVariant and the digest-keyed
+     * VEP/gnomAD/ClinVar annotation map for the full molecular picture.
+     *
+     * Streamed as NDJSON (like the annotated-variant exports) so a large score set downloads without
+     * materializing every envelope server-side and a client can process it line by line. ``as_of``
+     * time-travels the molecular layer only (scores/classifications are immutable); the resolved value is
+     * echoed in ``X-As-Of`` and the variant count in ``X-Total-Count``.
+     */
+    get: operations["get_score_set_variant_details_api_v1_score_sets__urn__variant_details_get"];
+  };
   "/api/v1/score-sets/{urn}/variants/data": {
     /**
      * Get score set variant data in CSV format
@@ -823,13 +842,6 @@ export interface paths {
      */
     get: operations["get_score_set_counts_csv_api_v1_score_sets__urn__counts_get"];
   };
-  "/api/v1/score-sets/{urn}/mapped-variants": {
-    /**
-     * Get mapped variants from score set by URN
-     * @description Return mapped variants from a score set, identified by URN.
-     */
-    get: operations["get_score_set_mapped_variants_api_v1_score_sets__urn__mapped_variants_get"];
-  };
   "/api/v1/score-sets/{urn}/annotated-variants/pathogenicity-statement": {
     /**
      * Get pathogenicity statement annotations for variants within a score set
@@ -1002,7 +1014,8 @@ export interface paths {
   "/api/v1/score-sets/{urn}/gnomad-variants": {
     /**
      * Get gnomad variants for a score set
-     * @description Fetch relevant gnomad variants for a given score set.
+     * @description Fetch relevant gnomad variants for a given score set, each paired with the score-set variants (and
+     * annotated allele digests) it links to over the allele substrate.
      */
     get: operations["get_gnomad_variants_for_score_set_api_v1_score_sets__urn__gnomad_variants_get"];
   };
@@ -3460,10 +3473,10 @@ export interface components {
       totalScoredVariants: number;
     };
     /**
-     * GnomADVariantWithMappedVariants
-     * @description GnomAD variant view model with mapped variants for non-admin clients.
+     * GnomADVariantWithVariantLinks
+     * @description GnomAD variant + its score-set variant links, for non-admin clients.
      */
-    GnomADVariantWithMappedVariants: {
+    GnomADVariantWithVariantLinks: {
       /** Dbname */
       dbName: string;
       /** Dbidentifier */
@@ -3494,8 +3507,8 @@ export interface components {
        * Format: date
        */
       modificationDate: string;
-      /** Mappedvariants */
-      mappedVariants: components["schemas"]["MappedVariant"][];
+      /** Variantlinks */
+      variantLinks: components["schemas"]["GnomadVariantLink"][];
     };
     /**
      * GnomadAnnotation
@@ -3515,6 +3528,19 @@ export interface components {
       /** Dbidentifier */
       dbIdentifier: string;
     };
+    /**
+     * GnomadVariantLink
+     * @description One score-set variant a gnomAD frequency record reaches, tagged with the annotated allele's digest.
+     *
+     * Mirrors :class:`clinical_control.ClinvarVariantLink`: a gnomAD variant fans out to every allele that
+     * resolved to it, and each allele belongs to a score-set variant.
+     */
+    GnomadVariantLink: {
+      /** Varianturn */
+      variantUrn: string;
+      /** Alleledigest */
+      alleleDigest?: string | null;
+    };
     /**
      * GroupBy
      * @enum {string}
@@ -3860,44 +3886,6 @@ export interface components {
       cdna?: components["schemas"]["HgvsField"] | null;
       protein?: components["schemas"]["HgvsField"] | null;
     };
-    /** MappedVariant */
-    MappedVariant: {
-      /** Premapped */
-      preMapped?: unknown;
-      /** Postmapped */
-      postMapped?: unknown;
-      /** Vrsversion */
-      vrsVersion?: string | null;
-      /** Errormessage */
-      errorMessage?: string | null;
-      /**
-       * Modificationdate
-       * Format: date
-       */
-      modificationDate: string;
-      /**
-       * Mappeddate
-       * Format: date
-       */
-      mappedDate: string;
-      /** Mappingapiversion */
-      mappingApiVersion: string;
-      /** Current */
-      current: boolean;
-      alignmentLevel?: components["schemas"]["SequenceLevel"] | null;
-      /** Atmismatchedlocus */
-      atMismatchedLocus?: boolean | null;
-      /** Neargap */
-      nearGap?: boolean | null;
-      /** Varianturn */
-      variantUrn: string;
-      /** Id */
-      id: number;
-      /** Clingenalleleid */
-      clingenAlleleId?: string | null;
-      /** Recordtype */
-      recordType?: string;
-    };
     /**
      * MappingState
      * @enum {string}
@@ -5820,15 +5808,22 @@ export interface components {
      * @description The assayed variant-detail envelope (``GET /variants/{urn}``).
      *
      * Two tiers: flat, UI-ergonomic assay fields (the ``targetHgvs``/``referenceHgvs`` coordinate pair
-     * is a client-side toggle, no refetch) plus the spec-pure GA4GH ``molecularRepresentation``
-     * (``CategoricalVariant``, no MaveDB fields inside). The MaveDB layer rides alongside, keyed by VRS
-     * digest: the ``alleles`` identity sidecar (per-allele ``level`` / ``hgvs`` / ``clingenAlleleId`` /
-     * ``relation`` — one entry per linked allele, sharing keys with ``annotations``) and the
-     * ``annotations`` map. ``isCurrent``/``supersededByScoreSet`` let a superseded variant self-describe:
-     * ``supersededByScoreSet`` is the superseding *score set*'s URN, not a variant URN. Supersession is
-     * versioned at the score-set level, and a newer version may add, drop, or renumber variants — so there
-     * is no stable superseding-*variant* pointer to hand back; a consumer resolves the current measurement
-     * by looking this variant up within that score set. Absent fields are omitted.
+     * is a client-side toggle, no refetch; the ``preMapped``/``postMapped`` raw VRS pair lets a
+     * VRS/bulk consumer read the assayed-level and measured VRS directly) plus the spec-pure GA4GH
+     * ``molecularRepresentation`` (``CategoricalVariant``, no MaveDB fields inside). The MaveDB layer
+     * rides alongside, keyed by VRS digest: the ``alleles`` identity sidecar (per-allele ``level`` /
+     * ``hgvs`` / ``clingenAlleleId`` / ``relation`` — one entry per linked allele, sharing keys with
+     * ``annotations``) and the ``annotations`` map. ``isCurrent``/``supersededByScoreSet`` let a
+     * superseded variant self-describe: ``supersededByScoreSet`` is the superseding *score set*'s URN,
+     * not a variant URN. Supersession is versioned at the score-set level, and a newer version may add,
+     * drop, or renumber variants — so there is no stable superseding-*variant* pointer to hand back; a
+     * consumer resolves the current measurement by looking this variant up within that score set.
+     *
+     * Unlike most MaveDB response models, this one serializes with ``exclude_none=False`` on both routes
+     * that emit it (``GET /variants/{urn}`` and the bulk ``GET /score-sets/{urn}/variant-details`` NDJSON
+     * stream): the shape is a stable, self-describing envelope, so every record carries the same key set
+     * and an unmapped variant reads ``preMapped``/``postMapped``/``molecularRepresentation`` as ``null``
+     * rather than dropping them. The two routes are kept in lockstep — the same object, one shape.
      */
     VariantDetail: {
       /** Urn */
@@ -5851,6 +5846,10 @@ export interface components {
       assayLevelDigest?: string | null;
       /** Clingenalleleid */
       clingenAlleleId?: string | null;
+      /** Premapped */
+      preMapped?: Record<string, never> | null;
+      /** Postmapped */
+      postMapped?: Record<string, never> | null;
       /** Molecularrepresentation */
       molecularRepresentation?: Record<string, never> | null;
       /** Mode */
@@ -10232,6 +10231,67 @@ export interface operations {
       };
     };
   };
+  /**
+   * Download a score set's variant details (VRS + Cat-VRS + annotations)
+   * @description Download the score set's variant details — the whole-set streaming pair of the single-variant
+   * ``GET /variants/{urn}`` detail endpoint, and the substrate-faithful replacement for the retired
+   * ``/mapped-variants`` export.
+   *
+   * One record per *mapped* variant (unmapped variants carry no VRS and are omitted): the same
+   * VariantDetail envelope the single-variant route serves — the flat ``preMapped``/``postMapped`` VRS
+   * pair for VRS consumers, plus the spec-pure GA4GH CategoricalVariant and the digest-keyed
+   * VEP/gnomAD/ClinVar annotation map for the full molecular picture.
+   *
+   * Streamed as NDJSON (like the annotated-variant exports) so a large score set downloads without
+   * materializing every envelope server-side and a client can process it line by line. ``as_of``
+   * time-travels the molecular layer only (scores/classifications are immutable); the resolved value is
+   * echoed in ``X-As-Of`` and the variant count in ``X-Total-Count``.
+   */
+  get_score_set_variant_details_api_v1_score_sets__urn__variant_details_get: {
+    parameters: {
+      query?: {
+        /** @description Reconstruct the molecular layer (VRS, Cat-VRS membership + VEP/gnomAD/ClinVar annotations) as it stood at this instant, over the score set's fixed scores. ISO 8601, ideally timezone-aware. Content valid-time only — it never re-selects a score-set version. Defaults to current. */
+        as_of?: string | null;
+      };
+      header?: {
+        "x-active-roles"?: string | null;
+      };
+      path: {
+        urn: string;
+      };
+    };
+    responses: {
+      /** @description Newline-delimited JSON: one VariantDetail per mapped variant — the same envelope the single-variant GET /variants/{urn} route serves, carrying the flat preMapped/postMapped VRS pair, the spec-pure GA4GH CategoricalVariant, and the digest-keyed VEP/gnomAD/ClinVar annotation map. */
+      200: {
+        content: {
+          "application/json": unknown;
+          "application/x-ndjson": unknown;
+        };
+      };
+      /** @description Authentication required. */
+      401: {
+        content: never;
+      };
+      /** @description Forbidden. Insufficient permissions. */
+      403: {
+        content: never;
+      };
+      /** @description Resource not found. */
+      404: {
+        content: never;
+      };
+      /** @description Validation Error */
+      422: {
+        content: {
+          "application/json": components["schemas"]["HTTPValidationError"];
+        };
+      };
+      /** @description Internal server error. */
+      500: {
+        content: never;
+      };
+    };
+  };
   /**
    * Get score set variant data in CSV format
    * @description Return tabular variant data from a score set, identified by URN, in CSV format.
@@ -10276,6 +10336,8 @@ export interface operations {
         drop_na_columns?: boolean | null;
         include_custom_columns?: boolean | null;
         include_post_mapped_hgvs?: boolean | null;
+        /** @description Reconstruct the annotation layer (post-mapped HGVS, VEP, gnomAD, ClinVar) as it stood at this instant, over the variant's immutable submitted HGVS/scores/counts. ISO 8601, ideally timezone-aware. No effect on the scores/counts namespaces. Defaults to current. */
+        as_of?: string | null;
       };
       header?: {
         "x-active-roles"?: string | null;
@@ -10497,50 +10559,6 @@ export interface operations {
       };
     };
   };
-  /**
-   * Get mapped variants from score set by URN
-   * @description Return mapped variants from a score set, identified by URN.
-   */
-  get_score_set_mapped_variants_api_v1_score_sets__urn__mapped_variants_get: {
-    parameters: {
-      header?: {
-        "x-active-roles"?: string | null;
-      };
-      path: {
-        urn: string;
-      };
-    };
-    responses: {
-      /** @description Successful Response */
-      200: {
-        content: {
-          "application/json": components["schemas"]["MappedVariant"][];
-        };
-      };
-      /** @description Authentication required. */
-      401: {
-        content: never;
-      };
-      /** @description Forbidden. Insufficient permissions. */
-      403: {
-        content: never;
-      };
-      /** @description Resource not found. */
-      404: {
-        content: never;
-      };
-      /** @description Validation Error */
-      422: {
-        content: {
-          "application/json": components["schemas"]["HTTPValidationError"];
-        };
-      };
-      /** @description Internal server error. */
-      500: {
-        content: never;
-      };
-    };
-  };
   /**
    * Get pathogenicity statement annotations for variants within a score set
    * @description Retrieve annotated variants with pathogenicity statements for a given score set.
@@ -11016,11 +11034,14 @@ export interface operations {
   };
   /**
    * Get gnomad variants for a score set
-   * @description Fetch relevant gnomad variants for a given score set.
+   * @description Fetch relevant gnomad variants for a given score set, each paired with the score-set variants (and
+   * annotated allele digests) it links to over the allele substrate.
    */
   get_gnomad_variants_for_score_set_api_v1_score_sets__urn__gnomad_variants_get: {
     parameters: {
       query?: {
+        /** @description Reconstruct the allele → gnomAD link state as it stood at this instant. ISO 8601, ideally timezone-aware. Defaults to current. */
+        as_of?: string | null;
         version?: string | null;
       };
       header?: {
@@ -11034,7 +11055,7 @@ export interface operations {
       /** @description Successful Response */
       200: {
         content: {
-          "application/json": components["schemas"]["GnomADVariantWithMappedVariants"][];
+          "application/json": components["schemas"]["GnomADVariantWithVariantLinks"][];
         };
       };
       /** @description Authentication required. */

From 16c1d92c0a4a35266f76a745b1a12e4db233664b Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Wed, 22 Jul 2026 23:37:03 -0700
Subject: [PATCH 63/84] feat(variant): level-gate ClinVar/gnomAD placement by
 assay level

The related-allele context on a variant's ClinVar and gnomAD cells
could leak the subject's own record back into its "related" list,
and ClinVar precedence would silently borrow a projection sibling's
call even when the measured allele sat at nucleotide level, where
its own absent record is real information rather than a fan-out gap.

- add annotation-subject.ts: a shared SubjectDigest type/helper for
  a measurement's own digest(s), including its c<->g projection twin,
  so gnomAD and ClinVar resolve "is this my own record" the same way
- resolveClinvarRecords/collectGnomadFrequencies now key off the full
  subject digest set instead of a single assayLevelDigest, and drop
  cross-frame duplicates of the subject's own record from the
  related-record enumeration
- reduceControlPlacement only falls through to projection siblings at
  protein assay level; at cdna/genomic level a missing direct record
  returns null (a new 'absent' ClinvarHeadline kind) instead of
  borrowing a sibling's call
- wire assayLevel/assayLevelDigest through VariantDetailPanel and
  VariantScreen to the gnomAD/ClinVar stat components
---
 src/components/screens/VariantScreen.vue      | 36 ++++++--
 src/components/variant/VariantClinvarStat.vue | 85 +++++++++++++------
 src/components/variant/VariantDetailPanel.vue | 11 ++-
 src/components/variant/VariantGnomadStat.vue  | 82 +++++++++++++-----
 src/composables/use-clinvar-controls.ts       |  2 +-
 src/lib/annotation-subject.ts                 | 14 +++
 src/lib/clinvar-control-placement.test.ts     | 60 +++++++++++++
 src/lib/clinvar-control-placement.ts          | 78 +++++++++++------
 src/lib/clinvar-controls.test.ts              | 23 ++++-
 src/lib/clinvar-controls.ts                   | 18 +++-
 src/lib/gnomad.test.ts                        | 29 +++++++
 src/lib/gnomad.ts                             | 19 ++++-
 12 files changed, 369 insertions(+), 88 deletions(-)
 create mode 100644 src/lib/annotation-subject.ts

diff --git a/src/components/screens/VariantScreen.vue b/src/components/screens/VariantScreen.vue
index 85a5b006..e57fefeb 100644
--- a/src/components/screens/VariantScreen.vue
+++ b/src/components/screens/VariantScreen.vue
@@ -317,6 +317,8 @@
               :alleles="lookup.selectedVariantDetail.value.alleles"
               :annotations="lookup.selectedVariantDetail.value.annotations"
               :assay-gnomad="assayGnomad"
+              :assay-level="lookup.selectedVariantDetail.value.assayLevel ?? null"
+              :assay-level-digest="primarySubjectDigests"
               plain
             >
               <template #label>
@@ -330,7 +332,8 @@
             <VariantClinvarStat
               :alleles="lookup.selectedVariantDetail.value.alleles"
               :annotations="lookup.selectedVariantDetail.value.annotations"
-              :assay-level-digest="lookup.selectedVariantDetail.value.assayLevelDigest"
+              :assay-level="lookup.selectedVariantDetail.value.assayLevel ?? null"
+              :assay-level-digest="primarySubjectDigests"
               :clinvar-version="clinvarControls.controlVersion"
               plain
             >
@@ -387,6 +390,19 @@
                 @calibration-changed="lookup.selectedCalibration.value = $event"
                 @selection-changed="() => {}"
               />
+              <!-- On a convergent-cousin/candidate page the highlighted point is a *measured* allele sharing
+                   this variant's protein consequence, not this allele — which was not itself assayed. Say so.
+                   TODO(histogram): the highlight is not deterministic when two distinct nucleotide variants
+                   that encode the same protein consequence were both measured — only one is highlighted here.
+                   Resolving that needs histogram multi-selection (highlight every measured sibling), a larger
+                   change deferred for now. -->
+              <p
+                v-if="primaryGroup && !primaryGroup.measured"
+                class="mt-2 text-xs italic leading-tight text-text-muted"
+              >
+                This allele was not directly measured — the highlighted point is a measured allele that shares
+                its protein consequence.
+              </p>
             </div>
             <div v-else class="flex min-h-[200px] items-center justify-center">
               <MvLoader text="Loading variant information..." />
@@ -538,17 +554,25 @@ export default defineComponent({
     primaryAnnotations(): AlleleAnnotations | null {
       return this.primaryGroup?.coalescedAnnotations ?? null
     },
+    // The subject the External Evidence cells anchor on: the page's own allele, as its digest(s). One physical
+    // allele is stored as a c↔g pair (two digests) and ClinVar/gnomAD attach to only one, so both count as the
+    // subject's own. This is the *page* allele, not the measured allele — on a convergent cousin's page they
+    // differ, and the cell should reflect the cousin (empty → context), not the allele that was assayed. The
+    // *level* that gates projection is the assay level (detail.assayLevel), passed separately — the assay's
+    // resolution, not the allele's molecular level, is what determines whether we may project.
+    primarySubjectDigests(): string[] {
+      return this.primaryGroup?.members.map((m) => m.digest) ?? []
+    },
     // VEP molecular consequence for the primary allele.
     primaryMolecularConsequence(): string | null {
       const consequence = this.primaryAnnotations?.vep?.consequence
       return consequence ? formatConsequence(consequence) : null
     },
-    // The measured allele's own gnomAD annotation — the headline the gnomAD cell shows straight up (siblings
-    // are enumerated by the cell itself when the measured allele has none, e.g. a protein-level assay).
+    // The page allele's own gnomAD annotation — the headline the gnomAD cell shows straight up (siblings are
+    // enumerated by the cell itself when the page allele has none). Coalesced across the allele's c↔g pair so
+    // a frequency on either representation counts; anchored on the page allele, not the measured allele.
     assayGnomad(): GnomadAnnotation | null {
-      const detail = this.lookup.selectedVariantDetail.value
-      const digest = detail?.assayLevelDigest
-      return (digest ? detail?.annotations?.[digest]?.gnomad : null) ?? null
+      return this.primaryAnnotations?.gnomad ?? null
     },
     // Whether any allele on the record carries a gnomAD or ClinVar annotation — gates the evidence card.
     hasExternalEvidence(): boolean {
diff --git a/src/components/variant/VariantClinvarStat.vue b/src/components/variant/VariantClinvarStat.vue
index 996e9fa8..aaa54279 100644
--- a/src/components/variant/VariantClinvarStat.vue
+++ b/src/components/variant/VariantClinvarStat.vue
@@ -10,7 +10,7 @@
          lean but flags a co-occurring uncertain record (differentiating a plain VUS from ClinVar's own
          Conflicting verdict); a concordant call gets a quiet aside. Show the lean rather than hide it. -->
     <template v-else-if="headline.kind === 'call'">
-      <MvClinvarSummary :clinvar="headline.clinvar" :show-provenance="false" />
+      <MvClinvarSummary :clinvar="headline.clinvar" :show-provenance="showHeadlineProvenance" />
       <span v-if="headline.note === 'soft-conflicting'" class="text-xs italic text-text-muted">
         ClinVar marks a record with the same protein consequence as conflicting.
       </span>
@@ -22,21 +22,31 @@
       </span>
     </template>
     <!-- No usable call, but a ClinVar record exists on an allele (a `-`, e.g. a somatic/oncogenicity-only
-         submission with no germline classification). MvClinvarSummary names the state and links out. -->
-    <MvClinvarSummary v-else-if="headline.kind === 'presence'" :clinvar="headline.record.clinvar" />
+         submission with no germline classification). MvClinvarSummary names the state; it links out inline
+         only when this record is shown directly (no underlying records), else the link lives in the popover. -->
+    <MvClinvarSummary
+      v-else-if="headline.kind === 'presence'"
+      :clinvar="headline.record.clinvar"
+      :show-provenance="showHeadlineProvenance"
+    />
+    <!-- Nucleotide measurement with no ClinVar record of its own: be explicit rather than borrow a related
+         allele's call. Related records (if any) are offered below as context, not promoted to a call. -->
+    <span v-else-if="headline.kind === 'absent'" class="stat-value text-sm italic text-text-muted">
+      No ClinVar record for this variant
+    </span>
     <span v-else class="stat-value">—</span>
 
-    <!-- The records on sibling alleles behind the headline — everything except the measured allele's own
-         record (germline-less `-` included), so a lone assayed record gets no popover. Mirrors gnomAD's. -->
+    <!-- Related-allele records offered as context: beside a direct call (records that did not drive it),
+         beneath a projected call (the siblings it folded over), or under an `absent` headline. -->
     <template v-if="underlyingClinvar.length">
       <button class="mt-auto text-left text-xs text-link hover:underline" type="button" @click="toggleClinvarPopover">
         {{ underlyingClinvar.length }}
-        {{ underlyingClinvar.length === 1 ? 'underlying record' : 'underlying records' }}
+        {{ underlyingLabel }}
       </button>
       <Popover ref="clinvarPopoverRef">
         <div class="flex max-w-xs flex-col gap-2">
           <span class="text-xs text-text-muted">{{ underlyingClinvarNote }}</span>
-          <!-- Lean rows: the prioritized call is the headline above, so each underlying record shows only its
+          <!-- Lean rows: the headline call is shown above, so each context record shows only its
                allele (HGVS), release, and a link out to ClinVar for the full classification. -->
           <div
             v-for="item in underlyingClinvar"
@@ -63,23 +73,26 @@ import {
   resolveClinvarRecords,
   type MeasurementClinvarRecord
 } from '@/lib/clinvar-controls'
+import type {SubjectDigest} from '@/lib/annotation-subject'
 import {resolveClinvarHeadline, type ClinvarHeadline} from '@/lib/clinvar-control-placement'
 import type {components} from '@/schema/openapi'
 
 type AlleleAnnotations = components['schemas']['AlleleAnnotations']
 type AlleleIdentity = components['schemas']['AlleleIdentity']
+type SequenceLevel = components['schemas']['SequenceLevel']
 
 /**
- * The ClinVar stat cell shared by the score-set variant panel and the variant screen. Runs the
- * concordant/discordant placement fold over the whole record so it agrees with the histogram:
- * Prefer the assayed allele's own call wins, then...
- * If the assayed allele is unannotated, a projected call from a sibling allele (same protein consequence) is used.
- * If it is unannotated it falls through to a related-level projection sibling.
- * If those siblings are discordant, note they are in conflict.
- * If no germline record exists but the variant has a somatic/oncogenicity-only submission, link but note 'No germline classification'.
- * Beneath the folded headline, a popover lists the sibling-allele records behind it (allele HGVS, release,
- * link) — every record except the measured allele's own; germline-less `-` included, only the fold drops those.
- * `clinvarVersion` is passed by the parent so this component resolves the same version as other histogram and stat cells.
+ * The ClinVar stat cell shared by the score-set variant panel and the variant screen. Runs the same
+ * level-gated placement fold as the histogram ({@link resolveClinvarHeadline}) so the two agree:
+ *  - the measured allele's own call wins as the headline, with its link inline;
+ *  - at *protein* level, an unannotated measured allele projects a representative from its encoding siblings
+ *    (flagged for soft/hard discordance); the popover lists the siblings it folded over;
+ *  - at *nucleotide* level, an unannotated measured allele stays explicit ('No ClinVar record for this
+ *    variant') — we don't borrow a related allele's call — and any related records show as context;
+ *  - a germline-less `-` record on the measured allele shows 'No germline classification' and links out.
+ * The popover always carries the related-allele records as context (allele HGVS, release, link), minus the
+ * measured allele's own record and its cross-frame duplicates.
+ * `clinvarVersion` is passed by the parent so this cell resolves the same release as other histogram and stat cells.
  * `plain` / the `#label` slot let a caller drop the `.stat` chrome and supply its own label.
  */
 export default defineComponent({
@@ -95,8 +108,12 @@ export default defineComponent({
     annotations: {type: Object as PropType<Record<string, AlleleAnnotations>>, default: () => ({})},
     // Digest-keyed allele identities. These supply a projected call's reference-frame HGVS.
     alleles: {type: Object as PropType<Record<string, AlleleIdentity>>, default: () => ({})},
-    // The measured allele's digest.
-    assayLevelDigest: {type: String as PropType<string | null>, default: null},
+    // The subject allele's digest(s) — the measured allele on the score-set panel, or the page's own allele
+    // (its c↔g pair) on the variant page. A ClinVar record on any of them is the subject's own.
+    assayLevelDigest: {type: [String, Array] as PropType<SubjectDigest>, default: null},
+    // The measured allele's sequence level. Gates projection: at nucleotide level a missing direct record
+    // stays explicit ('absent') rather than borrowing a related allele's call. `null` → project (unknown).
+    assayLevel: {type: String as PropType<SequenceLevel | null>, default: null},
     // The ClinVar release to reduce over (raw `MM_YYYY`), so this cell agrees with all parents.
     // `null` (store not ready / no controls) → fall back to the latest release per allele.
     clinvarVersion: {type: String as PropType<string | null>, default: null}
@@ -107,17 +124,37 @@ export default defineComponent({
     records(): MeasurementClinvarRecord[] {
       return resolveClinvarRecords(this.annotations, this.alleles, this.assayLevelDigest, this.clinvarVersion)
     },
-    // What the single headline shows: the fold's call, a `-` presence fallback, "conflicting", or nothing.
+    // What the single headline shows: the fold's call, a `-` presence, an explicit `absent`, "conflicting", or nothing.
     headline(): ClinvarHeadline {
-      return resolveClinvarHeadline(this.records, this.assayLevelDigest)
+      return resolveClinvarHeadline(this.records, this.assayLevelDigest, this.assayLevel)
     },
-    // The records on sibling alleles behind the headline — enumerateUnderlyingClinvar excludes the measured
-    // allele's own record (the primary), so a lone assayed record gets no popover.
+    // The related-allele records shown as context — enumerateUnderlyingClinvar excludes the measured allele's
+    // own record and its cross-frame duplicates.
     underlyingClinvar(): MeasurementClinvarRecord[] {
       return enumerateUnderlyingClinvar(this.records)
     },
+    // True when the headline is a projected call — the representative is a related allele, and the context
+    // records below are the siblings it folded over (protein level). Otherwise the context records are just
+    // that: related records that did not drive a direct call (or an `absent` headline).
+    isProjectedHeadline(): boolean {
+      return this.headline.kind === 'call' && this.headline.placement.projected
+    },
+    // The headline record links inline only when it *is* the measured allele's own record — a direct call or
+    // the measured allele's `-` presence. A projected call's links live in the context popover.
+    showHeadlineProvenance(): boolean {
+      const h = this.headline
+      if (h.kind === 'call') return !h.placement.projected
+      if (h.kind === 'presence') return h.record.onAssayed
+      return false
+    },
+    underlyingLabel(): string {
+      const noun = this.isProjectedHeadline ? 'underlying record' : 'related record'
+      return this.underlyingClinvar.length === 1 ? noun : `${noun}s`
+    },
     underlyingClinvarNote(): string {
-      return "ClinVar records for variants with this allele's protein consequence. Open each in ClinVar to view its full classification."
+      return this.isProjectedHeadline
+        ? "ClinVar records for variants with this allele's protein consequence. Open each in ClinVar to view its full classification."
+        : 'Other variants with the same protein consequence that also carry ClinVar records. Open each in ClinVar for its full classification.'
     }
   },
 
diff --git a/src/components/variant/VariantDetailPanel.vue b/src/components/variant/VariantDetailPanel.vue
index b2f108ec..e19f322e 100644
--- a/src/components/variant/VariantDetailPanel.vue
+++ b/src/components/variant/VariantDetailPanel.vue
@@ -64,10 +64,17 @@
           </template>
         </div>
 
-        <VariantGnomadStat :alleles="detail.alleles" :annotations="detail.annotations" :assay-gnomad="gnomad" />
+        <VariantGnomadStat
+          :alleles="detail.alleles"
+          :annotations="detail.annotations"
+          :assay-gnomad="gnomad"
+          :assay-level="detail.assayLevel"
+          :assay-level-digest="detail.assayLevelDigest"
+        />
         <VariantClinvarStat
           :alleles="detail.alleles"
           :annotations="detail.annotations"
+          :assay-level="detail.assayLevel"
           :assay-level-digest="detail.assayLevelDigest"
           :clinvar-version="clinvarVersion"
         />
@@ -212,7 +219,7 @@ export default defineComponent({
         this.detail?.assayLevelDigest ?? null,
         this.clinvarVersion
       )
-      const headline = resolveClinvarHeadline(records, this.detail?.assayLevelDigest ?? null)
+      const headline = resolveClinvarHeadline(records, this.detail?.assayLevelDigest ?? null, this.detail?.assayLevel ?? null)
       return headline.kind !== 'none' || enumerateUnderlyingClinvar(records).length > 0
     },
     // The facts grid only earns its place when a cell resolves; otherwise it's four dashes (clutter), and the
diff --git a/src/components/variant/VariantGnomadStat.vue b/src/components/variant/VariantGnomadStat.vue
index 59a7de33..483f10e5 100644
--- a/src/components/variant/VariantGnomadStat.vue
+++ b/src/components/variant/VariantGnomadStat.vue
@@ -2,15 +2,26 @@
   <div :class="plain ? 'flex h-full flex-col gap-0.5' : 'stat'">
     <!-- Label defaults to the score-set stat label; callers (e.g. the variant screen) inject their own. -->
     <slot name="label"><span v-key-term="'population'" class="stat-label">gnomAD</span></slot>
-    <!-- The measured allele's own frequency (a nucleotide-level assay): the canonical stat, straight up. -->
-    <MvGnomadSummary v-if="assayGnomad" :gnomad="assayGnomad" />
-    <!-- No gnomAD on the measured allele itself, but sibling variants carry frequencies (protein level assay). 
-         Enumerate them: a max-AF headline + a popover of full allele-level frequencies. -->
-    <template v-else-if="underlyingGnomad.length">
-      <span class="stat-value font-semibold">Up to AF {{ formatFrequency(underlyingGnomadMaxAf) }}</span>
+    <!-- The subject allele's own frequency: the canonical statistic. -->
+    <MvGnomadSummary v-if="headlineState === 'direct'" :gnomad="assayGnomad!" />
+    <!-- No frequency on the subject itself, but its encoding variants carry frequencies (protein level assay):
+         enumerate them as a max-AF headline + a popover of full allele-level frequencies. -->
+    <span v-else-if="headlineState === 'enumerated'" class="stat-value font-semibold"
+      >Up to AF {{ formatFrequency(underlyingGnomadMaxAf) }}</span
+    >
+    <!-- Nucleotide subject with no frequency of its own but related variants carry frequencies: be explicit 
+     rather than borrow related variants' frequencies. Related frequencies, if any, show below as context. -->
+    <span v-else-if="headlineState === 'absent'" class="stat-value text-sm italic text-text-muted">
+      No gnomAD record for this variant
+    </span>
+    <span v-else class="stat-value">—</span>
+
+    <!-- Related-allele frequencies as context: the encoding variants behind an enumerated headline, or
+         other same-consequence variants' frequencies beside a direct/absent headline. -->
+    <template v-if="underlyingGnomad.length">
       <button class="mt-auto text-left text-xs text-link hover:underline" type="button" @click="toggleGnomadPopover">
         {{ underlyingGnomad.length }}
-        {{ underlyingGnomad.length === 1 ? 'underlying frequency' : 'underlying frequencies' }}
+        {{ underlyingLabel }}
       </button>
       <Popover ref="gnomadPopoverRef">
         <div class="flex max-w-xs flex-col gap-2">
@@ -26,7 +37,6 @@
         </div>
       </Popover>
     </template>
-    <span v-else class="stat-value">—</span>
   </div>
 </template>
 
@@ -35,18 +45,23 @@ import {defineComponent, type PropType} from 'vue'
 import Popover from 'primevue/popover'
 
 import MvGnomadSummary from '@/components/variant/MvGnomadSummary.vue'
+import {type SubjectDigest, toSubjectDigestSet} from '@/lib/annotation-subject'
 import {collectGnomadFrequencies, formatFrequency, type UnderlyingGnomad} from '@/lib/gnomad'
 import type {components} from '@/schema/openapi'
 
 type GnomadAnnotation = components['schemas']['GnomadAnnotation']
 type AlleleAnnotations = components['schemas']['AlleleAnnotations']
 type AlleleIdentity = components['schemas']['AlleleIdentity']
+type SequenceLevel = components['schemas']['SequenceLevel']
 
 /**
- * The score-set variant panel's gnomAD stat cell. Shows the measured allele's own frequency when it has one;
- * for a protein-level assay (where gnomAD annotates the *genomic* encoding variants, not the protein allele)
- * it enumerates the codon siblings' distinct frequencies behind a popover along with a note that it isn't
- * established which underlies the measurement.
+ * The gnomAD stat cell. Placement rules mirror {@link VariantClinvarStat}:
+ *  - the subject allele's own frequency wins as the headline, with its link;
+ *  - at *protein* level, a subject with no frequency of its own enumerates its encoding variants' distinct
+ *    frequencies (max-AF headline + popover), noting it isn't established which underlies the measurement;
+ *  - at *nucleotide* level, a subject with no frequency stays explicit ('No gnomAD record for this variant') —
+ *    we don't borrow a related variant's frequency — and any related frequencies show below as context.
+ * The subject is the measured allele on the score-set panel, or the page's own allele on the variant page.
  */
 export default defineComponent({
   name: 'VariantGnomadStat',
@@ -57,29 +72,52 @@ export default defineComponent({
     // Drop the score-set `.stat` chrome (bg/padding) so the cell can be embedded on its own (e.g. the
     // variant screen's evidence panel), where the caller supplies the wrapper and a `#label` slot.
     plain: {type: Boolean, default: false},
-    // The measured allele's own gnomAD annotation, or null (e.g. a protein-level assay).
+    // The subject allele's own gnomAD annotation, or null (e.g. a protein-level assay).
     assayGnomad: {type: Object as PropType<GnomadAnnotation | null>, default: null},
     // Digest-keyed annotations for the whole record. Source for the encoding-variant enumeration.
     annotations: {type: Object as PropType<Record<string, AlleleAnnotations>>, default: () => ({})},
     // Digest-keyed allele identities. Supplies each underlying frequency's HGVS label.
-    alleles: {type: Object as PropType<Record<string, AlleleIdentity>>, default: () => ({})}
+    alleles: {type: Object as PropType<Record<string, AlleleIdentity>>, default: () => ({})},
+    // The subject allele's digest(s) — excluded (with its c↔g twin) from the related-frequency enumeration,
+    // so the subject's own frequency never reappears as "related".
+    assayLevelDigest: {type: [String, Array] as PropType<SubjectDigest>, default: null},
+    // The subject allele's sequence level. Gates the enumeration: at nucleotide level a missing frequency
+    // stays explicit ('absent') rather than borrowing related variants'. `null` → enumerate (unknown).
+    assayLevel: {type: String as PropType<SequenceLevel | null>, default: null}
   },
 
   computed: {
     underlyingGnomad(): UnderlyingGnomad[] {
-      return collectGnomadFrequencies(this.annotations, this.alleles)
+      return collectGnomadFrequencies(this.annotations, this.alleles, toSubjectDigestSet(this.assayLevelDigest))
     },
-    // Sorted highest-first, so the leading entry is the max. This becomes the headline stat in the cell,
-    // with the rest enumerated in the popover.
+    // Only enumerate related frequencies as a headline at protein level (or unknown); at nucleotide level a
+    // missing direct frequency is final — mirrors the ClinVar projection gate.
+    canEnumerate(): boolean {
+      return this.assayLevel !== 'cdna' && this.assayLevel !== 'genomic'
+    },
+    // The headline: the subject's own frequency, an enumerated max-AF (protein), an explicit absence
+    // (nucleotide), or nothing.
+    headlineState(): 'direct' | 'enumerated' | 'absent' | 'none' {
+      if (this.assayGnomad) return 'direct'
+      if (this.canEnumerate && this.underlyingGnomad.length) return 'enumerated'
+      if (this.underlyingGnomad.length) return 'absent'
+      return 'none'
+    },
+    // Sorted highest-first, so the leading entry is the max — the enumerated headline stat.
     underlyingGnomadMaxAf(): number | null {
       return this.underlyingGnomad[0]?.gnomad.alleleFrequency ?? null
     },
-    // Nucleotide variants that *could* encode the measured protein change; only those present in gnomAD
-    // are shown, and it's not established which (if any) actually underly the measurement.
+    underlyingLabel(): string {
+      const kind = this.headlineState === 'enumerated' ? 'underlying' : 'related'
+      return `${kind} ${this.underlyingGnomad.length === 1 ? 'frequency' : 'frequencies'}`
+    },
     underlyingGnomadNote(): string {
-      return this.underlyingGnomad.length === 1
-        ? 'The frequency of any variants in gnomAD which can encode this protein change. This assay does not establish which one underlies the measurement.'
-        : 'Frequencies of any variants in gnomAD which can encode this protein change. This assay does not establish which of them underlie the measurement.'
+      if (this.headlineState === 'enumerated') {
+        return this.underlyingGnomad.length === 1
+          ? 'The frequency of any variants in gnomAD which can encode this protein change. This assay does not establish which one underlies the measurement.'
+          : 'Frequencies of any variants in gnomAD which can encode this protein change. This assay does not establish which of them underlie the measurement.'
+      }
+      return 'Other variants with the same protein consequence that also have gnomAD frequencies.'
     }
   },
 
diff --git a/src/composables/use-clinvar-controls.ts b/src/composables/use-clinvar-controls.ts
index 8b868e02..b08a6942 100644
--- a/src/composables/use-clinvar-controls.ts
+++ b/src/composables/use-clinvar-controls.ts
@@ -148,7 +148,7 @@ export function useClinvarControls(
     let usableAny = false
     for (const variant of list) {
       const links = linksByUrn.get(variant.variantUrn)
-      const placement = links ? reduceControlPlacement(links, variant.assayLevelDigest) : null
+      const placement = links ? reduceControlPlacement(links, variant.assayLevelDigest, variant.assayLevel) : null
       variant.control = placement
       // "Has clinical significance" gates the clinical view — a hard-discordant variant carries ClinVar
       // data but is not a usable control, so it doesn't count toward showing the view.
diff --git a/src/lib/annotation-subject.ts b/src/lib/annotation-subject.ts
new file mode 100644
index 00000000..a9791554
--- /dev/null
+++ b/src/lib/annotation-subject.ts
@@ -0,0 +1,14 @@
+/**
+ * The subject allele of an annotation surface (ClinVar, gnomAD), as its digest(s).
+ *
+ * Usually a single digest — the measured allele. But a variant page's subject is one physical allele stored
+ * as two digests: its coding and genomic representations (a c↔g projection pair). External databases attach
+ * to only one of them (no fixed level→source mapping), so both must count as "the subject's own" or a record
+ * on the twin reads as a related allele.
+ */
+export type SubjectDigest = string | string[] | null | undefined
+
+/** Normalize a {@link SubjectDigest} to a set for membership tests. */
+export function toSubjectDigestSet(subject: SubjectDigest): Set<string> {
+  return new Set(subject == null ? [] : Array.isArray(subject) ? subject : [subject])
+}
diff --git a/src/lib/clinvar-control-placement.test.ts b/src/lib/clinvar-control-placement.test.ts
index 7b665974..8e97ade8 100644
--- a/src/lib/clinvar-control-placement.test.ts
+++ b/src/lib/clinvar-control-placement.test.ts
@@ -312,11 +312,71 @@ function rec(significance: string, digest: string, reviewStatus: string = ONE_ST
   }
 }
 
+describe('reduceControlPlacement — assay-level gating of projection', () => {
+  test('protein level projects a sibling call when the measured allele has none', () => {
+    const p = reduceControlPlacement([link(P, SIB)], ASSAY, 'protein')
+    expect(p?.projected).toBe(true)
+    expect(usable(p!).clinicalSignificance).toBe(P)
+  })
+
+  test('nucleotide level does not project — no direct record → null', () => {
+    expect(reduceControlPlacement([link(P, SIB)], ASSAY, 'cdna')).toBeNull()
+    expect(reduceControlPlacement([link(P, SIB)], ASSAY, 'genomic')).toBeNull()
+  })
+
+  test('nucleotide level still honors the measured allele`s own direct call', () => {
+    const p = reduceControlPlacement([link(P, ASSAY), link(VUS, SIB)], ASSAY, 'cdna')
+    expect(usable(p!).clinicalSignificance).toBe(P)
+    expect(usable(p!).projected).toBe(false)
+  })
+
+  test('unknown level preserves the prior behavior — projects', () => {
+    expect(reduceControlPlacement([link(P, SIB)], ASSAY)?.projected).toBe(true)
+  })
+
+  test('a subject digest *set* (c↔g twin) counts a record on either representation as direct', () => {
+    // The physical allele is stored as ASSAY (coding) + SIB (its genomic twin); ClinVar linked the record to
+    // the twin. Anchoring on both digests keeps it a direct call, not a projection off a "sibling".
+    const p = reduceControlPlacement([link(P, SIB)], [ASSAY, SIB], 'cdna')
+    expect(usable(p!).clinicalSignificance).toBe(P)
+    expect(usable(p!).projected).toBe(false)
+  })
+})
+
 describe('resolveClinvarHeadline — the display decision', () => {
   test('no records → none', () => {
     expect(resolveClinvarHeadline([], ASSAY)).toEqual({kind: 'none'})
   })
 
+  test('nucleotide level, no direct record but classified siblings → kind "absent"', () => {
+    expect(resolveClinvarHeadline([rec(P, SIB)], ASSAY, 'cdna')).toEqual({kind: 'absent'})
+    expect(resolveClinvarHeadline([rec(P, SIB), rec(VUS, SIB2)], ASSAY, 'genomic')).toEqual({kind: 'absent'})
+  })
+
+  test('protein level, no direct record → projects to kind "call"', () => {
+    expect(resolveClinvarHeadline([rec(P, SIB)], ASSAY, 'protein').kind).toBe('call')
+  })
+
+  test('measured allele has no record, only germline-less related records → absent (not a sibling presence)', () => {
+    // The measured variant has no record of its own; a sibling`s `-` must not be shown as this variant`s state.
+    expect(resolveClinvarHeadline([rec('-', SIB)], ASSAY, 'cdna')).toEqual({kind: 'absent'})
+    expect(resolveClinvarHeadline([rec('-', SIB)], ASSAY, 'protein')).toEqual({kind: 'absent'})
+  })
+
+  test('nucleotide level, measured allele carries a `-` record → presence, not absent', () => {
+    const headline = resolveClinvarHeadline([rec('-', ASSAY), rec(P, SIB)], ASSAY, 'cdna')
+    expect(headline.kind).toBe('presence')
+    if (headline.kind !== 'presence') throw new Error('expected presence')
+    expect(headline.record.onAssayed).toBe(true)
+  })
+
+  test('nucleotide level, measured allele has its own call → kind "call" (direct, not projected)', () => {
+    const headline = resolveClinvarHeadline([rec(P, ASSAY), rec(VUS, SIB)], ASSAY, 'cdna')
+    expect(headline.kind).toBe('call')
+    if (headline.kind !== 'call') throw new Error('expected a call')
+    expect(headline.placement.projected).toBe(false)
+  })
+
   test('a usable call → kind "call", carrying the representative record and placement', () => {
     const headline = resolveClinvarHeadline([rec(P, ASSAY), rec(VUS, SIB)], ASSAY)
     expect(headline.kind).toBe('call')
diff --git a/src/lib/clinvar-control-placement.ts b/src/lib/clinvar-control-placement.ts
index 6e0cffc6..6e523358 100644
--- a/src/lib/clinvar-control-placement.ts
+++ b/src/lib/clinvar-control-placement.ts
@@ -11,7 +11,6 @@
 
 import {
   BENIGN_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS,
-  clinvarVariantUrl,
   CLINVAR_REVIEW_STATUS_STARS,
   CONFLICTING_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS,
   DEFAULT_CLNREVSTAT_FIELD,
@@ -20,9 +19,11 @@ import {
   type MeasurementClinvarRecord,
   PATHOGENIC_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS
 } from '@/lib/clinvar-controls'
+import {type SubjectDigest, toSubjectDigestSet} from '@/lib/annotation-subject'
 import type {components} from '@/schema/openapi'
 
 type ClinvarAnnotation = components['schemas']['ClinvarAnnotation']
+type SequenceLevel = components['schemas']['SequenceLevel']
 
 /**
  * How the ClinVar calls reaching a measurement disagree, ordered by placement difficulty.
@@ -100,10 +101,16 @@ const starsOf = (reviewStatus: string) => CLINVAR_REVIEW_STATUS_STARS[reviewStat
 /**
  * Reduce the ClinVar controls reaching one variant to a single {@link ClinvarControlPlacement}.
  *
- * **Precedence:** if any control annotates the variant's own assayed-level allele
- * (`alleleDigest === assayLevelDigest`), those controls are the winning set and the projection siblings
- * are ignored — a direct call on the assayed entity is not diluted by the fan-out. Otherwise the
- * siblings are the winning set. Over the winning set:
+ * **Precedence:** if any control annotates the variant's own subject allele (`alleleDigest` ∈ the subject
+ * digest set — the measured/page allele, including its c↔g twin), those controls are the winning set and the
+ * projection siblings are ignored — a direct call on the assayed entity is not diluted by the fan-out.
+ *
+ * **Projection is level-gated.** Falling through to sibling controls is only legitimate at the *protein*
+ * assay level, where ClinVar (a nucleotide resource) cannot annotate the measured allele itself, so the
+ * encoding siblings are the only available signal. At nucleotide level (`cdna`/`genomic`) the measured
+ * variant *can* carry its own record, so its absence is real information: we do **not** borrow a sibling's
+ * call (which would both overreach and double-count — that sibling is its own scored row). With no direct
+ * record at nucleotide level, this returns `null`. Otherwise the siblings are the winning set. Over it:
  *   - **hard** (both a P/LP and a B/LB call) → `discordance: 'hard'`, not a usable control;
  *   - **soft** (a directional lean + an uncertain record — a VUS or a ClinVar-*Conflicting* call) →
  *     `discordance: 'soft'`, usable — the lean is the representative, but the surface can flag the soft conflict;
@@ -116,7 +123,8 @@ const starsOf = (reviewStatus: string) => CLINVAR_REVIEW_STATUS_STARS[reviewStat
  */
 export function reduceControlPlacement(
   links: ControlLink[],
-  assayLevelDigest: string | null | undefined
+  subject: SubjectDigest,
+  assayLevel?: SequenceLevel | null
 ): ClinvarControlPlacement | null {
   // Drop ClinVar "no classification" placeholders (a literal `-`/empty) up front, so they neither become a
   // call nor — as a `-` on the assayed allele — block fall-through to a real projection sibling.
@@ -125,11 +133,19 @@ export function reduceControlPlacement(
     return null
   }
 
-  const assayedLevel = assayLevelDigest ? classified.filter((link) => link.alleleDigest === assayLevelDigest) : []
-  const winning = assayedLevel.length > 0 ? assayedLevel : classified
-  // Fell through to siblings — but only *claim* projection when the assayed digest is known; an absent
+  const subjectSet = toSubjectDigestSet(subject)
+  const assayedLevel =
+    subjectSet.size > 0 ? classified.filter((link) => link.alleleDigest && subjectSet.has(link.alleleDigest)) : []
+  // Only project at protein level (or when the level is unknown, to avoid silently dropping controls);
+  // at nucleotide level a missing direct record is final.
+  const canProject = assayLevel !== 'cdna' && assayLevel !== 'genomic'
+  const winning = assayedLevel.length > 0 ? assayedLevel : canProject ? classified : []
+  if (winning.length === 0) {
+    return null
+  }
+  // Fell through to siblings — but only *claim* projection when the subject digest is known; an absent
   // digest means unknown provenance, which we don't surface as "related variant" (avoids mislabeling).
-  const projected = Boolean(assayLevelDigest) && assayedLevel.length === 0
+  const projected = subjectSet.size > 0 && assayedLevel.length === 0
 
   // Distinct calls, preserving first-seen order.
   const seen = new Set<string>()
@@ -201,13 +217,18 @@ export type ClinvarCallNote = 'none' | 'concordant' | 'soft-vus' | 'soft-conflic
  * - `conflicting` — hard-discordant winning set; no single call to show.
  * - `call` — the representative usable call (assayed-level or a projection sibling), with a {@link ClinvarCallNote}
  *   qualifying it (concordant aside, or a soft-conflict flag). The lib owns that decision so the template renders it.
- * - `presence` — no usable call, but a ClinVar record exists (a `-` germline-less submission); link out.
+ * - `presence` — no usable call, but a ClinVar record exists on the measurement (a `-` germline-less
+ *   submission); name the state and link out.
+ * - `absent` — a nucleotide-level measurement whose own allele has no ClinVar record, while related alleles
+ *   do: we decline to project (see reduceControlPlacement), so the surface says the record is absent and
+ *   offers the related records as context rather than promoting one to a call.
  * - `none` — nothing reaches the measurement.
  */
 export type ClinvarHeadline =
   | {kind: 'conflicting'; placement: HardDiscordantPlacement}
   | {kind: 'call'; clinvar: ClinvarAnnotation; placement: UsableControlPlacement; note: ClinvarCallNote}
   | {kind: 'presence'; record: MeasurementClinvarRecord}
+  | {kind: 'absent'}
   | {kind: 'none'}
 
 /** Derive the {@link ClinvarCallNote} for a usable placement — the lib's single display decision for a call. */
@@ -219,21 +240,21 @@ function resolveCallNote(placement: UsableControlPlacement): ClinvarCallNote {
   return 'none'
 }
 
-/** Pick the germline-less record to represent a measurement when the fold yields no call: the measured
- *  allele's own record wins, then any linkable one, else first-seen. */
-function selectPresence(records: MeasurementClinvarRecord[]): MeasurementClinvarRecord | null {
-  if (records.length === 0) return null
-  return records.find((r) => r.onAssayed) ?? records.find((r) => Boolean(clinvarVariantUrl(r.clinvar))) ?? records[0]
-}
-
 /**
- * Resolve what a one-headline ClinVar surface shows, over a resolved walk. Runs the fold and, when it yields
- * no usable call, falls back to a `-` presence record — the single precedence decision every such surface
- * reads, so the stat cell and variant screen agree.
+ * Resolve what a one-headline ClinVar surface shows, over a resolved walk. Runs the level-gated fold, then
+ * falls back through a fixed precedence so every such surface (stat cell, variant screen) agrees:
+ *   1. a usable/hard placement → `call`/`conflicting`;
+ *   2. the measured allele's *own* record (a `-`, since a classification would have folded above) → `presence`,
+ *      naming the germline-less state and linking out;
+ *   3. no record on the measured allele, but records reach related alleles (a nucleotide measurement we
+ *      declined to project) → `absent` — the measured variant has no ClinVar record; the related records are
+ *      offered as context, never promoted to a call or a germline-less state on this variant;
+ *   4. nothing reaches the measurement → `none`.
  */
 export function resolveClinvarHeadline(
   records: MeasurementClinvarRecord[],
-  assayLevelDigest: string | null | undefined
+  subject: SubjectDigest,
+  assayLevel?: SequenceLevel | null
 ): ClinvarHeadline {
   const placement = reduceControlPlacement(
     records.map((r) => ({
@@ -241,7 +262,8 @@ export function resolveClinvarHeadline(
       reviewStatus: r.clinvar.clinicalReviewStatus,
       alleleDigest: r.digest
     })),
-    assayLevelDigest
+    subject,
+    assayLevel
   )
   if (placement?.discordance === 'hard') return {kind: 'conflicting', placement}
   if (placement) {
@@ -250,7 +272,11 @@ export function resolveClinvarHeadline(
       return {kind: 'call', clinvar: representative.clinvar, placement, note: resolveCallNote(placement)}
     }
   }
-  // No usable call — a real classification would have folded above, so any surviving record is a `-`.
-  const presence = selectPresence(records)
-  return presence ? {kind: 'presence', record: presence} : {kind: 'none'}
+  // The subject allele's own record (if any) is germline-less — a classification would have folded above.
+  // `onAssayed` was tagged against this same subject, so it covers the c↔g twin too.
+  const assayedRecord = records.find((r) => r.onAssayed)
+  if (assayedRecord) return {kind: 'presence', record: assayedRecord}
+  // No record on the measured allele. Any records that reach it are on *related* alleles — we won't promote
+  // one to a call or a germline-less state on this variant; say the record is absent and offer them as context.
+  return records.length > 0 ? {kind: 'absent'} : {kind: 'none'}
 }
diff --git a/src/lib/clinvar-controls.test.ts b/src/lib/clinvar-controls.test.ts
index 50912e84..2de332dc 100644
--- a/src/lib/clinvar-controls.test.ts
+++ b/src/lib/clinvar-controls.test.ts
@@ -113,12 +113,31 @@ describe('enumerateUnderlyingClinvar — the popover projection', () => {
     expect(ids(enumerate(annotations, {}))).toEqual(['b', 'a'])
   })
 
-  test('excludes the measured allele`s own record — the primary is not "underlying"', () => {
+  test('keeps a distinct related sibling as context beside the measured allele`s own call', () => {
     const annotations = {
       assayed: {clinvar: [clinvar({clinvarAlleleId: 'assayed', clinicalSignificance: 'Pathogenic'})]},
       sib: {clinvar: [clinvar({clinvarAlleleId: 'sib', clinicalSignificance: 'Uncertain significance'})]}
     }
-    // Only the sibling is underlying; a lone assayed record would leave this empty (→ no popover).
+    // The measured allele's own call is the headline; the genuinely distinct sibling is offered as context.
+    expect(ids(enumerateUnderlyingClinvar(resolveClinvarRecords(annotations, {}, 'assayed')))).toEqual(['sib'])
+  })
+
+  test('the same record under a non-assayed reference frame is not "underlying" the assayed call', () => {
+    const annotations = {
+      // One ClinVar record (variation V1), annotated on the measured protein allele `p` and again on its
+      // genomic frame `g`. `g` is not a distinct sibling — it's the same record you're already looking at.
+      p: {clinvar: [clinvar({clinvarAlleleId: 'x', clinvarVariationId: 'V1'})]},
+      g: {clinvar: [clinvar({clinvarAlleleId: 'x', clinvarVariationId: 'V1'})]}
+    }
+    expect(ids(enumerateUnderlyingClinvar(resolveClinvarRecords(annotations, {}, 'p')))).toEqual([])
+  })
+
+  test('an unclassified (`-`) assayed record does not win — siblings still surface', () => {
+    const annotations = {
+      assayed: {clinvar: [clinvar({clinvarAlleleId: 'assayed', clinicalSignificance: '-'})]},
+      sib: {clinvar: [clinvar({clinvarAlleleId: 'sib', clinicalSignificance: 'Uncertain significance'})]}
+    }
+    // A `-` on the measured allele carries no call, so the fold projects from the sibling — which is underlying.
     expect(ids(enumerateUnderlyingClinvar(resolveClinvarRecords(annotations, {}, 'assayed')))).toEqual(['sib'])
   })
 
diff --git a/src/lib/clinvar-controls.ts b/src/lib/clinvar-controls.ts
index c68651a1..e61b3c98 100644
--- a/src/lib/clinvar-controls.ts
+++ b/src/lib/clinvar-controls.ts
@@ -1,4 +1,5 @@
 import type {KeySection} from '@/composables/use-key-drawer'
+import {type SubjectDigest, toSubjectDigestSet} from '@/lib/annotation-subject'
 import {hgvsLabelRank} from '@/lib/formats'
 import type {components} from '@/schema/openapi'
 
@@ -239,22 +240,24 @@ export function clinvarRecordId(clinvar: {clinvarVariationId?: string | null; cl
  * Resolve the ClinVar records reaching one measurement at `version` — the single walk over the annotations
  * map that the fold, the underlying-record popover, and the `-` headline fallback all project from, so no
  * surface re-walks it. One record per annotated allele digest (unclassified `-` records included, tagged);
- * downstream projections filter/fold as they need.
+ * downstream projections filter/fold as they need. `subject` is the measured/page allele's digest(s);
+ * a record on any of them is the subject's own (`onAssayed`).
  */
 export function resolveClinvarRecords(
   annotations: Record<string, {clinvar?: ClinvarAnnotation[] | null}> | null | undefined,
   alleles: Record<string, {hgvs?: string | null}> | null | undefined,
-  assayLevelDigest: string | null | undefined,
+  subject: SubjectDigest,
   version?: string | null
 ): MeasurementClinvarRecord[] {
   if (!annotations) return []
+  const subjectSet = toSubjectDigestSet(subject)
   const records: MeasurementClinvarRecord[] = []
   for (const [digest, ann] of Object.entries(annotations)) {
     const clinvar = selectClinvar(ann.clinvar, version)
     if (!clinvar) continue
     records.push({
       digest,
-      onAssayed: digest === assayLevelDigest,
+      onAssayed: subjectSet.has(digest),
       hgvs: alleles?.[digest]?.hgvs ?? null,
       classified: isClassifiedSignificance(clinvar.clinicalSignificance),
       clinvar
@@ -269,15 +272,24 @@ export function resolveClinvarRecords(
  * primary, already shown as the headline, not "underlying" — so a lone assayed record yields no popover, and
  * a protein-level allele's projected headline still lists the nucleotide sibling it was drawn from.
  *
+ * These are the *related-allele* records offered as context — beside a direct call (transparency: records
+ * that did not drive it), beneath a projected call (the siblings it folded over), or under an `absent`
+ * nucleotide headline. Excludes the measured allele's own record (`onAssayed`) **and its cross-frame
+ * duplicates**: the same ClinVar record seen under another reference-frame digest is the very record already
+ * shown, not a distinct sibling, so it must not reappear here.
+ *
  * Germline-less `-` submissions are kept (a record that exists is worth linking to; only the control fold
  * drops `-`). Dedupes by ClinVar record id across the DNA/protein frames that share one record (preferring a
  * coding HGVS for the label), and sorts directional calls (P/LP, B/LB) ahead of VUS and `-`, then by stars.
  */
 export function enumerateUnderlyingClinvar(records: MeasurementClinvarRecord[]): MeasurementClinvarRecord[] {
+  // The measured allele's own record id(s): exclude these and any other frame carrying the same record.
+  const assayedIds = new Set(records.filter((r) => r.onAssayed).map((r) => clinvarRecordId(r.clinvar)))
   const byRecord = new Map<string, MeasurementClinvarRecord>()
   for (const rec of records) {
     if (rec.onAssayed) continue
     const key = clinvarRecordId(rec.clinvar)
+    if (assayedIds.has(key)) continue
     const existing = byRecord.get(key)
     if (!existing) byRecord.set(key, {...rec})
     else if (hgvsLabelRank(rec.hgvs) > hgvsLabelRank(existing.hgvs)) existing.hgvs = rec.hgvs
diff --git a/src/lib/gnomad.test.ts b/src/lib/gnomad.test.ts
index 00c0537c..6e8fa47d 100644
--- a/src/lib/gnomad.test.ts
+++ b/src/lib/gnomad.test.ts
@@ -93,6 +93,35 @@ describe('collectGnomadFrequencies — enumeration of encoding-variant frequenci
       expect(collectGnomadFrequencies(annotations, {'g-digest': {hgvs: 'g.100A>G'}})[0]?.hgvs).toBe('g.100A>G')
     })
   })
+
+  describe('subject exclusion — the subject`s own frequency is the headline, not a "related" one', () => {
+    test('excludes the subject digest', () => {
+      const annotations = {
+        subject: {gnomad: gnomad({dbIdentifier: 'S'})},
+        sib: {gnomad: gnomad({dbIdentifier: 'B'})}
+      }
+      expect(ids(collectGnomadFrequencies(annotations, {}, ['subject']))).toEqual(['B'])
+    })
+
+    test('excludes the subject`s cross-frame twin (same gnomAD id on a non-subject digest)', () => {
+      // The subject (coding) has no gnomAD of its own; its genomic twin carries the record. Anchoring on both
+      // subject digests drops the twin so the subject`s own frequency is never listed as related.
+      const annotations = {
+        'subject-c': {gnomad: null},
+        'subject-g': {gnomad: gnomad({dbIdentifier: 'S'})},
+        sib: {gnomad: gnomad({dbIdentifier: 'B'})}
+      }
+      expect(ids(collectGnomadFrequencies(annotations, {}, ['subject-c', 'subject-g']))).toEqual(['B'])
+    })
+
+    test('no subject given → collects everything (backward compatible)', () => {
+      const annotations = {
+        subject: {gnomad: gnomad({dbIdentifier: 'S'})},
+        sib: {gnomad: gnomad({dbIdentifier: 'B', alleleFrequency: 0.002})}
+      }
+      expect(ids(collectGnomadFrequencies(annotations, {}))).toEqual(['B', 'S'])
+    })
+  })
 })
 
 describe('formatFrequency', () => {
diff --git a/src/lib/gnomad.ts b/src/lib/gnomad.ts
index 6ce51204..794521e1 100644
--- a/src/lib/gnomad.ts
+++ b/src/lib/gnomad.ts
@@ -44,21 +44,36 @@ export interface UnderlyingGnomad {
 }
 
 /**
- * Collect the distinct gnomAD measurements across a variant record's alleles.
+ * Collect the distinct gnomAD measurements across a variant record's alleles — the *related* frequencies
+ * shown as context.
  *
  * A protein change is encoded by several genomic variants, each with its own gnomAD frequency. Enumerate
  * this set of distinct frequencies, deduplicating by gnomAD variant id and preferring a coding HGVS for
  * the label. Sort by descending allele frequency.
+ *
+ * `subjectDigests` names the subject allele (the measured/page allele, including its c↔g twin); its own
+ * frequency is the headline, so it — and any other frame carrying the same gnomAD record — is excluded here,
+ * mirroring the ClinVar underlying-record enumeration.
  */
 export function collectGnomadFrequencies(
   annotations: Record<string, {gnomad?: GnomadAnnotation | null}> | null | undefined,
-  alleles: Record<string, {hgvs?: string | null}> | null | undefined
+  alleles: Record<string, {hgvs?: string | null}> | null | undefined,
+  subjectDigests?: Iterable<string>
 ): UnderlyingGnomad[] {
   if (!annotations) return []
+  const subjectSet = new Set(subjectDigests ?? [])
+  // The subject's own gnomAD id(s): exclude these so the subject's frequency (or its cross-frame twin) never
+  // reappears as a "related" one.
+  const subjectIds = new Set<string>()
+  for (const digest of subjectSet) {
+    const id = annotations[digest]?.gnomad?.dbIdentifier
+    if (id) subjectIds.add(id)
+  }
   const byVariant = new Map<string, UnderlyingGnomad>()
   for (const [digest, ann] of Object.entries(annotations)) {
     const gnomad = ann.gnomad
     if (!gnomad) continue
+    if (subjectSet.has(digest) || subjectIds.has(gnomad.dbIdentifier)) continue
 
     const hgvs = alleles?.[digest]?.hgvs ?? null
     const existing = byVariant.get(gnomad.dbIdentifier)

From 1a2c7095ae8b68769c1af1f55d455a804dc60ced Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Wed, 22 Jul 2026 23:44:03 -0700
Subject: [PATCH 64/84] feat(score-set-downloads): stream variant-details
 export, add annotation columns

Replace the retired /mapped-variants JSON download with the
substrate-faithful streaming NDJSON /variant-details export, and
extend the custom CSV download with the new annotation namespaces
(gnomAD, VEP, ClinGen, ClinVar).

- remove downloadMappedVariants; the Variant Details button now
  streams GET /score-sets/{urn}/variant-details via streamNdjson,
  driving a progress bar off the server's X-Total-Count
- fix progress overshooting 100%: count '\n' characters per chunk
  instead of split() segments, which overcounted by one per chunk
  and double-counted lines split across fetch chunk boundaries;
  also clamp the computed percentage to 100
- fix the progress bar rendering under both the Variant Details and
  Annotated Variants buttons at once; track which button's stream
  is active (streamTarget) and gate each bar on its own target
  instead of the shared in-progress flag
- add gnomAD/VEP/ClinGen/ClinVar options to the custom CSV dialog,
  wiring ScoreSetView's resolved clinvarVersion through so the
  versioned ClinVar column can be offered
- update the downloading and API quickstart docs to describe the
  Variant Details export in place of the old mapped-variants JSON
---
 docs/content/finding-data/downloading.md      |   8 +-
 docs/content/finding-data/index.md            |   2 +-
 .../programmatic-access/api-quickstart.md     |  19 ++--
 src/api/mavedb/score-sets.ts                  |   5 -
 .../score-set/ScoreSetDownloads.vue           |  46 +++++---
 src/components/screens/ScoreSetView.vue       |   1 +
 src/composables/use-score-set-downloads.ts    | 106 +++++++++++++-----
 7 files changed, 123 insertions(+), 64 deletions(-)

diff --git a/docs/content/finding-data/downloading.md b/docs/content/finding-data/downloading.md
index 8ecea328..412d9a69 100644
--- a/docs/content/finding-data/downloading.md
+++ b/docs/content/finding-data/downloading.md
@@ -8,21 +8,21 @@ Each [score set](../getting-started/key-concepts.md#score-sets) page in MaveDB i
 
 <figure markdown="span">
   ![Download buttons on a MaveDB score set page](../images/download_buttons.png)
-  <figcaption>Download options available on a score set page, including score/count CSV, mapped variants JSON, and annotated variant exports.</figcaption>
+  <figcaption>Download options available on a score set page, including score/count CSV, variant details, and annotated variant exports.</figcaption>
 </figure>
 
 ### Score and count data
 
 MaveDB allows users to download variant effect score data along with associated count data in **CSV** (Comma-Separated Values) format.
 
-The downloaded file contains the same data that was uploaded by the submitter, with an additional column for variant [URNs](../reference/accession-numbers.md) that uniquely identify each variant in MaveDB. Users may also choose to include other MaveDB-generated columns in this output, such as mapped variant HGVS strings and VRS identifiers, if available.
+The downloaded file contains the same data that was uploaded by the submitter, with an additional column for variant [URNs](../reference/accession-numbers.md) that uniquely identify each variant in MaveDB. Using the **Custom Data** option, users may also choose to include other MaveDB-generated columns in this output, such as mapped variant HGVS strings and VRS identifiers, and — where available — annotation columns for gnomAD allele frequency, Ensembl VEP consequence, ClinGen allele IDs, and ClinVar clinical significance.
 
 !!! warning
     Score and count columns are non-prescriptive and may vary between datasets. Columns may mean different things between datasets, so users should refer to the dataset methods section for details on the specific columns included in each download.
 
-### Mapped variants (VRS JSON)
+### Variant details (VRS JSON)
 
-MaveDB stores [mapped variants](../reference/variant-mapping.md) using the [GA4GH VRS](https://vrs.ga4gh.org/) standard for representing genetic variants. For datasets that have been mapped, users may download a JSON file containing all mapped variants associated with the score set. This provides a structured representation of each variant including genomic coordinates, alleles, and reference sequences.
+MaveDB represents [mapped variants](../reference/variant-mapping.md) using the [GA4GH VRS](https://vrs.ga4gh.org/) standard. For datasets that have been mapped, the **Variant Details** button downloads a [newline-delimited JSON](https://jsonlines.org/) (NDJSON) file — one record per mapped variant, the bulk counterpart of a single variant's detail page. Each record carries the assayed-level (pre-mapped) and measured (post-mapped) VRS objects, the full [GA4GH Cat-VRS](https://vrs.ga4gh.org/) categorical variant (the variant's equivalence class of related alleles), and its gnomAD, Ensembl VEP, and ClinVar annotations.
 
 ### Annotated variants (VA-Spec)
 
diff --git a/docs/content/finding-data/index.md b/docs/content/finding-data/index.md
index c3aa642f..74bc0843 100644
--- a/docs/content/finding-data/index.md
+++ b/docs/content/finding-data/index.md
@@ -6,7 +6,7 @@ MaveDB provides several ways to discover, explore, and download MAVE datasets. W
 
 - **[Searching Datasets](searching.md)** -- Find MAVE datasets by gene name, target organism, publication, or keywords using the MaveDB search interface.
 - **[Visualizations](visualizations.md)** -- Explore variant effect data through interactive histograms, heatmaps, and 3D protein structure views on score set pages.
-- **[Downloading Data](downloading.md)** -- Download variant scores, counts, mapped variants, and annotated data in CSV, VRS JSON, and VA-Spec formats, or access a bulk archive via Zenodo.
+- **[Downloading Data](downloading.md)** -- Download variant scores, counts, variant details, and annotated data in CSV, VRS JSON, and VA-Spec formats, or access a bulk archive via Zenodo.
 - **[External Integrations](external-integrations.md)** -- Learn how MaveDB connects with ClinGen, ClinVar, gnomAD, Ensembl VEP, DECIPHER, and other resources.
 
 Looking for a specific variant? Use the [MaveMD variant search](../mavemd/variant-search.md) to look up individual variants by HGVS, ClinVar ID, dbSNP RSID, or ClinGen Allele ID.
diff --git a/docs/content/programmatic-access/api-quickstart.md b/docs/content/programmatic-access/api-quickstart.md
index 7972dfb2..e857bb4e 100644
--- a/docs/content/programmatic-access/api-quickstart.md
+++ b/docs/content/programmatic-access/api-quickstart.md
@@ -164,21 +164,22 @@ The search endpoint uses POST with a JSON body:
       -d '{"text": "BRCA1"}'
     ```
 
-### Download mapped variants (VRS format)
+### Download variant details (VRS format)
 
-For datasets with human targets, [mapped variants](../reference/variant-mapping.md) are available in [GA4GH VRS](https://vrs.ga4gh.org/) format:
+For datasets with human targets, the mapped [variant details](../reference/variant-mapping.md) are available in [GA4GH VRS](https://vrs.ga4gh.org/) format. The `/variant-details` endpoint is the bulk pair of `GET /variants/{urn}`: it streams [newline-delimited JSON](https://jsonlines.org/) (NDJSON), one `VariantDetail` per mapped variant, each carrying the flat `preMapped`/`postMapped` VRS pair, the full [GA4GH Cat-VRS](https://vrs.ga4gh.org/) categorical variant (its equivalence class of related alleles), and the VEP, gnomAD, and ClinVar annotations:
 
 === "Python"
 
     ```python
+    import json
     import requests
 
     response = requests.get(
-        "https://api.mavedb.org/api/v1/score-sets/urn:mavedb:00000003-a-1/mapped-variants"
+        "https://api.mavedb.org/api/v1/score-sets/urn:mavedb:00000003-a-1/variant-details"
     )
 
-    with open("mapped_variants.json", "w") as f:
-        f.write(response.text)
+    # NDJSON: one VariantDetail object per line.
+    variants = [json.loads(line) for line in response.text.splitlines() if line]
     ```
 
 === "R"
@@ -186,15 +187,15 @@ For datasets with human targets, [mapped variants](../reference/variant-mapping.
     ```r
     library(httr)
 
-    response <- GET("https://api.mavedb.org/api/v1/score-sets/urn:mavedb:00000003-a-1/mapped-variants")
-    writeLines(content(response, as = "text"), "mapped_variants.json")
+    response <- GET("https://api.mavedb.org/api/v1/score-sets/urn:mavedb:00000003-a-1/variant-details")
+    writeLines(content(response, as = "text"), "variant_details.ndjson")
     ```
 
 === "curl"
 
     ```bash
-    curl -o mapped_variants.json \
-      https://api.mavedb.org/api/v1/score-sets/urn:mavedb:00000003-a-1/mapped-variants
+    curl -o variant_details.ndjson \
+      https://api.mavedb.org/api/v1/score-sets/urn:mavedb:00000003-a-1/variant-details
     ```
 
 ### List score sets in an experiment
diff --git a/src/api/mavedb/score-sets.ts b/src/api/mavedb/score-sets.ts
index 9a7f0b78..8c590f44 100644
--- a/src/api/mavedb/score-sets.ts
+++ b/src/api/mavedb/score-sets.ts
@@ -156,11 +156,6 @@ export async function getScoreSetCountsPreview(urn: string, limit?: number): Pro
   return response.data
 }
 
-export async function downloadMappedVariants(urn: string) {
-  const response = await axios.get(`${config.apiBaseUrl}/score-sets/${encodeURIComponent(urn)}/mapped-variants`)
-  return response.data
-}
-
 export async function getRecentlyPublishedScoreSets(
   signal?: AbortSignal
 ): Promise<components['schemas']['ScoreSet'][]> {
diff --git a/src/components/score-set/ScoreSetDownloads.vue b/src/components/score-set/ScoreSetDownloads.vue
index 79b98bf9..2550058c 100644
--- a/src/components/score-set/ScoreSetDownloads.vue
+++ b/src/components/score-set/ScoreSetDownloads.vue
@@ -19,18 +19,24 @@
         size="small"
         @click="downloadMetadata"
       />
-      <PButton
-        icon="pi pi-download"
-        label="Mapped Variants"
-        severity="secondary"
-        size="small"
-        @click="downloadMappedVariantsFile"
-      />
+      <div class="relative inline-block">
+        <PButton
+          :disabled="streamDownloadInProgress"
+          icon="pi pi-download"
+          label="Variant Details"
+          severity="secondary"
+          size="small"
+          @click="streamVariantDetails"
+        />
+        <div v-if="streamTarget === 'variantDetails'" class="absolute inset-x-0 top-full mt-1">
+          <ProgressBar show-value style="height: 1.5em" :value="streamDownloadProgress" />
+        </div>
+      </div>
 
       <div class="relative inline-block">
         <SplitButton
           :button-props="{class: 'p-button-sm p-button-secondary'}"
-          :disabled="annotatedDownloadInProgress"
+          :disabled="streamDownloadInProgress"
           label="Annotated Variants"
           :menu-button-props="{class: 'p-button-sm p-button-secondary'}"
           :model="annotatedVariantDownloadOptions"
@@ -41,8 +47,8 @@
             })
           "
         />
-        <div v-if="annotatedDownloadInProgress" class="absolute inset-x-0 top-full mt-1">
-          <ProgressBar show-value style="height: 1.5em" :value="annotatedDownloadProgress" />
+        <div v-if="streamTarget === 'annotatedVariants'" class="absolute inset-x-0 top-full mt-1">
+          <ProgressBar show-value style="height: 1.5em" :value="streamDownloadProgress" />
         </div>
       </div>
 
@@ -61,7 +67,7 @@
       <div class="mt-1.5 flex flex-wrap gap-2">
         <PButton label="Scores" severity="secondary" size="small" @click="sendToGalaxy('scores')" />
         <PButton v-if="hasCounts" label="Counts" severity="secondary" size="small" @click="sendToGalaxy('counts')" />
-        <PButton label="Mapped Variants" severity="secondary" size="small" @click="sendToGalaxy('mappedVariants')" />
+        <PButton label="Variant Details" severity="secondary" size="small" @click="sendToGalaxy('variantDetails')" />
       </div>
     </div>
 
@@ -113,13 +119,21 @@ export default defineComponent({
     hasPathogenicityCalibrations: {type: Boolean, default: false},
     hasFunctionalImpactCalibrations: {type: Boolean, default: false},
     isMetaDataEmpty: {type: Boolean, default: true},
-    scoreSet: {type: Object as PropType<ScoreSet>, required: true}
+    scoreSet: {type: Object as PropType<ScoreSet>, required: true},
+    // The ClinVar control version the page resolved (histogram controlVersion), MM_YYYY form; enables
+    // the ClinVar column in the custom CSV download.
+    clinvarVersion: {type: String as PropType<string | null>, default: null}
   },
 
   setup(props) {
     const scoreSetRef = toRef(props, 'scoreSet')
     const hasCountsRef = toRef(props, 'hasCounts')
-    const downloads = useScoreSetDownloads({scoreSet: scoreSetRef, hasCounts: hasCountsRef})
+    const clinvarVersionRef = toRef(props, 'clinvarVersion')
+    const downloads = useScoreSetDownloads({
+      scoreSet: scoreSetRef,
+      hasCounts: hasCountsRef,
+      clinvarVersion: clinvarVersionRef
+    })
 
     const routeProps = store.state.routeProps as {galaxyUrl: string; toolId: string; requestFromGalaxy: string}
 
@@ -184,8 +198,10 @@ export default defineComponent({
             endpoint = 'scores'
             outputType = 'table'
             break
-          case 'mappedVariants':
-            endpoint = 'mapped-variants'
+          case 'variantDetails':
+            // /mapped-variants was retired in #743; /variant-details is the replacement (VRS pair + Cat-VRS + annotations),
+            // streamed as NDJSON.
+            endpoint = 'variant-details'
             outputType = 'json'
             break
           default:
diff --git a/src/components/screens/ScoreSetView.vue b/src/components/screens/ScoreSetView.vue
index 7030ba67..cd095930 100644
--- a/src/components/screens/ScoreSetView.vue
+++ b/src/components/screens/ScoreSetView.vue
@@ -336,6 +336,7 @@
         <!-- Downloads -->
         <div class="mb-6">
           <ScoreSetDownloads
+            :clinvar-version="clinvarControls.controlVersion"
             :has-counts="hasCounts"
             :has-functional-impact-calibrations="hasFunctionalImpactCalibrations"
             :has-pathogenicity-calibrations="hasPathogenicityCalibrations"
diff --git a/src/composables/use-score-set-downloads.ts b/src/composables/use-score-set-downloads.ts
index c1b95e93..7be838bb 100644
--- a/src/composables/use-score-set-downloads.ts
+++ b/src/composables/use-score-set-downloads.ts
@@ -1,6 +1,6 @@
 import {computed, ref, type Ref} from 'vue'
 
-import {downloadScoreSetFile, downloadScoreSetVariantData, downloadMappedVariants} from '@/api/mavedb'
+import {downloadScoreSetFile, downloadScoreSetVariantData} from '@/api/mavedb'
 import config from '@/config'
 import {triggerDownload} from '@/lib/downloads'
 import type {components} from '@/schema/openapi'
@@ -12,25 +12,49 @@ export const TEXT_COLUMNS = ['hgvs_nt', 'hgvs_splice', 'hgvs_pro']
 interface UseScoreSetDownloadsOptions {
   scoreSet: Ref<ScoreSet | null>
   hasCounts?: Ref<boolean>
+  // The ClinVar control version the page has resolved via the histogram.
+  clinvarVersion?: Ref<string | null>
 }
 
-export function useScoreSetDownloads({scoreSet, hasCounts}: UseScoreSetDownloadsOptions) {
+// Convert and pad the ClinVar version, or return null if the version isn't in the expected shape.
+function clinvarNamespace(version: string | null | undefined): string | null {
+  if (!version) return null
+  const match = /^(\d{1,2})_(\d{4})$/.exec(version)
+  if (!match) return null
+  return `clinvar.${match[2]}_${match[1].padStart(2, '0')}`
+}
+
+export function useScoreSetDownloads({scoreSet, hasCounts, clinvarVersion}: UseScoreSetDownloadsOptions) {
   const customDialogVisible = ref(false)
   const selectedDataOptions = ref<string[]>([])
-  const annotatedDownloadInProgress = ref(false)
-  const annotatedDownloadProgress = ref(0)
+  // Shared progress state for the NDJSON streaming downloads (variant details + annotated variants).
+  // Only one stream runs at a time — starting a new one aborts any in-flight stream. `streamTarget`
+  // identifies which button's stream is running, so only that element renders the progress bar.
+  const streamDownloadInProgress = ref(false)
+  const streamDownloadProgress = ref(0)
+  const streamTarget = ref<'variantDetails' | 'annotatedVariants' | null>(null)
   const streamController = ref<AbortController | null>(null)
 
   const dataTypeOptions = computed(() => {
     const options = [
       {label: 'Scores', value: 'scores'},
       {label: 'Reference-frame HGVS', value: 'mappedHgvs'},
+      // Annotation namespaces served by the reworked CSV export. gnomAD / VEP / ClinGen are unversioned;
+      // ClinVar is versioned and only offered when the page has resolved a control version to target.
+      {label: 'gnomAD allele frequency', value: 'gnomad'},
+      {label: 'VEP consequence', value: 'vep'},
+      {label: 'ClinGen allele ID', value: 'clingen'},
       {label: 'Custom columns', value: 'includeCustomColumns'},
       {label: 'Without NA columns', value: 'dropNaColumns'}
     ]
     if (hasCounts?.value) {
       options.splice(1, 0, {label: 'Counts', value: 'counts'})
     }
+    if (clinvarNamespace(clinvarVersion?.value)) {
+      // Place ClinVar right after ClinGen alongside other annotation namespaces.
+      const clingenIndex = options.findIndex((opt) => opt.value === 'clingen')
+      options.splice(clingenIndex + 1, 0, {label: 'ClinVar significance', value: 'clinvar'})
+    }
     return options
   })
 
@@ -44,24 +68,25 @@ export function useScoreSetDownloads({scoreSet, hasCounts}: UseScoreSetDownloads
     if (!scoreSet.value) return
     const params = new URLSearchParams()
     for (const opt of selectedDataOptions.value) {
-      if (opt === 'scores') params.append('data_type', 'scores')
-      else if (opt === 'counts') params.append('data_type', 'counts')
-      else if (opt === 'mappedHgvs') params.append('include_post_mapped_hgvs', 'true')
+      if (opt === 'scores') params.append('namespaces', 'scores')
+      else if (opt === 'counts') params.append('namespaces', 'counts')
+      else if (opt === 'gnomad') params.append('namespaces', 'gnomad')
+      else if (opt === 'vep') params.append('namespaces', 'vep')
+      else if (opt === 'clingen') params.append('namespaces', 'clingen')
+      else if (opt === 'clinvar') {
+        const namespace = clinvarNamespace(clinvarVersion?.value)
+        if (namespace) params.append('namespaces', namespace)
+      } else if (opt === 'mappedHgvs') params.append('include_post_mapped_hgvs', 'true')
       else if (opt === 'includeCustomColumns') params.append('include_custom_columns', 'true')
       else if (opt === 'dropNaColumns') params.append('drop_na_columns', 'true')
     }
-    if (!params.has('data_type')) params.append('data_type', 'scores')
+    // Guarantee at least the core HGVS + score columns when only flags (no namespace) were selected.
+    if (!params.has('namespaces')) params.append('namespaces', 'scores')
     const data = await downloadScoreSetVariantData(scoreSet.value.urn, params)
     triggerDownload(data, `${scoreSet.value.urn}_custom.csv`)
     customDialogVisible.value = false
   }
 
-  async function downloadMappedVariantsFile() {
-    if (!scoreSet.value) return
-    const data = await downloadMappedVariants(scoreSet.value.urn)
-    triggerDownload(JSON.stringify(data), `${scoreSet.value.urn}_mapped_variants.json`, 'text/json')
-  }
-
   function downloadMetadata() {
     if (!scoreSet.value) return
     const metadata = JSON.stringify(scoreSet.value.extraMetadata)
@@ -71,22 +96,26 @@ export function useScoreSetDownloads({scoreSet, hasCounts}: UseScoreSetDownloads
   function abortStream() {
     if (streamController.value) {
       streamController.value.abort()
-      annotatedDownloadInProgress.value = false
-      annotatedDownloadProgress.value = 0
+      streamDownloadInProgress.value = false
+      streamDownloadProgress.value = 0
+      streamTarget.value = null
     }
   }
 
-  async function streamVariantAnnotations(annotationType: string) {
+  // Stream an NDJSON export (variant details, annotated variants) from a score-set sub-path to a file,
+  // driving the shared progress bar off the server's X-Total-Count. Aborts any in-flight stream first.
+  async function streamNdjson(subPath: string, filename: string, target: 'variantDetails' | 'annotatedVariants') {
     if (!scoreSet.value) return
     abortStream()
     streamController.value = new AbortController()
 
     try {
-      annotatedDownloadInProgress.value = true
-      const response = await fetch(
-        `${config.apiBaseUrl}/score-sets/${scoreSet.value.urn}/annotated-variants/${annotationType}`,
-        {signal: streamController.value.signal, headers: {Accept: 'application/x-ndjson'}}
-      )
+      streamDownloadInProgress.value = true
+      streamTarget.value = target
+      const response = await fetch(`${config.apiBaseUrl}/score-sets/${scoreSet.value.urn}/${subPath}`, {
+        signal: streamController.value.signal,
+        headers: {Accept: 'application/x-ndjson'}
+      })
 
       if (!response.ok) {
         throw new Error(`HTTP ${response.status}: ${response.statusText}`)
@@ -107,15 +136,16 @@ export function useScoreSetDownloads({scoreSet, hasCounts}: UseScoreSetDownloads
           const url = URL.createObjectURL(blob)
           const anchor = document.createElement('a')
           anchor.href = url
-          anchor.download = `${scoreSet.value!.urn}_annotated_variants_${annotationType}.ndjson`
+          anchor.download = filename
           anchor.click()
           URL.revokeObjectURL(url)
           break
         }
         const chunk = decoder.decode(value)
         chunks.push(chunk)
-        processedCount += chunk.split('\n').length
-        annotatedDownloadProgress.value = Math.round((processedCount / totalCount) * 100)
+        // Count newline characters, and clamp to 100% for progress tracking.
+        processedCount += chunk.split('\n').length - 1
+        streamDownloadProgress.value = totalCount ? Math.min(100, Math.round((processedCount / totalCount) * 100)) : 0
       }
     } catch (error: unknown) {
       const message = error instanceof Error ? error.message : 'Unknown error'
@@ -124,17 +154,33 @@ export function useScoreSetDownloads({scoreSet, hasCounts}: UseScoreSetDownloads
       }
     } finally {
       streamController.value = null
-      annotatedDownloadInProgress.value = false
-      annotatedDownloadProgress.value = 0
+      streamDownloadInProgress.value = false
+      streamDownloadProgress.value = 0
+      streamTarget.value = null
     }
   }
 
+  function streamVariantDetails() {
+    if (!scoreSet.value) return
+    return streamNdjson('variant-details', `${scoreSet.value.urn}_variant_details.ndjson`, 'variantDetails')
+  }
+
+  function streamVariantAnnotations(annotationType: string) {
+    if (!scoreSet.value) return
+    return streamNdjson(
+      `annotated-variants/${annotationType}`,
+      `${scoreSet.value.urn}_annotated_variants_${annotationType}.ndjson`,
+      'annotatedVariants'
+    )
+  }
+
   return {
     // State
     customDialogVisible,
     selectedDataOptions,
-    annotatedDownloadInProgress,
-    annotatedDownloadProgress,
+    streamDownloadInProgress,
+    streamDownloadProgress,
+    streamTarget,
 
     // Computed
     dataTypeOptions,
@@ -142,8 +188,8 @@ export function useScoreSetDownloads({scoreSet, hasCounts}: UseScoreSetDownloads
     // Methods
     downloadFile,
     downloadMultipleData,
-    downloadMappedVariantsFile,
     downloadMetadata,
+    streamVariantDetails,
     streamVariantAnnotations,
     abortStream
   }

From fc493bd89e88623bc6f78910a2ca6c825cf0e833 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 23 Jul 2026 18:40:11 -0700
Subject: [PATCH 65/84] feat(variant): rename "Your variant" to "This variant",
 rework confidence-badge palette
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

"Your variant" read oddly once the same badge could appear on other pages/contexts,
so the direct-relationship label and its Key-drawer entry are now phrased as "This
variant" instead, with its own dedicated subject color rather than reusing brand
sage. MvMeasurementCard's relationship badge now derives its color from the shared
RELATIONSHIPS dict instead of a hardcoded class, which is what let the two drift
out of sync in the first place.

On the confidence axis (measured/resolved/convergent/candidate), "Resolved" gets
its own dedicated slate rather than reusing the assay-level "Nucleotide" color —
the two answer different questions (was this coordinate measured or derived? vs.
what level was it assayed at?) and coloring them identically read as redundant on
the same card. "Convergent" and "Candidate" are unified onto one shared color: both
represent genuine variant-identity ambiguity, as opposed to "Resolved"'s certain,
deterministic re-expression of the same variant.
---
 src/assets/app.css                           | 10 +++++++---
 src/components/variant/MvMeasurementCard.vue | 11 +++++------
 src/glossary.ts                              |  4 ++--
 src/lib/allele-grouping.test.ts              |  2 +-
 src/lib/allele-grouping.ts                   | 16 ++++++++++------
 src/lib/glossary-prose.ts                    | 10 +++++-----
 src/lib/measurement-types.ts                 | 14 +++++++-------
 7 files changed, 37 insertions(+), 30 deletions(-)

diff --git a/src/assets/app.css b/src/assets/app.css
index 6c008a96..ff35e004 100644
--- a/src/assets/app.css
+++ b/src/assets/app.css
@@ -121,9 +121,9 @@
   --color-ga4gh-light: #e3f0f9;
 
   /* ── Measurement Types (variant screen) ────────────────────── */
-  --color-nucleotide: #2e7d32;
-  --color-nucleotide-light: #e8f5e9;
-  --color-nucleotide-border: #c8e4c6;
+  --color-nucleotide: #a8247c;
+  --color-nucleotide-light: #fce8f4;
+  --color-nucleotide-border: #eec3e0;
   --color-amino-acid: #7e5daf;
   --color-amino-acid-light: #f1ecf8;
   --color-amino-acid-border: #b5a0d0;
@@ -145,6 +145,10 @@
 
   /* ── Semantic colors ─────────────────────────────────────────── */
   --color-link: #0074d9;
+  --color-subject: #4a9ba8;
+  --color-subject-light: #ddecee;
+  --color-resolved: #475569;
+  --color-resolved-light: #eef1f5;
   --color-border: #dee2e6;
   --color-border-light: #f0f0f0;
   --color-bg: #f7f7f7;
diff --git a/src/components/variant/MvMeasurementCard.vue b/src/components/variant/MvMeasurementCard.vue
index 8d4e431d..e1901d3b 100644
--- a/src/components/variant/MvMeasurementCard.vue
+++ b/src/components/variant/MvMeasurementCard.vue
@@ -22,7 +22,7 @@
       <span
         v-key-term="'relationship'"
         class="inline-block rounded-sm px-2 py-0.5 text-[10px] font-semibold uppercase tracking-[0.3px]"
-        :class="relationship === 'direct' ? 'bg-sage/15 text-sage' : 'bg-border-light text-text-muted'"
+        :class="relationshipClass"
       >
         {{ relationshipLabel }}
       </span>
@@ -74,11 +74,7 @@ import {defineComponent, type PropType} from 'vue'
 
 import MvClassificationTag from '@/components/common/MvClassificationTag.vue'
 import MvEvidenceTag from '@/components/common/MvEvidenceTag.vue'
-import {
-  assayLevelDisplay,
-  RELATIONSHIPS,
-  type MeasurementRelationship
-} from '@/lib/measurement-types'
+import {assayLevelDisplay, RELATIONSHIPS, type MeasurementRelationship} from '@/lib/measurement-types'
 import type {components} from '@/schema/openapi'
 
 type SavedFunctionalClassification = components['schemas']['SavedFunctionalClassification']
@@ -125,6 +121,9 @@ export default defineComponent({
     relationshipLabel(): string {
       return RELATIONSHIPS[this.relationship]?.label ?? this.relationship
     },
+    relationshipClass(): string {
+      return RELATIONSHIPS[this.relationship]?.class ?? 'bg-border-light text-text-muted'
+    },
     classification(): string | null {
       return this.preferredClassification?.functionalClassification ?? null
     },
diff --git a/src/glossary.ts b/src/glossary.ts
index fd8560c5..a3228bdd 100644
--- a/src/glossary.ts
+++ b/src/glossary.ts
@@ -5,7 +5,7 @@ import {ACMG_KEY_SECTION} from '@/lib/acmg'
 import {CONFIDENCE_KEY_SECTION} from '@/lib/allele-grouping'
 import {CLINICAL_SIGNIFICANCE_KEY_SECTION, SIBLING_CONTROL_KEY_SECTION} from '@/lib/clinvar-controls'
 import {FUNCTIONAL_IMPACT_KEY_SECTION} from '@/lib/functional-impact'
-import {AS_OF_KEY_SECTION, CONSEQUENCE_KEY_SECTION, SELECTED_ALLELE_KEY_SECTION, SUPERSEDED_KEY_SECTION} from '@/lib/glossary-prose'
+import {AS_OF_KEY_SECTION, CONSEQUENCE_KEY_SECTION, THIS_VARIANT_KEY_SECTION, SUPERSEDED_KEY_SECTION} from '@/lib/glossary-prose'
 import {POPULATION_KEY_SECTION} from '@/lib/gnomad'
 import {ASSAY_LEVEL_KEY_SECTION, RELATIONSHIP_KEY_SECTION} from '@/lib/measurement-types'
 
@@ -15,7 +15,7 @@ export const GLOSSARY_SECTIONS: KeySection[] = [
   RELATIONSHIP_KEY_SECTION,
   ASSAY_LEVEL_KEY_SECTION,
   CONFIDENCE_KEY_SECTION,
-  SELECTED_ALLELE_KEY_SECTION,
+  THIS_VARIANT_KEY_SECTION,
   COORDINATE_FRAME_KEY_SECTION,
   CONSEQUENCE_KEY_SECTION,
   FUNCTIONAL_IMPACT_KEY_SECTION,
diff --git a/src/lib/allele-grouping.test.ts b/src/lib/allele-grouping.test.ts
index a0f4542c..ed7d0ad1 100644
--- a/src/lib/allele-grouping.test.ts
+++ b/src/lib/allele-grouping.test.ts
@@ -130,7 +130,7 @@ describe('groupAlleles — projection pairing + confidence', () => {
   })
 
   it('badges measured over derivation, maps projection→Resolved / convergent→Convergent / candidate→Candidate, else null', () => {
-    // `measured` wins even if a derivation is also present (a stray measured sibling still reads "Measured").
+    // `measured` wins even if a derivation is also present (a stray measured sibling still reads "This measurement").
     expect(confidenceBadge({measured: true, derivation: 'projection'})).toBe(ALLELE_CONFIDENCE.measured)
     expect(confidenceBadge({measured: false, derivation: 'projection'})).toBe(ALLELE_CONFIDENCE.projection)
     // A synonymous cousin under a nucleotide assay: a distinct change sharing the consequence, not ambiguous.
diff --git a/src/lib/allele-grouping.ts b/src/lib/allele-grouping.ts
index 74c51db5..cafae9b7 100644
--- a/src/lib/allele-grouping.ts
+++ b/src/lib/allele-grouping.ts
@@ -61,14 +61,18 @@ export interface ConfidenceBadge {
   definition: string
 }
 
-// Single source for the confidence axis (badges + the Key drawer's "confidence" section). Keyed by
-// outcome, not raw `Derivation`: the focus/measured allele reads "Measured" (it has no derivation); the
-// derived states map straight from `derivation`. Insertion order is the drawer's display order.
+// Single source for the confidence axis (badges + the Key drawer's "confidence" section), keyed by outcome
+// rather than raw `Derivation`. `convergent` and `candidate` share a color (identity ambiguity);
+// `projection` gets its own (certain but derived). Insertion order is the drawer's display order.
 export const ALLELE_CONFIDENCE: Record<string, ConfidenceBadge> = {
-  measured: {label: 'Measured', class: 'bg-sage/15 text-sage', definition: 'Directly assayed in this score set.'},
+  measured: {
+    label: 'This measurement',
+    class: 'bg-sage/15 text-sage',
+    definition: 'An allele that was directly measured in this assay.'
+  },
   projection: {
     label: 'Resolved',
-    class: 'bg-nucleotide-light text-nucleotide',
+    class: 'bg-resolved-light text-resolved',
     definition: 'Derived from the measured allele — the same change expressed at another coordinate level.'
   },
   convergent: {
@@ -79,7 +83,7 @@ export const ALLELE_CONFIDENCE: Record<string, ConfidenceBadge> = {
   },
   candidate: {
     label: 'Candidate',
-    class: 'bg-amber-100 text-amber-700',
+    class: 'bg-synonymous-nucleotide-light text-synonymous-nucleotide',
     definition:
       'A possible nucleotide change behind a protein-level measurement — one of several synonymous codons; which was actually assayed is unknown.'
   }
diff --git a/src/lib/glossary-prose.ts b/src/lib/glossary-prose.ts
index 0f50bb04..f2ee18d9 100644
--- a/src/lib/glossary-prose.ts
+++ b/src/lib/glossary-prose.ts
@@ -1,13 +1,13 @@
 import type {KeySection} from '@/composables/use-key-drawer'
 
-export const SELECTED_ALLELE_KEY_SECTION: KeySection = {
-  id: 'selected-allele',
-  title: 'Selected allele',
+export const THIS_VARIANT_KEY_SECTION: KeySection = {
+  id: 'this-variant',
+  title: 'This variant',
   terms: [
     {
-      label: 'Selected allele',
+      label: 'This variant',
       definition: 'The allele this page is anchored on — the ClinGen allele you navigated to.',
-      class: 'bg-link/10 text-link'
+      class: 'bg-subject/15 text-subject'
     }
   ]
 }
diff --git a/src/lib/measurement-types.ts b/src/lib/measurement-types.ts
index fbc31764..73759194 100644
--- a/src/lib/measurement-types.ts
+++ b/src/lib/measurement-types.ts
@@ -15,28 +15,28 @@ export function assayLevelBucket(level: string | null | undefined): LevelBucket
 
 /**
  * Single source of truth for the measurement-to-query relationship vocabulary (the RT asymmetry): the
- * card label, an optional chip class, and the Key-drawer gloss. Phrased relative to the user's variant so
- * the labels self-explain under the "relative to your variant" anchor. Insertion order is display order.
+ * card label, an optional chip class, and the Key-drawer gloss. Phrased relative to the page's own variant
+ * so the labels self-explain under the "relative to this variant" anchor. Insertion order is display order.
  */
 export const RELATIONSHIPS: Record<MeasurementRelationship, {label: string; class?: string; definition: string}> = {
   direct: {
-    label: 'Your variant',
-    class: 'bg-sage/15 text-sage',
+    label: 'This variant',
+    class: 'bg-subject/15 text-subject',
     definition: 'The result assayed exactly the allele you searched.'
   },
   protein_consequence: {
     label: 'Its protein consequence',
-    definition: 'The result assayed the protein change your variant produces.'
+    definition: 'The result assayed the protein change this variant produces.'
   },
   nucleotide_encoding: {
     label: 'Encodes the protein consequence',
-    definition: 'The result assayed a nucleotide allele that encodes the same protein change as your variant.'
+    definition: 'The result assayed a nucleotide allele that encodes the same protein change as this variant.'
   }
 }
 
 export const RELATIONSHIP_KEY_SECTION: KeySection = {
   id: 'relationship',
-  title: 'Relationship to your variant',
+  title: 'Relationship to this variant',
   gloss: 'How each result relates to the allele you searched.',
   terms: Object.values(RELATIONSHIPS).map((r) => ({label: r.label, definition: r.definition, class: r.class}))
 }

From f32ef02707fd14536b6e48da52f305f9eb62d802 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 23 Jul 2026 18:40:28 -0700
Subject: [PATCH 66/84] feat(variant): promote the redesigned detail page to
 production

Replaces the old VariantScreen with the functional-first redesign: functional
evidence leads, re-anchoring is per-section and always labeled, and clinical/
population reference is shown per allele rather than pooled across a group.

- MvAlleleLedger combines the old separate "related alleles" panel and per-allele
  clinical/population cells into one card per allele group (this-variant/
  this-measurement/collapsed others), each with a role badge and a facts grid.
- VariantConsequenceStat factors the molecular-consequence cell out of
  VariantDetailPanel so the ledger and the score-set panel render it identically.
- VariantClinvarStat/VariantGnomadStat fold their "pooled from N related variants"
  provenance into the stat trigger itself instead of a separate caption.
- use-clingen-allele now surfaces every mapped reference-genome build
  (allGenomicLocationsText) instead of silently keeping only the first, closing a
  gap versus the old VariantInfoSection card.
- clingen.ts extracts the ClinGen registry URL helpers shared by the page and
  search results.
- VariantInfoSection and MvRelatedAlleles are deleted; the ledger fully supersedes
  both.
---
 src/components/screens/VariantScreen.vue      | 302 +++++++-----------
 src/components/variant/MvAlleleLedger.vue     | 232 ++++++++++++++
 src/components/variant/MvRelatedAlleles.vue   | 147 ---------
 src/components/variant/VariantClinvarStat.vue |  61 +++-
 .../variant/VariantConsequenceStat.vue        |  75 +++++
 src/components/variant/VariantDetailPanel.vue |  22 +-
 src/components/variant/VariantGnomadStat.vue  |  43 ++-
 src/components/variant/VariantInfoSection.vue |  70 ----
 src/composables/use-clingen-allele.ts         |  16 +-
 src/lib/clingen.ts                            |  10 +
 10 files changed, 525 insertions(+), 453 deletions(-)
 create mode 100644 src/components/variant/MvAlleleLedger.vue
 delete mode 100644 src/components/variant/MvRelatedAlleles.vue
 create mode 100644 src/components/variant/VariantConsequenceStat.vue
 delete mode 100644 src/components/variant/VariantInfoSection.vue
 create mode 100644 src/lib/clingen.ts

diff --git a/src/components/screens/VariantScreen.vue b/src/components/screens/VariantScreen.vue
index e57fefeb..fc11b4fb 100644
--- a/src/components/screens/VariantScreen.vue
+++ b/src/components/screens/VariantScreen.vue
@@ -21,22 +21,30 @@
         <template v-if="lookup.variants.value.length > 0" #subtitle>
           <p class="mt-2 text-sm text-text-muted">
             <template v-if="lookup.geneName.value">{{ lookup.geneName.value }} &middot; </template>
-            <template v-if="lookup.clingenAllele.genomicLocationText.value"
-              >{{ lookup.clingenAllele.genomicLocationText.value }} &middot;
+            <template v-if="lookup.clingenAllele.allGenomicLocationsText.value"
+              >{{ lookup.clingenAllele.allGenomicLocationsText.value }} &middot;
             </template>
             {{ lookup.variants.value.length }}
             {{ lookup.variants.value.length === 1 ? 'measurement' : 'measurements' }}
             <template v-if="lookup.uniqueAssayCount.value > 1">
               across {{ lookup.uniqueAssayCount.value }} score sets</template
             >
+            <template v-if="clingenAlleleId">
+              &middot;
+              <a
+                class="inline-flex items-center gap-0.5 text-link hover:underline"
+                :href="clingenRegistryUrl"
+                target="_blank"
+                >View in ClinGen Allele Registry&nbsp;<i class="pi pi-external-link !text-[11px]"
+              /></a>
+            </template>
           </p>
         </template>
       </MvPageHeader>
     </template>
 
     <div class="mx-auto w-full px-4 tablet:px-6 py-6 tablet:py-8" style="max-width: 1000px">
-      <!-- ── CONTROL ROW (query axes: content valid-time + superseded scope) — always rendered so the
-           as_of / superseded controls stay reachable even when the query returns no measurements ── -->
+      <!-- ── CONTROL ROW (query axes) ── -->
       <div
         class="mave-gradient-bar relative overflow-hidden mb-4 flex flex-col gap-3 rounded-lg border border-border bg-surface px-4 py-3 tablet:flex-row tablet:flex-wrap tablet:items-center tablet:gap-x-5 tablet:gap-y-2 tablet:px-5 tablet:py-2.5"
       >
@@ -91,13 +99,9 @@
         </button>
       </div>
 
-      <!-- Error state -->
+      <!-- Error / loading / empty -->
       <MvErrorState v-if="lookup.variantsStatus.value === 'Error'" @retry="lookup.fetchVariants" />
-
-      <!-- Loading state -->
       <MvPageLoading v-else-if="lookup.variantsStatus.value === 'Loading'" text="Loading variant measurements..." />
-
-      <!-- Empty state -->
       <MvEmptyState
         v-else-if="lookup.variants.value.length === 0"
         :description="emptyStateDescription"
@@ -105,7 +109,8 @@
       />
 
       <template v-else>
-        <!-- ── MEASUREMENTS SECTION ───────────────────────────── -->
+        <!-- ═══ MEASUREMENTS — the body; strongly about the measured variant (Y) ═══ -->
+        <!-- Switcher -->
         <div class="rounded-lg border border-border bg-surface">
           <div class="flex flex-wrap items-center gap-2.5 border-b border-border-light px-4 tablet:px-5 py-3.5">
             <span class="text-sm font-bold text-text-primary"
@@ -134,20 +139,19 @@
             </div>
           </div>
           <!-- Anchor heading: names the frame of reference so the per-card relationship badges
-               ("Your variant" / "Its protein consequence" / "Encodes the protein consequence") read as
+               ("This variant" / "Its protein consequence" / "Encodes the protein consequence") read as
                self-explaining rather than needing a per-badge tooltip. -->
           <div class="px-4 tablet:px-5 pt-3.5 text-xs-minus text-text-muted">
-            What each result assayed, relative to your variant:
+            What each result assayed, relative to this variant:
           </div>
-          <!-- Desktop: horizontal scroll strip -->
           <div class="measurement-switcher hidden tablet:flex gap-3 overflow-x-auto px-5 py-4">
             <MvMeasurementCard
               v-for="m in lookup.filteredVariants.value"
               :key="'desktop-' + m.variantUrn"
               :active="lookup.selectedVariantUrn.value === m.variantUrn"
-              :loading="lookup.selectedVariantUrn.value === m.variantUrn && lookup.selectedLoading.value"
               :assay-level="m.assayLevel"
               :assay-type="lookup.getKeyword(m.scoreSetUrn, 'Phenotypic Assay Method')"
+              :loading="lookup.selectedVariantUrn.value === m.variantUrn && lookup.selectedLoading.value"
               :mechanism="lookup.getKeyword(m.scoreSetUrn, 'Molecular Mechanism Assessed')"
               :model-system="lookup.getKeyword(m.scoreSetUrn, 'Phenotypic Assay Model System')"
               :preferred-classification="m.preferredClassification ?? null"
@@ -174,12 +178,22 @@
               class="pi pi-spin pi-spinner text-sage"
             />
           </div>
+
+          <!-- ── RELATIONSHIP LINE ── a plain sentence relating the selected measurement (Y) to the page
+               subject (X). -->
+          <div
+            v-if="lookup.selectedVariantDetail.value"
+            class="border-t border-border-light bg-sage/[0.06] px-4 tablet:px-5 py-3 text-sm text-text-secondary"
+          >
+            {{ relationshipPrefix }} <span class="font-semibold text-text-primary">this variant</span
+            >{{ isDirectMeasurement ? ' directly' : '' }}.
+          </div>
         </div>
 
-        <!-- ── SUPERSESSION BANNER ───────────────────────────── -->
+        <!-- Supersession banner (about the selected measurement (Y) ) -->
         <div
           v-if="lookup.selectedVariantDetail.value && !lookup.selectedVariantDetail.value.isCurrent"
-          class="mt-6 flex items-start gap-2 rounded-lg border border-amber-200 bg-amber-50 px-4 py-3 text-sm text-amber-800"
+          class="mt-4 flex items-start gap-2 rounded-lg border border-amber-200 bg-amber-50 px-4 py-3 text-sm text-amber-800"
         >
           <i class="pi pi-exclamation-triangle mt-0.5 text-xs" />
           <div>
@@ -196,12 +210,10 @@
           </div>
         </div>
 
-        <!-- ── FUNCTIONAL EVIDENCE (MaveDB) ───────────────────── First-class: the functional measurement is
-             MaveDB's own contribution, so it leads the page. Descriptive annotations (VEP) sit in the identity 
-             section below; external reference evidence sits in its own card below. -->
+        <!-- ── FUNCTIONAL EVIDENCE ── MaveDB's own contribution, centered as the lead of the body. -->
         <div
           v-if="lookup.selectedVariantDetail.value"
-          class="relative mt-6 rounded-lg border bg-surface px-[18px] py-3.5"
+          class="relative mt-4 rounded-lg border bg-surface px-[18px] py-3.5"
         >
           <div class="mb-2.5 flex flex-wrap items-center gap-2">
             <h3 class="mave-section-title !mb-0">Functional evidence</h3>
@@ -247,118 +259,40 @@
           <p v-else class="text-xs-plus italic text-text-muted">No score available</p>
         </div>
 
-        <!-- ── VARIANT & ASSAY DETAILS ──────────────────────── -->
-        <template v-if="lookup.selectedVariantDetail.value">
-          <!-- Desktop: single card with two columns -->
-          <div class="relative mt-6 hidden tablet:block rounded-lg border border-border bg-surface px-[18px] py-3.5">
-            <div class="grid grid-cols-2">
-              <div class="border-r border-border-light pr-[18px]">
-                <VariantInfoSection
-                  :allele-name="lookup.clingenAllele.alleleName.value"
-                  :clingen-allele-id="lookup.selectedClingenAlleleId.value"
-                  :clinvar-allele-ids="lookup.clingenAllele.clinvarAlleleIds.value"
-                  :genomic-locations="lookup.clingenAllele.genomicLocations.value"
-                  :molecular-consequence="primaryMolecularConsequence"
-                />
-              </div>
-              <div class="pl-[18px]">
-                <MvAssayFactsCard
-                  :assay-level="lookup.selectedVariantDetail.value?.assayLevel ?? null"
-                  :columns="1"
-                  :score-set="lookup.selectedScoreSet.value ?? undefined"
-                  show-urn
-                  :variant-urn="lookup.selectedVariantDetail.value?.urn ?? undefined"
-                />
-              </div>
-            </div>
-          </div>
-
-          <!-- Mobile: separate cards -->
-          <div class="mt-6 tablet:hidden relative rounded-lg border border-border bg-surface px-4 py-3.5">
-            <VariantInfoSection
-              :allele-name="lookup.clingenAllele.alleleName.value"
-              :clingen-allele-id="lookup.selectedClingenAlleleId.value"
-              :clinvar-allele-ids="lookup.clingenAllele.clinvarAlleleIds.value"
-              :genomic-locations="lookup.clingenAllele.genomicLocations.value"
-              :molecular-consequence="primaryMolecularConsequence"
-            />
-          </div>
-          <div class="mt-4 tablet:hidden relative rounded-lg border border-border bg-surface px-4 py-3.5">
-            <MvAssayFactsCard
-              :assay-level="lookup.selectedVariantDetail.value?.assayLevel ?? null"
-              :columns="1"
-              :score-set="lookup.selectedScoreSet.value ?? undefined"
-              show-urn
-              :variant-urn="lookup.selectedVariantDetail.value?.urn ?? undefined"
-            />
-          </div>
-        </template>
-
-        <!-- ── EXTERNAL EVIDENCE ──────────────────────────────── Reference data pulled from other databases,
-             for comparison against the functional evidence above. Rendered only when there is at least one 
-             external annotation. -->
+        <!-- Assay facts (about the selected measurement) -->
         <div
-          v-if="lookup.selectedVariantDetail.value && hasExternalEvidence"
+          v-if="lookup.selectedVariantDetail.value"
           class="relative mt-4 rounded-lg border border-border bg-surface px-[18px] py-3.5"
         >
-          <div class="mb-2.5 flex flex-wrap items-center gap-2">
-            <h3 class="mave-section-title !mb-0">External evidence</h3>
-            <span class="text-xs-minus text-text-muted">from reference databases</span>
-            <span
-              v-if="primaryGroup && !primaryGroup.annotationsMatch"
-              class="ml-auto text-[10px] font-semibold uppercase tracking-[0.3px] text-amber-600"
-              >differ by level</span
-            >
-          </div>
-          <!-- Same fold + underlying-annotations popovers as the score-set variant panel, so both surfaces
-               apply identical placement rules and expose the precise underlying gnomAD/ClinVar records. -->
-          <div class="grid grid-cols-1 gap-x-8 gap-y-4 tablet:grid-cols-2">
-            <VariantGnomadStat
-              :alleles="lookup.selectedVariantDetail.value.alleles"
-              :annotations="lookup.selectedVariantDetail.value.annotations"
-              :assay-gnomad="assayGnomad"
-              :assay-level="lookup.selectedVariantDetail.value.assayLevel ?? null"
-              :assay-level-digest="primarySubjectDigests"
-              plain
-            >
-              <template #label>
-                <span
-                  v-key-term="'population'"
-                  class="w-fit text-[10px] font-semibold uppercase tracking-[0.3px] text-[#aaa]"
-                  >Population frequency</span
-                >
-              </template>
-            </VariantGnomadStat>
-            <VariantClinvarStat
-              :alleles="lookup.selectedVariantDetail.value.alleles"
-              :annotations="lookup.selectedVariantDetail.value.annotations"
-              :assay-level="lookup.selectedVariantDetail.value.assayLevel ?? null"
-              :assay-level-digest="primarySubjectDigests"
-              :clinvar-version="clinvarControls.controlVersion"
-              plain
-            >
-              <template #label>
-                <span
-                  v-key-term="'clinical'"
-                  class="w-fit text-[10px] font-semibold uppercase tracking-[0.3px] text-[#aaa]"
-                  >Clinical significance</span
-                >
-              </template>
-            </VariantClinvarStat>
-          </div>
+          <MvAssayFactsCard
+            :assay-level="lookup.selectedVariantDetail.value?.assayLevel ?? null"
+            :columns="2"
+            :score-set="lookup.selectedScoreSet.value ?? undefined"
+            show-urn
+            :variant-urn="lookup.selectedVariantDetail.value?.urn ?? undefined"
+          />
         </div>
 
-        <!-- ── RELATED ALLELES ───────────────────────────────── Sibling alleles used as context;
-             subordinate to the evidence panel above (lighter, collapsed by default). -->
+        <!-- ═══ CLINICAL, POPULATION & RELATED VARIATION ═══ 
+             This variant (X) is pinned with its own clinical/population data (a property of this exact allele, so it never follows the selection). 
+             The measured allele (Y) is pinned when the selection assayed a different allele. 
+             All other alleles and the rest of the equivalence class collapses underneath, each carrying its own per-level reference so the same 
+             information is available at every level. ═══ -->
         <div
-          v-if="lookup.selectedVariantDetail.value && siblingGroups.length > 0"
-          class="relative mt-4 rounded-lg border border-border-light bg-surface px-[18px] py-3.5"
+          v-if="lookup.selectedVariantDetail.value && alleleGroups.length > 0"
+          class="relative mt-4 rounded-lg border border-border bg-surface px-[18px] py-3.5"
         >
-          <MvRelatedAlleles :groups="siblingGroups" :variant-urn="lookup.selectedVariantDetail.value.urn" />
+          <MvAlleleLedger
+            :alleles="lookup.selectedVariantDetail.value.alleles"
+            :annotations="lookup.selectedVariantDetail.value.annotations"
+            :clinvar-version="clinvarControls.controlVersion"
+            :groups="alleleGroups"
+            :variant-urn="lookup.selectedVariantDetail.value.urn"
+          />
         </div>
 
-        <!-- ── SCORE DISTRIBUTION CHART ──────────────────────── -->
-        <div v-if="lookup.selectedScoreSet.value" class="mt-6 rounded-lg border border-border bg-surface">
+        <!-- ── SCORE DISTRIBUTION ── -->
+        <div v-if="lookup.selectedScoreSet.value" class="mt-4 rounded-lg border border-border bg-surface">
           <div
             class="flex flex-wrap items-center justify-between gap-3 border-b border-border-light px-4 tablet:px-5 py-3.5"
           >
@@ -390,18 +324,12 @@
                 @calibration-changed="lookup.selectedCalibration.value = $event"
                 @selection-changed="() => {}"
               />
-              <!-- On a convergent-cousin/candidate page the highlighted point is a *measured* allele sharing
-                   this variant's protein consequence, not this allele — which was not itself assayed. Say so.
-                   TODO(histogram): the highlight is not deterministic when two distinct nucleotide variants
-                   that encode the same protein consequence were both measured — only one is highlighted here.
-                   Resolving that needs histogram multi-selection (highlight every measured sibling), a larger
-                   change deferred for now. -->
               <p
                 v-if="primaryGroup && !primaryGroup.measured"
                 class="mt-2 text-xs italic leading-tight text-text-muted"
               >
-                This allele was not directly measured — the highlighted point is a measured allele that shares
-                its protein consequence.
+                This allele was not directly measured — the highlighted point is a measured allele that shares its
+                protein consequence.
               </p>
             </div>
             <div v-else class="flex min-h-[200px] items-center justify-center">
@@ -417,7 +345,6 @@
         </div>
       </template>
     </div>
-
   </MvLayout>
 </template>
 
@@ -443,33 +370,34 @@ import MvBadgeToggle from '@/components/common/MvBadgeToggle.vue'
 import ScoreSetHistogram from '@/components/score-set/ScoreSetHistogram.vue'
 import {useClinvarControls} from '@/composables/use-clinvar-controls'
 import {useKeyDrawer} from '@/composables/use-key-drawer'
-import MvRelatedAlleles from '@/components/variant/MvRelatedAlleles.vue'
+import MvAlleleLedger from '@/components/variant/MvAlleleLedger.vue'
 import MvClassificationTag from '@/components/common/MvClassificationTag.vue'
-import VariantGnomadStat from '@/components/variant/VariantGnomadStat.vue'
-import VariantClinvarStat from '@/components/variant/VariantClinvarStat.vue'
 import MvMeasurementCard from '@/components/variant/MvMeasurementCard.vue'
 import MvRowActionMenu, {type RowAction} from '@/components/common/MvRowActionMenu.vue'
-import VariantInfoSection from '@/components/variant/VariantInfoSection.vue'
 import {useVariantLookup} from '@/composables/use-variant-lookup'
 import {assayLevelDisplay} from '@/lib/measurement-types'
 import {hasFunctionalCalibrations, hasPathogenicityCalibrations} from '@/lib/calibrations'
 import {confidenceBadge, groupAlleles, type AlleleGroup, type ConfidenceBadge} from '@/lib/allele-grouping'
-import {formatConsequence} from '@/lib/formats'
 import type {components} from '@/schema/openapi'
+import {clingenAlleleUrlFromCanonicalId} from '@/lib/clingen'
 
-type AlleleAnnotations = components['schemas']['AlleleAnnotations']
-type GnomadAnnotation = components['schemas']['GnomadAnnotation']
+type SequenceLevel = components['schemas']['SequenceLevel']
 
+/**
+ * The variant detail page. It is critical that this page makes clear the seam between the PAGE VARIANT (X)
+ * and the SELECTED MEASURED VARIANT (Y). The page header for the PAGE variant (X) with its identity and
+ * registry link; the measurement body (which follows the selection, i.e. the measured variant Y) and how
+ * it relates to X; a combined clinical/population + related-alleles ledger anchored back on X; and the
+ * score distribution last. Each section names its subject so the per-section re-anchoring reads as intentional.
+ */
 export default defineComponent({
   name: 'VariantScreen',
 
   components: {
     CalibrationTable,
     DatePicker,
-    MvRelatedAlleles,
+    MvAlleleLedger,
     MvClassificationTag,
-    VariantGnomadStat,
-    VariantClinvarStat,
     MvAssayFactsCard,
     MvBadgeToggle,
     MvEmptyState,
@@ -483,8 +411,7 @@ export default defineComponent({
     MvPageLoading,
     PSelect: Select,
     ScoreSetHistogram,
-    SplitButton,
-    VariantInfoSection
+    SplitButton
   },
 
   props: {
@@ -504,7 +431,6 @@ export default defineComponent({
 
     const lookup = useVariantLookup(toRef(props, 'clingenAlleleId'), {
       highlightUrn: toRef(props, 'highlightVariantUrn'),
-      // Seed the query-axis controls from the URL so shared links load in a single fetch.
       initialIncludeSuperseded: (route.query.include_superseded as string)?.toLowerCase() === 'true',
       initialAsOf: typeof route.query.as_of === 'string' ? route.query.as_of : null,
       toast: useToast()
@@ -513,7 +439,7 @@ export default defineComponent({
     const clinvarControls = useClinvarControls(lookup.selectedScoreSetUrn, lookup.scores)
 
     return {
-      head: useHead({title: 'Variant search results'}),
+      head: useHead({title: 'Variant'}),
       lookup,
       clinvarControls,
       keyDrawer: useKeyDrawer()
@@ -528,8 +454,9 @@ export default defineComponent({
         selectedVariantUrn: this.lookup.selectedVariantUrn.value
       }
     },
+    // Anchor to the page allele (X); never shift to the measured allele on selection.
     pageTitle(): string {
-      return this.lookup.clingenAllele.alleleName.value || this.lookup.selectedVariantName.value || 'Variant'
+      return this.lookup.clingenAllele.alleleName.value || this.clingenAlleleId || 'Variant'
     },
     // Allele groups for the selected measurement (c↔g projection pairs collapsed, annotations coalesced).
     alleleGroups(): AlleleGroup[] {
@@ -541,54 +468,48 @@ export default defineComponent({
         pageClingenAlleleId: this.clingenAlleleId
       })
     },
-    // The subject of the page: the searched (page-root) allele, falling back to the measured allele. Its
-    // annotations are promoted into the evidence panel; everything else is a "related allele" control.
+    // The page's own allele group (page-root preferred, falling back to the measured allele).
     primaryGroup(): AlleleGroup | null {
       const groups = this.alleleGroups
       return groups.find((g) => g.pageRoot) ?? groups.find((g) => g.measured) ?? groups[0] ?? null
     },
-    siblingGroups(): AlleleGroup[] {
-      const primary = this.primaryGroup
-      return this.alleleGroups.filter((g) => g !== primary)
+    // The page allele's (X) own sequence level, read off its pageRoot member — null if the selected
+    // measurement's envelope doesn't happen to carry X's own identity.
+    pageLevel(): SequenceLevel | null {
+      const group = this.alleleGroups.find((g) => g.pageRoot)
+      const root = group?.members.find((m) => m.pageRoot)
+      return (root?.level ?? null) as SequenceLevel | null
     },
-    primaryAnnotations(): AlleleAnnotations | null {
-      return this.primaryGroup?.coalescedAnnotations ?? null
+    // True when the page itself is anchored on the protein-level entity (a PA id) — X *is* the protein
+    // change, not a nucleotide variant that separately produces one.
+    pageIsProteinRooted(): boolean {
+      return this.pageLevel === 'protein'
     },
-    // The subject the External Evidence cells anchor on: the page's own allele, as its digest(s). One physical
-    // allele is stored as a c↔g pair (two digests) and ClinVar/gnomAD attach to only one, so both count as the
-    // subject's own. This is the *page* allele, not the measured allele — on a convergent cousin's page they
-    // differ, and the cell should reflect the cousin (empty → context), not the allele that was assayed. The
-    // *level* that gates projection is the assay level (detail.assayLevel), passed separately — the assay's
-    // resolution, not the allele's molecular level, is what determines whether we may project.
-    primarySubjectDigests(): string[] {
-      return this.primaryGroup?.members.map((m) => m.digest) ?? []
+    // ClinGen Allele Registry deep link for the page allele (X).
+    clingenRegistryUrl(): string {
+      return clingenAlleleUrlFromCanonicalId(this.clingenAlleleId)
     },
-    // VEP molecular consequence for the primary allele.
-    primaryMolecularConsequence(): string | null {
-      const consequence = this.primaryAnnotations?.vep?.consequence
-      return consequence ? formatConsequence(consequence) : null
+    // True when the selected measurement assayed the page allele itself (X == Y).
+    isDirectMeasurement(): boolean {
+      return this.lookup.selectedVariant.value?.relationship === 'direct'
     },
-    // The page allele's own gnomAD annotation — the headline the gnomAD cell shows straight up (siblings are
-    // enumerated by the cell itself when the page allele has none). Coalesced across the allele's c↔g pair so
-    // a frequency on either representation counts; anchored on the page allele, not the measured allele.
-    assayGnomad(): GnomadAnnotation | null {
-      return this.primaryAnnotations?.gnomad ?? null
-    },
-    // Whether any allele on the record carries a gnomAD or ClinVar annotation — gates the evidence card.
-    hasExternalEvidence(): boolean {
-      const annotations = this.lookup.selectedVariantDetail.value?.annotations
-      if (!annotations) return false
-      return Object.values(annotations).some((a) => a.gnomad || (a.clinvar?.length ?? 0) > 0)
+    // Leading half of the relationship line — everything up to the bold "this variant".
+    relationshipPrefix(): string {
+      const rel = this.lookup.selectedVariant.value?.relationship
+      if (rel === 'protein_consequence') return 'The selected measurement measured the protein consequence of'
+      if (rel === 'nucleotide_encoding') {
+        return this.pageIsProteinRooted
+          ? 'The selected measurement measured a variant that encodes'
+          : 'The selected measurement measured a variant that encodes the same protein consequence as'
+      }
+      return 'The selected measurement measured'
     },
-    // Confidence/provenance badge for the primary allele (Measured / Resolved / Candidate).
     primaryConfidenceBadge(): ConfidenceBadge | null {
       return this.primaryGroup ? confidenceBadge(this.primaryGroup) : null
     },
     today(): Date {
       return new Date()
     },
-    // Points the empty state back at the active query controls, since an as_of / superseded filter is a
-    // common reason a valid allele returns nothing.
     emptyStateDescription(): string {
       if (this.lookup.asOf.value) {
         return this.lookup.includeSuperseded.value
@@ -600,9 +521,6 @@ export default defineComponent({
       }
       return 'No measurements were found for this allele.'
     },
-    // Maps the DatePicker's Date|null ⇄ the composable's `as_of` date string (null = current). A date-only
-    // string is valid ISO 8601; the API reconstructs the molecular/annotation layer at that instant.
-    // Built from local Y/M/D to avoid a UTC off-by-one.
     asOfDate: {
       get(): Date | null {
         return this.lookup.asOf.value ? new Date(`${this.lookup.asOf.value}T00:00:00`) : null
@@ -628,7 +546,6 @@ export default defineComponent({
       const activeVariant = this.lookup.selectedVariantDetail.value
       if (!activeVariant) return options
 
-      // Mapping is present iff the envelope built a molecular representation (Cat-VRS) for the variant.
       const hasMappingData = !!activeVariant.molecularRepresentation
       const scoreSet = this.lookup.selectedScoreSet.value
       const hasScore = this.lookup.selectedVariantScore.value !== null
@@ -657,10 +574,15 @@ export default defineComponent({
   },
 
   watch: {
-    // Reflect the query-axis controls + selected measurement in the URL (shareable/citation). Guarded
-    // against redundant nav. Writing `variant` keeps the selection ↔ `?variant=` highlight in sync, so the
-    // URL always points at the card the user is on.
-    queryAxisState({includeSuperseded, asOf, selectedVariantUrn}: {includeSuperseded: boolean; asOf: string | null; selectedVariantUrn: string | null}) {
+    queryAxisState({
+      includeSuperseded,
+      asOf,
+      selectedVariantUrn
+    }: {
+      includeSuperseded: boolean
+      asOf: string | null
+      selectedVariantUrn: string | null
+    }) {
       const query = {...this.$route.query}
       if (includeSuperseded) query.include_superseded = 'true'
       else delete query.include_superseded
@@ -670,11 +592,11 @@ export default defineComponent({
       else delete query.variant
       if (JSON.stringify(query) !== JSON.stringify(this.$route.query)) this.$router.replace({query})
     },
-    // Pull external URL changes (back/forward, edited link) back into the controls.
     '$route.query'(query: Record<string, string | string[] | null | undefined>) {
       const includeSuperseded = (query.include_superseded as string)?.toLowerCase() === 'true'
       const asOf = typeof query.as_of === 'string' ? query.as_of : null
-      if (this.lookup.includeSuperseded.value !== includeSuperseded) this.lookup.includeSuperseded.value = includeSuperseded
+      if (this.lookup.includeSuperseded.value !== includeSuperseded)
+        this.lookup.includeSuperseded.value = includeSuperseded
       if ((this.lookup.asOf.value ?? null) !== asOf) this.lookup.asOf.value = asOf
     },
     'lookup.clingenAllele.alleleName.value'(name: string | undefined) {
diff --git a/src/components/variant/MvAlleleLedger.vue b/src/components/variant/MvAlleleLedger.vue
new file mode 100644
index 00000000..766e7499
--- /dev/null
+++ b/src/components/variant/MvAlleleLedger.vue
@@ -0,0 +1,232 @@
+<template>
+  <div>
+    <div class="mb-3 flex flex-wrap items-baseline gap-x-2">
+      <h3 class="mave-section-title !mb-0">Clinical &amp; population data</h3>
+      <span class="text-xs-minus text-text-muted">a property of the exact allele, shown at every level</span>
+    </div>
+
+    <!-- One uniform card per allele group. This variant (X) leads; the measured allele (Y) follows when the
+         selection assayed a different allele; the rest of the equivalence class collapses underneath. Every
+         card renders the same full clinical/population stat components — the only difference is the role
+         badge and emphasis. -->
+    <div class="flex flex-col gap-2">
+      <div
+        v-for="entry in entries"
+        v-show="entry.role !== 'other' || expanded"
+        :key="entry.group.key"
+        class="rounded-md px-3.5 py-3"
+        :class="cardClass(entry.role)"
+      >
+        <div class="mb-2 flex flex-wrap items-center gap-x-2 gap-y-1">
+          <span
+            v-key-term="entry.role === 'page' ? 'this-variant' : 'confidence'"
+            class="rounded-sm px-1.5 py-0.5 text-[10px] font-bold uppercase tracking-[0.3px]"
+            :class="roleBadge(entry).class"
+            >{{ roleBadge(entry).label }}</span
+          >
+          <span
+            v-key-term="'assay-level'"
+            class="inline-block rounded-sm px-1.5 py-0.5 text-[10px] font-semibold uppercase tracking-[0.3px]"
+            :class="levelClass(titleMember(entry.group)?.level)"
+            >{{ levelLabel(titleMember(entry.group)?.level) }}</span
+          >
+          <span class="font-mono text-xs-plus font-semibold text-text-primary" :title="allHgvsTitle(entry.group)">{{
+            titleMember(entry.group)?.hgvs || '—'
+          }}</span>
+          <!-- This variant (X) is the page you're already on — no link out. Related alleles link to their
+               own variant page. -->
+          <router-link
+            v-for="caid in entry.role === 'page' ? [] : entry.group.clingenLinks"
+            :key="caid"
+            class="ml-auto inline-flex items-center gap-0.5 font-mono text-xs font-semibold text-link hover:underline"
+            :to="{name: 'variant', params: {clingenAlleleId: caid}, query: variantUrn ? {variant: variantUrn} : {}}"
+          >
+            {{ caid }}<i class="pi pi-arrow-up-right text-xs" />
+          </router-link>
+        </div>
+
+        <div class="grid grid-cols-1 gap-x-8 gap-y-4 tablet:grid-cols-3">
+          <VariantConsequenceStat plain :vep="entry.group.coalescedAnnotations?.vep ?? null">
+            <template #label>
+              <span
+                v-key-term="'consequence'"
+                class="w-fit text-[10px] font-semibold uppercase tracking-[0.3px] text-[#aaa]"
+                >Molecular consequence</span
+              >
+            </template>
+          </VariantConsequenceStat>
+          <VariantGnomadStat
+            :alleles="alleles"
+            :annotations="annotations"
+            :assay-level="groupLevel(entry.group)"
+            :assay-level-digest="digestsOf(entry.group)"
+            plain
+            :show-underlying-popover="false"
+          >
+            <template #label>
+              <span
+                v-key-term="'population'"
+                class="w-fit text-[10px] font-semibold uppercase tracking-[0.3px] text-[#aaa]"
+                >Population frequency</span
+              >
+            </template>
+          </VariantGnomadStat>
+          <VariantClinvarStat
+            :alleles="alleles"
+            :annotations="annotations"
+            :assay-level="groupLevel(entry.group)"
+            :assay-level-digest="digestsOf(entry.group)"
+            :clinvar-version="clinvarVersion"
+            plain
+            :show-underlying-popover="false"
+          >
+            <template #label>
+              <span
+                v-key-term="'clinical'"
+                class="w-fit text-[10px] font-semibold uppercase tracking-[0.3px] text-[#aaa]"
+                >Clinical significance</span
+              >
+            </template>
+          </VariantClinvarStat>
+        </div>
+      </div>
+    </div>
+
+    <button
+      v-if="otherGroups.length"
+      class="mt-2 cursor-pointer border-none bg-transparent text-xs font-semibold text-link hover:underline"
+      type="button"
+      @click="expanded = !expanded"
+    >
+      {{
+        expanded
+          ? 'Hide other related alleles'
+          : `Show ${otherGroups.length} other related ${otherGroups.length === 1 ? 'allele' : 'alleles'}`
+      }}
+    </button>
+  </div>
+</template>
+
+<script lang="ts">
+import {defineComponent, type PropType} from 'vue'
+
+import VariantConsequenceStat from '@/components/variant/VariantConsequenceStat.vue'
+import VariantGnomadStat from '@/components/variant/VariantGnomadStat.vue'
+import VariantClinvarStat from '@/components/variant/VariantClinvarStat.vue'
+import {type AlleleGroup, type AlleleMember, confidenceBadge} from '@/lib/allele-grouping'
+import {assayLevelDisplay} from '@/lib/measurement-types'
+import type {components} from '@/schema/openapi'
+
+type AlleleAnnotations = components['schemas']['AlleleAnnotations']
+type AlleleIdentity = components['schemas']['AlleleIdentity']
+type SequenceLevel = components['schemas']['SequenceLevel']
+
+type LedgerRole = 'page' | 'measured' | 'other'
+type LedgerEntry = {group: AlleleGroup; role: LedgerRole}
+
+/**
+ * Combined clinical/population + related-alleles ledger. Presents the whole equivalence class in one
+ * place, at every level, with a *uniform* card per allele group: this variant (X) leads, the measured
+ * allele (Y) follows when the selection assayed a different allele, and the rest collapse underneath.
+ * Every card renders the same three-cell facts grid — molecular consequence, then
+ * {@link VariantGnomadStat}/{@link VariantClinvarStat} keyed to that group's own digests — mirroring
+ * {@link VariantDetailPanel}'s facts grid on the score-set page, so the only thing split out elsewhere on
+ * this page is the functional evidence itself.
+ */
+export default defineComponent({
+  name: 'MvAlleleLedger',
+
+  components: {
+    VariantConsequenceStat,
+    VariantGnomadStat,
+    VariantClinvarStat
+  },
+
+  props: {
+    // Every allele group in the selected measurement's equivalence class.
+    groups: {type: Array as PropType<AlleleGroup[]>, default: () => []},
+    // Raw alleles/annotations from the selected measurement detail — the stat components resolve each
+    // group's subject out of these maps by digest.
+    alleles: {type: Object as PropType<Record<string, AlleleIdentity>>, default: () => ({})},
+    annotations: {type: Object as PropType<Record<string, AlleleAnnotations>>, default: () => ({})},
+    clinvarVersion: {type: [String, null] as PropType<string | null>, default: null},
+    // The selected measurement's URN. Carried as the `?variant=` highlight on each allele's link-out.
+    variantUrn: {type: [String, null] as PropType<string | null>, default: null}
+  },
+
+  data() {
+    return {expanded: false}
+  },
+
+  computed: {
+    // The page allele's group (X) — pageRoot preferred, falling back to the measured/first group.
+    primaryGroup(): AlleleGroup | null {
+      return this.groups.find((g) => g.pageRoot) ?? this.groups.find((g) => g.measured) ?? this.groups[0] ?? null
+    },
+    // The measured allele's group (Y), only when it differs from X (otherwise the headline already is it).
+    pinnedMeasured(): AlleleGroup | null {
+      const measured = this.groups.find((g) => g.measured) ?? null
+      return measured && measured !== this.primaryGroup ? measured : null
+    },
+    // Everything that is neither the headline (X) nor the pinned measured allele (Y).
+    otherGroups(): AlleleGroup[] {
+      return this.groups.filter((g) => g !== this.primaryGroup && g !== this.pinnedMeasured)
+    },
+    // The ordered render list: X, then measured Y, then the rest (collapsed). Roles drive badge + emphasis.
+    entries(): LedgerEntry[] {
+      const list: LedgerEntry[] = []
+      if (this.primaryGroup) list.push({group: this.primaryGroup, role: 'page'})
+      if (this.pinnedMeasured) list.push({group: this.pinnedMeasured, role: 'measured'})
+      for (const g of this.otherGroups) list.push({group: g, role: 'other'})
+      return list
+    }
+  },
+
+  methods: {
+    digestsOf(group: AlleleGroup): string[] {
+      return group.members.map((m) => m.digest)
+    },
+    // The representative level for a group's stat resolution — the title member's level (cDNA-preferred).
+    groupLevel(group: AlleleGroup): SequenceLevel | null {
+      return (this.titleMember(group)?.level ?? null) as SequenceLevel | null
+    },
+    // The single member whose HGVS titles the card. A projection pair holds the same allele in two
+    // coordinate frames (genomic + cDNA). Lead with cDNA (community-preferred), then protein, then genomic.
+    titleMember(group: AlleleGroup): AlleleMember | null {
+      return (
+        group.members.find((m) => m.level === 'cdna') ??
+        group.members.find((m) => m.level === 'protein') ??
+        group.members[0] ??
+        null
+      )
+    },
+    allHgvsTitle(group: AlleleGroup): string {
+      return group.members.map((m) => `${this.levelLabel(m.level)}: ${m.hgvs || '—'}`).join('  ·  ')
+    },
+    // The page role gets its own fixed (teal "subject") badge, distinct from the green confidence axis and
+    // from every clinical-classification color — "This variant" (the page's own subject) and "This
+    // measurement" (what was actually assayed) are deliberately different colors so the two are never
+    // confused. Every other role (measured, resolved, convergent, candidate) reads its label/class off the shared
+    // confidence axis, so "This measurement" here is the same badge — and the same Key entry — as
+    // everywhere else in the app.
+    roleBadge(entry: LedgerEntry): {label: string; class: string} {
+      if (entry.role === 'page') return {label: 'This variant', class: 'bg-subject/15 text-subject'}
+      const badge = confidenceBadge(entry.group)
+      return badge
+        ? {label: badge.label, class: badge.class}
+        : {label: 'Related', class: 'bg-border-light text-text-muted'}
+    },
+    cardClass(role: LedgerRole): string {
+      if (role === 'page') return 'border-2 border-subject/40 bg-subject/[0.05]'
+      if (role === 'measured') return 'border border-sage/30 bg-sage/[0.03]'
+      return 'border border-border-light bg-surface'
+    },
+    levelLabel(level: string | null | undefined): string {
+      return level ? assayLevelDisplay(level).label : '—'
+    },
+    levelClass(level: string | null | undefined): string {
+      return level ? assayLevelDisplay(level).class : ''
+    }
+  }
+})
+</script>
diff --git a/src/components/variant/MvRelatedAlleles.vue b/src/components/variant/MvRelatedAlleles.vue
deleted file mode 100644
index 2b82b70f..00000000
--- a/src/components/variant/MvRelatedAlleles.vue
+++ /dev/null
@@ -1,147 +0,0 @@
-<template>
-  <div>
-    <div class="mb-1 flex flex-wrap items-baseline gap-x-2">
-      <span class="text-sm font-bold text-text-primary">Related alleles</span>
-      <span class="text-xs-minus text-text-muted">other variation sharing this variant's protein consequence</span>
-    </div>
-    <!-- Collapsed by default: these are additional context, secondary to the measured/selected allele shown in parallel. -->
-    <button
-      class="cursor-pointer border-none bg-transparent text-xs font-semibold text-link hover:underline"
-      type="button"
-      @click="expanded = !expanded"
-    >
-      {{
-        expanded
-          ? 'Hide related alleles'
-          : `Show ${groups.length} related ${groups.length === 1 ? 'allele' : 'alleles'}`
-      }}
-    </button>
-
-    <div v-if="expanded" class="mt-2 flex flex-col gap-2">
-      <div
-        v-for="group in groups"
-        :key="group.key"
-        class="rounded-md border border-border-light bg-surface px-3 py-2.5"
-      >
-        <!-- Confidence badge (Resolved/Candidate; a stray measured sibling still reads "Measured"). -->
-        <div class="mb-1.5 flex flex-wrap items-center gap-x-2 gap-y-1">
-          <span
-            v-if="confidenceBadge(group)"
-            v-key-term="'confidence'"
-            class="rounded-sm px-1.5 py-0.5 text-[10px] font-bold uppercase tracking-[0.3px]"
-            :class="confidenceBadge(group)!.class"
-            >{{ confidenceBadge(group)!.label }}</span
-          >
-          <router-link
-            v-for="caid in group.clingenLinks"
-            :key="caid"
-            class="ml-auto inline-flex items-center gap-0.5 font-mono text-xs font-semibold text-link hover:underline"
-            :to="{name: 'variant', params: {clingenAlleleId: caid}, query: variantUrn ? {variant: variantUrn} : {}}"
-          >
-            {{ caid }}<i class="pi pi-arrow-up-right text-xs" />
-          </router-link>
-        </div>
-
-        <!-- Identity: one line per level (a projection pair shows both), never the digest. -->
-        <div class="mb-1.5 flex flex-col gap-1">
-          <div v-for="m in group.members" :key="m.digest" class="flex flex-wrap items-center gap-x-2 gap-y-1">
-            <span
-              v-key-term="'assay-level'"
-              class="inline-block rounded-sm px-1.5 py-0.5 text-[10px] font-semibold uppercase tracking-[0.3px]"
-              :class="levelClass(m.level)"
-              >{{ levelLabel(m.level) }}</span
-            >
-            <span class="font-mono text-xs-plus font-semibold text-text-primary">{{ m.hgvs || '—' }}</span>
-          </div>
-        </div>
-
-        <!-- Annotations: one deduplicated block when the pair agrees, else per-level so divergence shows. -->
-        <div class="flex flex-col gap-1">
-          <div
-            v-if="!group.annotationsMatch"
-            class="text-[10px] font-semibold uppercase tracking-[0.3px] text-amber-600"
-          >
-            Annotations differ by level
-          </div>
-          <div v-for="line in annotationLines(group)" :key="line.label ?? 'shared'">
-            <div class="flex flex-col gap-0.5 text-xs-minus text-text-muted tablet:flex-row tablet:gap-5">
-              <span v-if="line.label" class="font-semibold text-[#aaa]">{{ line.label }}</span>
-              <span>
-                <span class="font-semibold text-[#aaa]">VEP:</span>
-                {{ line.annotations?.vep?.consequence ? formatConsequence(line.annotations.vep.consequence) : '—' }}
-              </span>
-              <span>
-                <span class="font-semibold text-[#aaa]">gnomAD:</span>
-                <template v-if="line.annotations?.gnomad">
-                  AF {{ formatFrequency(line.annotations.gnomad.alleleFrequency) }}</template
-                >
-                <template v-else> —</template>
-              </span>
-              <span>
-                <span class="font-semibold text-[#aaa]">ClinVar:</span>
-                <template v-if="latestClinvar(line.annotations)"
-                  >&nbsp;{{ formatClinicalSignificance(latestClinvar(line.annotations)!.clinicalSignificance) }}</template
-                >
-                <template v-else> —</template>
-              </span>
-            </div>
-          </div>
-        </div>
-      </div>
-    </div>
-  </div>
-</template>
-
-<script lang="ts">
-import {defineComponent, type PropType} from 'vue'
-
-import {type AlleleGroup, confidenceBadge} from '@/lib/allele-grouping'
-import {formatClinicalSignificance, latestClinvar} from '@/lib/clinvar-controls'
-import {formatConsequence} from '@/lib/formats'
-import {formatFrequency} from '@/lib/gnomad'
-import {assayLevelDisplay} from '@/lib/measurement-types'
-import type {components} from '@/schema/openapi'
-
-type AlleleAnnotations = components['schemas']['AlleleAnnotations']
-
-/**
- * Subordinate "Related alleles" panel: the sibling allele groups (everything that is not the page's
- * primary/selected allele — those are promoted into the evidence panel above). Collapsed by default and
- * visually lighter, so they read as context rather than co-equal evidence. Grouping is done by the
- * parent ({@link groupAlleles}); this component only renders the groups it is handed.
- */
-export default defineComponent({
-  name: 'MvRelatedAlleles',
-
-  props: {
-    // Sibling allele groups (pre-grouped and filtered by the parent).
-    groups: {type: Array as PropType<AlleleGroup[]>, default: () => []},
-    // The selected measurement's URN. Carried as the `?variant=` highlight on each group's link-out.
-    variantUrn: {type: [String, null] as PropType<string | null>, default: null}
-  },
-
-  data() {
-    return {expanded: false}
-  },
-
-  methods: {
-    formatConsequence,
-    formatFrequency,
-    latestClinvar,
-    formatClinicalSignificance,
-    confidenceBadge,
-    // The annotation blocks to render: one coalesced block (present-wins union across levels) when there
-    // is no real divergence, else one per level so an actual present-vs-present disagreement shows.
-    annotationLines(group: AlleleGroup): Array<{label: string | null; annotations: AlleleAnnotations | null}> {
-      if (group.annotationsMatch) return [{label: null, annotations: group.coalescedAnnotations}]
-      return group.members.map((m) => ({label: this.levelLabel(m.level), annotations: m.annotations}))
-    },
-    levelLabel(level: string | null | undefined): string {
-      return level ? assayLevelDisplay(level).label : '—'
-    },
-    levelClass(level: string | null | undefined): string {
-      return assayLevelDisplay(level).class
-    }
-  }
-})
-</script>
diff --git a/src/components/variant/VariantClinvarStat.vue b/src/components/variant/VariantClinvarStat.vue
index aaa54279..a07f8511 100644
--- a/src/components/variant/VariantClinvarStat.vue
+++ b/src/components/variant/VariantClinvarStat.vue
@@ -1,6 +1,6 @@
 <template>
   <div :class="plain ? 'flex h-full flex-col gap-0.5' : 'stat'">
-    <!-- Label defaults to the score-set stat label; callers (e.g. the variant screen) inject their own. -->
+    <!-- Label defaults to the score-set stat label; callers (e.g. the variant screen) may inject their own. -->
     <slot name="label"><span v-key-term="'clinical'" class="stat-label">ClinVar</span></slot>
     <!-- Hard discordance: related variants carry both pathogenic and benign calls — no single call to show. -->
     <span v-if="headline.kind === 'conflicting'" class="stat-value text-sm font-semibold">
@@ -36,12 +36,33 @@
     </span>
     <span v-else class="stat-value">—</span>
 
-    <!-- Related-allele records offered as context: beside a direct call (records that did not drive it),
-         beneath a projected call (the siblings it folded over), or under an `absent` headline. -->
-    <template v-if="underlyingClinvar.length">
-      <button class="mt-auto text-left text-xs text-link hover:underline" type="button" @click="toggleClinvarPopover">
-        {{ underlyingClinvar.length }}
-        {{ underlyingLabel }}
+    <!-- Related-allele records. For a projected headline this control doubles as a caveat about the projections provenance.
+         It states the headline is inferred, not a direct assertion on this variant, and opens the records it was pooled from. 
+         For a non-projected headline it's pure context (records that did not drive the call), and a caller can suppress it 
+         for a *direct* headline where those alleles are already laid out elsewhere (e.g. MvAlleleLedger). -->
+    <template v-if="underlyingClinvar.length && (showUnderlyingPopover || isProjectedHeadline)">
+      <button
+        class="text-xs text-link"
+        :class="
+          isProjectedHeadline
+            ? 'mt-auto flex items-center gap-1 italic underline-offset-2'
+            : 'mt-auto text-left hover:underline'
+        "
+        type="button"
+        @click="toggleClinvarPopover"
+      >
+        <template v-if="isProjectedHeadline">
+          <i class="pi pi-info-circle shrink-0 !text-xs not-italic" />
+          <span class="underline decoration-dotted"
+            >inferred from {{ underlyingClinvar.length }} related
+            {{ underlyingClinvar.length === 1 ? 'variant' : 'variants' }}</span
+          >
+        </template>
+        <template v-else
+          ><span class="underline decoration-dotted"
+            >{{ underlyingClinvar.length }} {{ underlyingLabel }}</span
+          ></template
+        >
       </button>
       <Popover ref="clinvarPopoverRef">
         <div class="flex max-w-xs flex-col gap-2">
@@ -116,7 +137,12 @@ export default defineComponent({
     assayLevel: {type: String as PropType<SequenceLevel | null>, default: null},
     // The ClinVar release to reduce over (raw `MM_YYYY`), so this cell agrees with all parents.
     // `null` (store not ready / no controls) → fall back to the latest release per allele.
-    clinvarVersion: {type: String as PropType<string | null>, default: null}
+    clinvarVersion: {type: String as PropType<string | null>, default: null},
+    // Hide the "N related record(s)" popover for a *direct* (non-projected) headline — for callers (e.g. the
+    // MvAlleleLedger) that already lay those alleles out as their own cards, where the popover would just
+    // restate what's one click away. Note that this prop has no effect on projected/pooled headlines. This
+    // popover is essential provenance for projected headlines.
+    showUnderlyingPopover: {type: Boolean, default: true}
   },
 
   computed: {
@@ -133,11 +159,14 @@ export default defineComponent({
     underlyingClinvar(): MeasurementClinvarRecord[] {
       return enumerateUnderlyingClinvar(this.records)
     },
-    // True when the headline is a projected call — the representative is a related allele, and the context
-    // records below are the siblings it folded over (protein level). Otherwise the context records are just
-    // that: related records that did not drive a direct call (or an `absent` headline).
+    // True when the headline (a usable call, or a hard-discordant "Conflicting") was pooled from related
+    // alleles rather than read off the subject's own record — the context records below are exactly the
+    // siblings that were pooled. Otherwise the context records are just that: related records that did
+    // not drive a direct call (or an `absent` headline).
     isProjectedHeadline(): boolean {
-      return this.headline.kind === 'call' && this.headline.placement.projected
+      if (this.headline.kind === 'call') return this.headline.placement.projected
+      if (this.headline.kind === 'conflicting') return this.headline.placement.projected
+      return false
     },
     // The headline record links inline only when it *is* the measured allele's own record — a direct call or
     // the measured allele's `-` presence. A projected call's links live in the context popover.
@@ -147,14 +176,14 @@ export default defineComponent({
       if (h.kind === 'presence') return h.record.onAssayed
       return false
     },
+    // Only the non-projected (context) trigger uses this — the projected trigger writes its own caveat copy.
     underlyingLabel(): string {
-      const noun = this.isProjectedHeadline ? 'underlying record' : 'related record'
-      return this.underlyingClinvar.length === 1 ? noun : `${noun}s`
+      return this.underlyingClinvar.length === 1 ? 'related record' : 'related records'
     },
     underlyingClinvarNote(): string {
       return this.isProjectedHeadline
-        ? "ClinVar records for variants with this allele's protein consequence. Open each in ClinVar to view its full classification."
-        : 'Other variants with the same protein consequence that also carry ClinVar records. Open each in ClinVar for its full classification.'
+        ? 'This variant has no ClinVar record. The classification above is pooled from these nucleotide variants that encode the same protein change and does not represent a ClinVar assertion for this variant.'
+        : 'Other variants with the same protein consequence that also carry ClinVar records.'
     }
   },
 
diff --git a/src/components/variant/VariantConsequenceStat.vue b/src/components/variant/VariantConsequenceStat.vue
new file mode 100644
index 00000000..646981b3
--- /dev/null
+++ b/src/components/variant/VariantConsequenceStat.vue
@@ -0,0 +1,75 @@
+<template>
+  <div :class="plain ? 'flex h-full flex-col gap-0.5' : 'stat'">
+    <!-- Label defaults to the score-set stat label; callers (e.g. MvAlleleLedger) may inject their own,
+         mirroring VariantGnomadStat/VariantClinvarStat. -->
+    <slot name="label"><span v-key-term="'consequence'" class="stat-label">Molecular consequence</span></slot>
+    <template v-if="consequence">
+      <span class="stat-value font-semibold">{{ formatConsequence(consequence) }}</span>
+      <span v-if="sourceVersion" class="mt-auto text-[10px] text-text-muted"
+        >As of VEP version {{ sourceVersion }}</span
+      >
+    </template>
+    <span v-else class="stat-value">—</span>
+  </div>
+</template>
+
+<script lang="ts">
+import {defineComponent, type PropType} from 'vue'
+
+import {formatConsequence} from '@/lib/formats'
+import type {components} from '@/schema/openapi'
+
+type AlleleAnnotations = components['schemas']['AlleleAnnotations']
+
+/**
+ * The molecular-consequence stat cell — the VEP consequence and the Ensembl/VEP release it resolved under.
+ * Shares the facts-grid `.stat` chrome with {@link VariantGnomadStat}/{@link VariantClinvarStat}; `plain`
+ * drops it so the ledger can supply its own wrapper + `#label` slot.
+ */
+export default defineComponent({
+  name: 'VariantConsequenceStat',
+
+  props: {
+    // Drop the score-set `.stat` chrome (bg/padding) so the cell can embed on its own (e.g. the allele
+    // ledger), where the caller supplies the wrapper and a `#label` slot.
+    plain: {type: Boolean, default: false},
+    // The subject's coalesced VEP annotation (consequence + sourceVersion), or null when absent.
+    vep: {type: Object as PropType<AlleleAnnotations['vep'] | null>, default: null}
+  },
+
+  computed: {
+    consequence(): string | null {
+      return this.vep?.consequence ?? null
+    },
+    sourceVersion(): string | null {
+      return this.vep?.sourceVersion ?? null
+    }
+  },
+
+  methods: {formatConsequence}
+})
+</script>
+
+<style scoped>
+/* Matches the panel's facts grid (see VariantDetailPanel), mirroring VariantGnomadStat/VariantClinvarStat. */
+.stat {
+  display: flex;
+  flex-direction: column;
+  gap: 3px;
+  background: var(--color-surface);
+  padding: 10px 14px;
+}
+
+.stat-label {
+  font-size: 10px;
+  font-weight: 700;
+  text-transform: uppercase;
+  letter-spacing: 0.5px;
+  color: var(--color-text-muted);
+}
+
+.stat-value {
+  font-size: 0.875rem;
+  color: var(--color-text-primary);
+}
+</style>
diff --git a/src/components/variant/VariantDetailPanel.vue b/src/components/variant/VariantDetailPanel.vue
index e19f322e..8672c0ed 100644
--- a/src/components/variant/VariantDetailPanel.vue
+++ b/src/components/variant/VariantDetailPanel.vue
@@ -37,16 +37,7 @@
         v-if="anyAnnotationsAvailable"
         class="grid grid-cols-2 gap-px border-t border-border-light bg-border-light tablet:grid-cols-4"
       >
-        <div class="stat">
-          <span v-key-term="'consequence'" class="stat-label">Molecular consequence</span>
-          <template v-if="consequence?.consequence">
-            <span class="stat-value font-semibold">{{ formatToken(consequence.consequence) }}</span>
-            <span class="mt-auto text-[10px] text-text-muted">
-              As of VEP version {{ consequence?.sourceVersion ?? '—' }}</span
-            >
-          </template>
-          <span v-else class="stat-value font-semibold">—</span>
-        </div>
+        <VariantConsequenceStat :vep="consequence" />
         <div class="stat">
           <span v-key-term="'functional-impact'" class="stat-label">Classification</span>
           <span v-if="selectedClassification" class="flex flex-wrap items-center gap-1.5">
@@ -115,6 +106,7 @@ import {defineComponent, type PropType} from 'vue'
 
 import MvEvidenceTag from '@/components/common/MvEvidenceTag.vue'
 import MvLoader from '@/components/common/MvLoader.vue'
+import VariantConsequenceStat from '@/components/variant/VariantConsequenceStat.vue'
 import VariantGnomadStat from '@/components/variant/VariantGnomadStat.vue'
 import VariantClinvarStat from '@/components/variant/VariantClinvarStat.vue'
 import {getVariantDetail} from '@/api/mavedb/variants'
@@ -130,7 +122,7 @@ type AlleleAnnotations = components['schemas']['AlleleAnnotations']
 /**
  * Compact selected-variant summary for the score-set page, consuming `GET /variants/{urn}`.
  *
- * Deliberately lean: assay-level facts (identity, consequence, the selected calibration's classification)
+ * Deliberately lean: assay-level facts (identity, consequence {@link VariantConsequenceStat}, the selected calibration's classification)
  * plus two annotation cells that reach past the assayed allele — {@link VariantGnomadStat} and
  * {@link VariantClinvarStat}. These each own their own presentation and their fold/enumeration wiring to sibling
  * alleles.
@@ -141,7 +133,7 @@ type AlleleAnnotations = components['schemas']['AlleleAnnotations']
 export default defineComponent({
   name: 'VariantDetailPanel',
 
-  components: {MvEvidenceTag, MvLoader, VariantGnomadStat, VariantClinvarStat},
+  components: {MvEvidenceTag, MvLoader, VariantConsequenceStat, VariantGnomadStat, VariantClinvarStat},
 
   props: {
     urn: {type: String, required: true},
@@ -219,7 +211,11 @@ export default defineComponent({
         this.detail?.assayLevelDigest ?? null,
         this.clinvarVersion
       )
-      const headline = resolveClinvarHeadline(records, this.detail?.assayLevelDigest ?? null, this.detail?.assayLevel ?? null)
+      const headline = resolveClinvarHeadline(
+        records,
+        this.detail?.assayLevelDigest ?? null,
+        this.detail?.assayLevel ?? null
+      )
       return headline.kind !== 'none' || enumerateUnderlyingClinvar(records).length > 0
     },
     // The facts grid only earns its place when a cell resolves; otherwise it's four dashes (clutter), and the
diff --git a/src/components/variant/VariantGnomadStat.vue b/src/components/variant/VariantGnomadStat.vue
index 483f10e5..5722b8aa 100644
--- a/src/components/variant/VariantGnomadStat.vue
+++ b/src/components/variant/VariantGnomadStat.vue
@@ -16,12 +16,33 @@
     </span>
     <span v-else class="stat-value">—</span>
 
-    <!-- Related-allele frequencies as context: the encoding variants behind an enumerated headline, or
-         other same-consequence variants' frequencies beside a direct/absent headline. -->
-    <template v-if="underlyingGnomad.length">
-      <button class="mt-auto text-left text-xs text-link hover:underline" type="button" @click="toggleGnomadPopover">
-        {{ underlyingGnomad.length }}
-        {{ underlyingLabel }}
+    <!-- Related-allele records. For a projected headline this control doubles as a caveat about the projections provenance.
+         It states the headline is inferred, not a direct assertion on this variant, and opens the records it was pooled from. 
+         For a non-projected headline it's pure context (records that did not drive the call), and a caller can suppress it 
+         for a *direct* headline where those alleles are already laid out elsewhere (e.g. MvAlleleLedger). -->
+    <template v-if="underlyingGnomad.length && (showUnderlyingPopover || headlineState === 'enumerated')">
+      <button
+        class="text-xs text-link"
+        :class="
+          headlineState === 'enumerated'
+            ? 'mt-auto flex items-center gap-1 italic underline-offset-2'
+            : 'mt-auto text-left hover:underline'
+        "
+        type="button"
+        @click="toggleGnomadPopover"
+      >
+        <template v-if="headlineState === 'enumerated'">
+          <i class="pi pi-info-circle shrink-0 !text-xs not-italic" />
+          <span class="underline decoration-dotted"
+            >pooled from {{ underlyingGnomad.length }} related
+            {{ underlyingGnomad.length === 1 ? 'variant' : 'variants' }}</span
+          >
+        </template>
+        <template v-else
+          ><span class="underline decoration-dotted"
+            >{{ underlyingGnomad.length }} {{ underlyingLabel }}</span
+          ></template
+        >
       </button>
       <Popover ref="gnomadPopoverRef">
         <div class="flex max-w-xs flex-col gap-2">
@@ -83,7 +104,11 @@ export default defineComponent({
     assayLevelDigest: {type: [String, Array] as PropType<SubjectDigest>, default: null},
     // The subject allele's sequence level. Gates the enumeration: at nucleotide level a missing frequency
     // stays explicit ('absent') rather than borrowing related variants'. `null` → enumerate (unknown).
-    assayLevel: {type: String as PropType<SequenceLevel | null>, default: null}
+    assayLevel: {type: String as PropType<SequenceLevel | null>, default: null},
+    // Hide the "N related frequencies" popover for a direct/absent headline — for callers (e.g. MvAlleleLedger)
+    // that already lay those alleles out as their own cards. An enumerated (pooled) headline always
+    // shows its popover regardless as it is essential provenance for the pooled number.
+    showUnderlyingPopover: {type: Boolean, default: true}
   },
 
   computed: {
@@ -107,9 +132,9 @@ export default defineComponent({
     underlyingGnomadMaxAf(): number | null {
       return this.underlyingGnomad[0]?.gnomad.alleleFrequency ?? null
     },
+    // Only the non-enumerated (context) trigger uses this — the enumerated trigger writes its own caveat copy.
     underlyingLabel(): string {
-      const kind = this.headlineState === 'enumerated' ? 'underlying' : 'related'
-      return `${kind} ${this.underlyingGnomad.length === 1 ? 'frequency' : 'frequencies'}`
+      return `related ${this.underlyingGnomad.length === 1 ? 'frequency' : 'frequencies'}`
     },
     underlyingGnomadNote(): string {
       if (this.headlineState === 'enumerated') {
diff --git a/src/components/variant/VariantInfoSection.vue b/src/components/variant/VariantInfoSection.vue
deleted file mode 100644
index aa7da2d4..00000000
--- a/src/components/variant/VariantInfoSection.vue
+++ /dev/null
@@ -1,70 +0,0 @@
-<template>
-  <div>
-    <h3 class="mave-section-title">Variant Information</h3>
-    <MvDetailRow label="ClinGen allele name" :value="alleleName" />
-    <MvDetailRow label="ClinGen allele ID">
-      <a
-        v-if="clingenAlleleId"
-        class="text-link"
-        :href="`https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_canonicalid?canonicalid=${clingenAlleleId}`"
-        target="_blank"
-        >{{ clingenAlleleId }}</a
-      >
-    </MvDetailRow>
-    <MvDetailRow :label="`ClinVar allele ${clinvarAlleleIds.length > 1 ? 'IDs' : 'ID'}`">
-      <template v-for="(cvId, i) in clinvarAlleleIds" :key="cvId">
-        <a class="text-link" :href="clinvarVariantUrl({clinvarAlleleId: cvId}) ?? undefined" target="_blank">{{
-          cvId
-        }}</a>
-        <template v-if="i < clinvarAlleleIds.length - 1">, </template>
-      </template>
-      <template v-if="clinvarAlleleIds.length === 0"><span class="text-text-muted">—</span></template>
-    </MvDetailRow>
-    <MvDetailRow label="Molecular consequence" term="consequence">
-      <span v-if="molecularConsequence">{{ formatConsequence(molecularConsequence) }}</span>
-      <span v-else class="italic text-text-muted">—</span>
-    </MvDetailRow>
-    <MvDetailRow :align="'flex-start'" :label="`Genomic ${genomicLocations.length > 1 ? 'locations' : 'location'}`">
-      <table v-if="genomicLocations.length > 0" class="border-collapse">
-        <tr v-for="(loc, i) in genomicLocations" :key="i">
-          <td class="py-px pr-2.5 text-xs-plus font-mono font-semibold">
-            chr{{ loc.chromosome }}:{{ Number(loc.start).toLocaleString() }}
-          </td>
-          <td>&nbsp;</td>
-          <td class="py-px text-xs text-text-muted">({{ loc.referenceGenome }})</td>
-        </tr>
-      </table>
-    </MvDetailRow>
-  </div>
-</template>
-
-<script lang="ts">
-import {defineComponent, type PropType} from 'vue'
-
-import MvDetailRow from '@/components/common/MvDetailRow.vue'
-import {clinvarVariantUrl} from '@/lib/clinvar-controls'
-import {formatConsequence} from '@/lib/formats'
-
-type GenomicLocation = {chromosome: string; start: string | number; referenceGenome: string}
-
-export default defineComponent({
-  name: 'VariantInfoSection',
-
-  components: {
-    MvDetailRow
-  },
-
-  props: {
-    alleleName: {type: [String, null] as PropType<string | null>, default: null},
-    clingenAlleleId: {type: [String, null] as PropType<string | null>, default: null},
-    clinvarAlleleIds: {type: Array as PropType<string[]>, default: () => []},
-    molecularConsequence: {type: [String, null] as PropType<string | null>, default: null},
-    genomicLocations: {type: Array as PropType<GenomicLocation[]>, default: () => []}
-  },
-
-  methods: {
-    clinvarVariantUrl,
-    formatConsequence
-  }
-})
-</script>
diff --git a/src/composables/use-clingen-allele.ts b/src/composables/use-clingen-allele.ts
index ab28058d..537bdd68 100644
--- a/src/composables/use-clingen-allele.ts
+++ b/src/composables/use-clingen-allele.ts
@@ -12,7 +12,7 @@ export interface GenomicLocation {
 export interface UseClingenAlleleReturn {
   allele: Ref<ClinGenAllele | undefined>
   alleleName: ComputedRef<string | undefined>
-  genomicLocationText: ComputedRef<string | null>
+  allGenomicLocationsText: ComputedRef<string | null>
   genomicLocations: ComputedRef<GenomicLocation[]>
   clinvarAlleleIds: ComputedRef<string[]>
   fetchAllele: () => Promise<void>
@@ -54,21 +54,21 @@ export function useClingenAllele(clingenAlleleId: Ref<string>): UseClingenAllele
       }))
   )
 
-  const genomicLocationText = computed(() => {
+  // Every mapped reference-genome build a variant mapped to.
+  const allGenomicLocationsText = computed(() => {
     const locs = genomicLocations.value
     if (locs.length === 0) return null
-    const loc = locs[0]
-    return `chr${loc.chromosome}:${Number(loc.start).toLocaleString()} (${loc.referenceGenome})`
+    return locs
+      .map((loc) => `chr${loc.chromosome}:${Number(loc.start).toLocaleString()} (${loc.referenceGenome})`)
+      .join(', ')
   })
 
-  const clinvarAlleleIds = computed(() =>
-    (allele.value?.externalRecords?.ClinVarAlleles || []).map((a) => a.alleleId)
-  )
+  const clinvarAlleleIds = computed(() => (allele.value?.externalRecords?.ClinVarAlleles || []).map((a) => a.alleleId))
 
   return {
     allele,
     alleleName,
-    genomicLocationText,
+    allGenomicLocationsText,
     genomicLocations,
     clinvarAlleleIds,
     fetchAllele
diff --git a/src/lib/clingen.ts b/src/lib/clingen.ts
new file mode 100644
index 00000000..13fbb774
--- /dev/null
+++ b/src/lib/clingen.ts
@@ -0,0 +1,10 @@
+export const clingenAlleleRegistryUrl = 'https://reg.clinicalgenome.org'
+export const clingenAlleleRegistryCanonicalIdUrl = `${clingenAlleleRegistryUrl}/redmine/projects/registry/genboree_registry/by_canonicalid?canonicalid=`
+
+export function clingenAlleleUrl(clingenAlleleId: string): string {
+  return `${clingenAlleleRegistryUrl}/allele/${clingenAlleleId}`
+}
+
+export function clingenAlleleUrlFromCanonicalId(canonicalId: string): string {
+  return `${clingenAlleleRegistryCanonicalIdUrl}${canonicalId}`
+}

From 07cd85fcdb7285a463508a57f1825962a25803d6 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 23 Jul 2026 18:53:06 -0700
Subject: [PATCH 67/84] fix(key-drawer): scroll to active term when drawer is
 already open

The `isOpen` watcher only re-fires on open/close transitions, so
clicking a badge while the drawer stays open updated `activeTerm`
without scrolling to it. Watch `activeTerm` directly and scroll
whenever the drawer is open.
---
 src/components/common/MvKeyDrawer.vue | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/components/common/MvKeyDrawer.vue b/src/components/common/MvKeyDrawer.vue
index 4d567d3b..bcd7fc29 100644
--- a/src/components/common/MvKeyDrawer.vue
+++ b/src/components/common/MvKeyDrawer.vue
@@ -100,6 +100,12 @@ export default defineComponent({
       } else {
         window.removeEventListener('keydown', this.onKeydown)
       }
+    },
+    // A badge click while the drawer is already open only changes `activeTerm` and the `isOpen`
+    // watcher above never re-fires. Watch active term as well so we can scroll to it even when
+    // the drawer is already open.
+    'drawer.activeTerm.value'() {
+      if (this.drawer.isOpen.value) void this.scrollToActiveTerm()
     }
   },
 

From e4bb4ec5e76c6a9c5f8a874e65cf52a7f25f86e9 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 23 Jul 2026 19:07:59 -0700
Subject: [PATCH 68/84] fix(SearchVariantsScreen): fix query parameter name
 from variantUrn to variant

---
 src/components/screens/SearchVariantsScreen.vue | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/components/screens/SearchVariantsScreen.vue b/src/components/screens/SearchVariantsScreen.vue
index 9719c355..44abbbd4 100644
--- a/src/components/screens/SearchVariantsScreen.vue
+++ b/src/components/screens/SearchVariantsScreen.vue
@@ -434,7 +434,7 @@
               :to="{
                 name: 'scoreSet',
                 params: {urn: scoreSetUrnFromVariantUrn(allele.variantUrn)},
-                query: {variantUrn: allele.variantUrn}
+                query: {variant: allele.variantUrn}
               }"
             >
               View score set &rarr;

From 1d4a3d588b09091436a1a5d86a27646f1f51bf89 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 23 Jul 2026 20:22:27 -0700
Subject: [PATCH 69/84] refactor(glossary): tighten Key drawer definitions for
 clarity and precision

Cuts redundant restatement (e.g. Convergent said the same thing twice
in different words) and fixes a couple of dangling clauses. Also
corrects the evidence-strength ladder, which only listed 4 of the 5
schema tiers (MODERATE_PLUS was missing despite being a live badge
value).
---
 src/lib/acmg.ts            | 5 ++++-
 src/lib/allele-grouping.ts | 8 ++++----
 src/lib/gnomad.ts          | 4 ++--
 3 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/src/lib/acmg.ts b/src/lib/acmg.ts
index f8e1cbde..a5129ce7 100644
--- a/src/lib/acmg.ts
+++ b/src/lib/acmg.ts
@@ -50,7 +50,10 @@ export const ACMG_KEY_SECTION: KeySection = {
   gloss: 'How the functional result maps onto clinical-classification evidence.',
   terms: [
     ...Object.values(ACMG_CRITERIA),
-    {label: 'Evidence strength', definition: 'How much weight the evidence carries: supporting → moderate → strong → very strong.'},
+    {
+      label: 'Evidence strength',
+      definition: 'How much weight the evidence carries: supporting → moderate → moderate+ → strong → very strong.'
+    },
     {label: 'OddsPath', definition: 'The odds of pathogenicity implied by the score; sets the evidence strength.'}
   ]
 }
diff --git a/src/lib/allele-grouping.ts b/src/lib/allele-grouping.ts
index cafae9b7..a26f6bc1 100644
--- a/src/lib/allele-grouping.ts
+++ b/src/lib/allele-grouping.ts
@@ -68,24 +68,24 @@ export const ALLELE_CONFIDENCE: Record<string, ConfidenceBadge> = {
   measured: {
     label: 'This measurement',
     class: 'bg-sage/15 text-sage',
-    definition: 'An allele that was directly measured in this assay.'
+    definition: 'Directly measured in this assay.'
   },
   projection: {
     label: 'Resolved',
     class: 'bg-resolved-light text-resolved',
-    definition: 'Derived from the measured allele — the same change expressed at another coordinate level.'
+    definition: 'Derived from the measured allele. The same change expressed at an un-measured coordinate level.'
   },
   convergent: {
     label: 'Convergent',
     class: 'bg-synonymous-nucleotide-light text-synonymous-nucleotide',
     definition:
-      'A distinct nucleotide change that produces the same protein change as the measured variant — a separate variant that converges on the same consequence, not the one assayed here.'
+      'A different nucleotide change than what was measured, which happens to produce the same protein change as the measured variant.'
   },
   candidate: {
     label: 'Candidate',
     class: 'bg-synonymous-nucleotide-light text-synonymous-nucleotide',
     definition:
-      'A possible nucleotide change behind a protein-level measurement — one of several synonymous codons; which was actually assayed is unknown.'
+      'A possible nucleotide change encoding a protein-level measurement. This variant is one of several synonymous codons. The assay did not report which one was measured.'
   }
 }
 
diff --git a/src/lib/gnomad.ts b/src/lib/gnomad.ts
index 794521e1..77602b8f 100644
--- a/src/lib/gnomad.ts
+++ b/src/lib/gnomad.ts
@@ -22,12 +22,12 @@ export const POPULATION_KEY_SECTION: KeySection = {
     {
       label: 'Allele frequency (AF)',
       definition:
-        'The fraction of sampled reference-population chromosomes carrying this allele in gnomAD (allele count ÷ allele number).'
+        "The fraction of gnomAD's sampled reference-population chromosomes that carry this allele (allele count ÷ allele number)."
     },
     {
       label: 'AC / AN',
       definition:
-        'Allele count and allele number: the observed carriers and the total chromosomes sampled that the frequency is computed from.'
+        'Allele count and allele number: the observed carriers and the total chromosomes sampled. The two inputs behind the frequency above.'
     },
     {
       label: 'FAF95',

From 2c2c8b52fee18ce985a0b797d43f9dfb0397cc1d Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 23 Jul 2026 20:23:51 -0700
Subject: [PATCH 70/84] refactor(glossary): merge duplicate "this variant"
 concept, reorder drawer
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

The allele ledger's page-role badge and a measurement's direct-
relationship badge were two names for the same fact (both use the
subject color) — collapse them onto one shared definition instead of
each carrying their own. Moves "This variant" to lead the drawer so
"Relationship to this variant" reads naturally right after it, and
routes MvMeasurementCard's direct-relationship badge to the
"this-variant" deep link (matching MvAlleleLedger's existing pattern)
instead of a "relationship" section that no longer defines it.
---
 src/components/variant/MvMeasurementCard.vue |  2 +-
 src/glossary.ts                              |  2 +-
 src/lib/glossary-prose.ts                    |  8 +++++++-
 src/lib/measurement-types.ts                 | 11 +++++++----
 4 files changed, 16 insertions(+), 7 deletions(-)

diff --git a/src/components/variant/MvMeasurementCard.vue b/src/components/variant/MvMeasurementCard.vue
index e1901d3b..d21bd17f 100644
--- a/src/components/variant/MvMeasurementCard.vue
+++ b/src/components/variant/MvMeasurementCard.vue
@@ -20,7 +20,7 @@
         {{ levelLabel }}
       </span>
       <span
-        v-key-term="'relationship'"
+        v-key-term="relationship === 'direct' ? 'this-variant' : 'relationship'"
         class="inline-block rounded-sm px-2 py-0.5 text-[10px] font-semibold uppercase tracking-[0.3px]"
         :class="relationshipClass"
       >
diff --git a/src/glossary.ts b/src/glossary.ts
index a3228bdd..ae837874 100644
--- a/src/glossary.ts
+++ b/src/glossary.ts
@@ -12,10 +12,10 @@ import {ASSAY_LEVEL_KEY_SECTION, RELATIONSHIP_KEY_SECTION} from '@/lib/measureme
 export const GLOSSARY_DOCS_URL = `${config.appBaseUrl}/docs/mavedb/getting-started/key-concepts.html`
 
 export const GLOSSARY_SECTIONS: KeySection[] = [
+  THIS_VARIANT_KEY_SECTION,
   RELATIONSHIP_KEY_SECTION,
   ASSAY_LEVEL_KEY_SECTION,
   CONFIDENCE_KEY_SECTION,
-  THIS_VARIANT_KEY_SECTION,
   COORDINATE_FRAME_KEY_SECTION,
   CONSEQUENCE_KEY_SECTION,
   FUNCTIONAL_IMPACT_KEY_SECTION,
diff --git a/src/lib/glossary-prose.ts b/src/lib/glossary-prose.ts
index f2ee18d9..e88e845d 100644
--- a/src/lib/glossary-prose.ts
+++ b/src/lib/glossary-prose.ts
@@ -1,12 +1,18 @@
 import type {KeySection} from '@/composables/use-key-drawer'
 
+// Single source for the "This variant" concept — the page's own subject allele — wherever it's badged:
+// the allele ledger's page-role entry (MvAlleleLedger) and a measurement's direct-relationship badge
+// (MvMeasurementCard) are the same fact from two objects, so they share this one definition rather than
+// each carrying their own. Leads GLOSSARY_SECTIONS (glossary.ts): establishing the subject first lets
+// "Relationship to this variant" read naturally right after it — how other results relate to the thing
+// this section just defined.
 export const THIS_VARIANT_KEY_SECTION: KeySection = {
   id: 'this-variant',
   title: 'This variant',
   terms: [
     {
       label: 'This variant',
-      definition: 'The allele this page is anchored on — the ClinGen allele you navigated to.',
+      definition: 'The ClinGen allele this page is anchored on.',
       class: 'bg-subject/15 text-subject'
     }
   ]
diff --git a/src/lib/measurement-types.ts b/src/lib/measurement-types.ts
index 73759194..04e2ef22 100644
--- a/src/lib/measurement-types.ts
+++ b/src/lib/measurement-types.ts
@@ -18,11 +18,12 @@ export function assayLevelBucket(level: string | null | undefined): LevelBucket
  * card label, an optional chip class, and the Key-drawer gloss. Phrased relative to the page's own variant
  * so the labels self-explain under the "relative to this variant" anchor. Insertion order is display order.
  */
-export const RELATIONSHIPS: Record<MeasurementRelationship, {label: string; class?: string; definition: string}> = {
+export const RELATIONSHIPS: Record<MeasurementRelationship, {label: string; class?: string; definition?: string}> = {
+  // No `definition`: a direct result is the page's own subject allele — the same concept as the Key
+  // drawer's "This variant" section (glossary-prose.ts), defined once there rather than twice.
   direct: {
     label: 'This variant',
-    class: 'bg-subject/15 text-subject',
-    definition: 'The result assayed exactly the allele you searched.'
+    class: 'bg-subject/15 text-subject'
   },
   protein_consequence: {
     label: 'Its protein consequence',
@@ -38,7 +39,9 @@ export const RELATIONSHIP_KEY_SECTION: KeySection = {
   id: 'relationship',
   title: 'Relationship to this variant',
   gloss: 'How each result relates to the allele you searched.',
-  terms: Object.values(RELATIONSHIPS).map((r) => ({label: r.label, definition: r.definition, class: r.class}))
+  terms: Object.values(RELATIONSHIPS)
+    .filter((r) => r.definition)
+    .map((r) => ({label: r.label, definition: r.definition!, class: r.class}))
 }
 
 /**

From 7f9d7dc7ab344a9343187fef8f0ed74dff12dfbd Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 23 Jul 2026 20:24:20 -0700
Subject: [PATCH 71/84] feat(variant-detail): consolidate Superseded badge into
 the Key drawer

Replaces the standalone tooltip (with its own duplicated wording) on
the Superseded badge with a deep link into the shared Key drawer, and
moves the supersession banner after the functional-evidence section
with copy refocused on the score set rather than the individual
measurement. Adds --color-superseded/-light tokens to app.css so the
badge, banner, and glossary chip share one source instead of three
copies of bg-amber-100/text-amber-800.
---
 src/assets/app.css                            |  2 +
 src/components/screens/VariantScreen.vue      | 45 ++++++++++---------
 src/components/variant/VariantDetailPanel.vue | 13 ++----
 src/lib/glossary-prose.ts                     |  3 +-
 4 files changed, 32 insertions(+), 31 deletions(-)

diff --git a/src/assets/app.css b/src/assets/app.css
index ff35e004..aa7d99f4 100644
--- a/src/assets/app.css
+++ b/src/assets/app.css
@@ -149,6 +149,8 @@
   --color-subject-light: #ddecee;
   --color-resolved: #475569;
   --color-resolved-light: #eef1f5;
+  --color-superseded: #92400e;
+  --color-superseded-light: #fef3c7;
   --color-border: #dee2e6;
   --color-border-light: #f0f0f0;
   --color-bg: #f7f7f7;
diff --git a/src/components/screens/VariantScreen.vue b/src/components/screens/VariantScreen.vue
index fc11b4fb..197dab36 100644
--- a/src/components/screens/VariantScreen.vue
+++ b/src/components/screens/VariantScreen.vue
@@ -190,26 +190,6 @@
           </div>
         </div>
 
-        <!-- Supersession banner (about the selected measurement (Y) ) -->
-        <div
-          v-if="lookup.selectedVariantDetail.value && !lookup.selectedVariantDetail.value.isCurrent"
-          class="mt-4 flex items-start gap-2 rounded-lg border border-amber-200 bg-amber-50 px-4 py-3 text-sm text-amber-800"
-        >
-          <i class="pi pi-exclamation-triangle mt-0.5 text-xs" />
-          <div>
-            This measurement is from a superseded version of its score set and may not reflect the current data.
-            <template v-if="lookup.selectedVariantDetail.value.supersededByScoreSet">
-              A newer version of this score set is available at
-              <router-link
-                class="font-semibold underline"
-                :to="{name: 'scoreSet', params: {urn: lookup.selectedVariantDetail.value.supersededByScoreSet}}"
-              >
-                {{ lookup.selectedVariantDetail.value.supersededByScoreSet }} </router-link
-              >. It is not guaranteed that it will contain a corresponding variant.
-            </template>
-          </div>
-        </div>
-
         <!-- ── FUNCTIONAL EVIDENCE ── MaveDB's own contribution, centered as the lead of the body. -->
         <div
           v-if="lookup.selectedVariantDetail.value"
@@ -225,6 +205,12 @@
               :class="primaryConfidenceBadge.class"
               >{{ primaryConfidenceBadge.label }}</span
             >
+            <span
+              v-if="lookup.selectedVariantDetail.value && !lookup.selectedVariantDetail.value.isCurrent"
+              v-key-term="'superseded'"
+              class="rounded-sm px-1.5 py-0.5 text-[10px] font-bold uppercase tracking-[0.3px] bg-superseded-light text-superseded"
+              >Superseded</span
+            >
           </div>
           <div v-if="lookup.selectedVariantScore.value != null" class="flex flex-wrap gap-x-10 gap-y-3">
             <div class="flex flex-col gap-0.5">
@@ -271,6 +257,25 @@
             show-urn
             :variant-urn="lookup.selectedVariantDetail.value?.urn ?? undefined"
           />
+          <!-- Supersession banner (about the score set of the selected measurement (Y) ) -->
+          <div
+            v-if="lookup.selectedVariantDetail.value && !lookup.selectedVariantDetail.value.isCurrent"
+            class="mt-4 flex items-start gap-2 rounded-lg border border-amber-200 bg-amber-50 px-4 py-3 text-sm text-superseded"
+          >
+            <i class="pi pi-exclamation-triangle mt-0.5 text-xs" />
+            <div>
+              This score set has been superseded and may not reflect current data.
+              <template v-if="lookup.selectedVariantDetail.value.supersededByScoreSet">
+                A newer version of this score set is available at
+                <router-link
+                  class="font-semibold underline"
+                  :to="{name: 'scoreSet', params: {urn: lookup.selectedVariantDetail.value.supersededByScoreSet}}"
+                >
+                  {{ lookup.selectedVariantDetail.value.supersededByScoreSet }} </router-link
+                >.
+              </template>
+            </div>
+          </div>
         </div>
 
         <!-- ═══ CLINICAL, POPULATION & RELATED VARIATION ═══ 
diff --git a/src/components/variant/VariantDetailPanel.vue b/src/components/variant/VariantDetailPanel.vue
index 8672c0ed..21219c5c 100644
--- a/src/components/variant/VariantDetailPanel.vue
+++ b/src/components/variant/VariantDetailPanel.vue
@@ -83,11 +83,11 @@
       >
         <span
           v-if="!detail.isCurrent"
-          v-tooltip.top="supersededTooltip"
-          class="inline-flex items-center gap-1 rounded-full bg-amber-100 px-2 py-0.5 text-xs font-semibold text-amber-800"
+          v-key-term="'superseded'"
+          class="inline-flex items-center gap-1 rounded-full bg-superseded-light px-2 py-0.5 text-xs font-semibold text-superseded"
         >
           <i class="pi pi-exclamation-triangle text-[10px]" />
-          <span v-key-term="'superseded'">Superseded</span>
+          <span>Superseded</span>
         </span>
         <router-link
           v-if="detail.clingenAlleleId"
@@ -193,13 +193,6 @@ export default defineComponent({
       if (!acmg?.evidenceStrength) return null
       return `${acmg.criterion}_${acmg.evidenceStrength.toUpperCase()}`
     },
-    supersededTooltip(): string {
-      // Supersession is anchored on the score set, not the variant: the newer version may not contain a
-      // corresponding variant, so we never imply a navigable superseding measurement.
-      return this.detail?.supersededByScoreSet
-        ? `Superseded by score set ${this.detail.supersededByScoreSet}. That version may not contain a corresponding variant.`
-        : 'This measurement is from a superseded version of its score set. The newer version may not contain a corresponding variant.'
-    },
     hasGnomad(): boolean {
       if (this.gnomad) return true
       return collectGnomadFrequencies(this.detail?.annotations ?? {}, this.detail?.alleles ?? {}).length > 0
diff --git a/src/lib/glossary-prose.ts b/src/lib/glossary-prose.ts
index e88e845d..2bfb6618 100644
--- a/src/lib/glossary-prose.ts
+++ b/src/lib/glossary-prose.ts
@@ -48,7 +48,8 @@ export const SUPERSEDED_KEY_SECTION: KeySection = {
     {
       label: 'Superseded',
       definition:
-        'The measurement comes from an older version of its score set. A newer version exists but may not contain a corresponding variant.'
+        'This measurement is from an older version of its score set and might have outdated scores or classifications. Note that the score set which supersedes the older version may not include this variant.',
+      class: 'bg-superseded-light text-superseded'
     }
   ]
 }

From 1bc6f874169ea92df324294c79f3138d2d717c52 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 23 Jul 2026 20:24:38 -0700
Subject: [PATCH 72/84] refactor(clinvar): standardize on "inferred" for
 sibling-derived calls

"Sibling allele" was scattered across the glossary, the histogram
caption/tooltip, and VariantClinvarStat under three different words
("sibling", "related", "pooled") for the same concept. Renames the
glossary section to "Inferred controls" and threads "inferred"
through the histogram tooltip and popover note so the same word
means the same thing everywhere it shows up.

Also fixes the histogram: the projected-control caption was a global
note that couldn't say which series it applied to; replaces it with a
per-series legend flag computed from that series' own classifier, and
teaches the legend to wrap a title across lines (HistogramSerieOptions
now accepts string | string[]) so the added text doesn't widen the
legend enough to cover plotted data. Drops the asterisk convention,
which collided with an unrelated footnote using the same glyph for a
different caveat.
---
 .../score-set/ScoreSetHistogram.vue           | 73 +++++++++++--------
 src/components/variant/VariantClinvarStat.vue |  2 +-
 src/glossary.ts                               |  4 +-
 src/lib/clinvar-controls.ts                   | 12 +--
 src/lib/histogram.ts                          | 43 ++++++++---
 5 files changed, 81 insertions(+), 53 deletions(-)

diff --git a/src/components/score-set/ScoreSetHistogram.vue b/src/components/score-set/ScoreSetHistogram.vue
index 78b67b39..85908435 100644
--- a/src/components/score-set/ScoreSetHistogram.vue
+++ b/src/components/score-set/ScoreSetHistogram.vue
@@ -169,10 +169,6 @@
     control variants used to derive the displayed calibration. For details on which variants were used, refer to the
     sources associated with each calibration.
   </span>
-  <span v-if="hasProjectedControlPlotted" class="mt-1 block text-center text-xs italic leading-tight">
-    Note: Some ClinVar controls shown (marked *) are carried over from a sibling allele that shares the protein
-    consequence — the assayed variant itself has no ClinVar record.
-  </span>
   <span v-if="selectedCalibrationIsClassBased" class="mavedb-class-based-calibration-note">
     *Class-based calibrations may not be visualized as thresholds. To view the distribution of variants within each
     class, select the
@@ -402,14 +398,6 @@ export default defineComponent({
         this.activeCalibration.value.functionalClassifications?.every((fc) => fc.class != null)
       )
     },
-    // True when a clinical-control view is active and at least one plotted control is a projection from a
-    // sibling allele. Gates the passthrough note.
-    hasProjectedControlPlotted: function (): boolean {
-      if (!this.vizOptions[this.activeViz]?.clinvarControlLegendNoteEnabled || !this.clinical.refreshed) {
-        return false
-      }
-      return (this.variants as DisplayVariant[]).some((v) => v.control?.projected)
-    },
     selectedCalibrationClassMap: function () {
       if (!this.selectedCalibrationIsClassBased) {
         return null
@@ -489,19 +477,21 @@ export default defineComponent({
             selectedSignificances: DEFAULT_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS,
             minStars: Number.NEGATIVE_INFINITY
           }
+          const isPathogenic = (d: HistogramDatum) => this.controlSeries(d, opts) === 'pathogenic'
+          const isBenign = (d: HistogramDatum) => this.controlSeries(d, opts) === 'benign'
           return [
             {
-              classifier: (d: HistogramDatum) => this.controlSeries(d, opts) === 'pathogenic',
+              classifier: isPathogenic,
               options: {
                 color: '#e41a1c',
-                title: 'Pathogenic/Likely Pathogenic'
+                title: this.seriesTitle('Pathogenic/Likely Pathogenic', isPathogenic)
               }
             },
             {
-              classifier: (d: HistogramDatum) => this.controlSeries(d, opts) === 'benign',
+              classifier: isBenign,
               options: {
                 color: '#377eb8',
-                title: 'Benign/Likely Benign'
+                title: this.seriesTitle('Benign/Likely Benign', isBenign)
               }
             }
           ]
@@ -522,21 +512,23 @@ export default defineComponent({
             selectedSignificances: this.customSelectedClinicalSignificanceClassifications,
             minStars: this.customMinStarRating
           }
+          const isPathogenic = (d: HistogramDatum) =>
+            this.controlSeries(d, opts) === 'pathogenic' && this.filterControlVariantByEffect(d)
+          const isBenign = (d: HistogramDatum) =>
+            this.controlSeries(d, opts) === 'benign' && this.filterControlVariantByEffect(d)
           const series = [
             {
-              classifier: (d: HistogramDatum) =>
-                this.controlSeries(d, opts) === 'pathogenic' && this.filterControlVariantByEffect(d),
+              classifier: isPathogenic,
               options: {
                 color: '#e41a1c',
-                title: 'Pathogenic/Likely Pathogenic'
+                title: this.seriesTitle('Pathogenic/Likely Pathogenic', isPathogenic)
               }
             },
             {
-              classifier: (d: HistogramDatum) =>
-                this.controlSeries(d, opts) === 'benign' && this.filterControlVariantByEffect(d),
+              classifier: isBenign,
               options: {
                 color: '#377eb8',
-                title: 'Benign/Likely Benign'
+                title: this.seriesTitle('Benign/Likely Benign', isBenign)
               }
             }
           ]
@@ -550,12 +542,13 @@ export default defineComponent({
                 UNCERTAIN_SIGNIFICANCE_CLASSIFICATIONS.includes(c)
               )
             ) {
+              const isUncertain = (d: HistogramDatum) =>
+                this.controlSeries(d, opts) === 'uncertain' && this.filterControlVariantByEffect(d)
               series.push({
-                classifier: (d: HistogramDatum) =>
-                  this.controlSeries(d, opts) === 'uncertain' && this.filterControlVariantByEffect(d),
+                classifier: isUncertain,
                 options: {
                   color: '#999999',
-                  title: 'Uncertain significance'
+                  title: this.seriesTitle('Uncertain significance', isUncertain)
                 }
               })
             }
@@ -566,12 +559,16 @@ export default defineComponent({
                 CONFLICTING_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS.includes(c)
               )
             ) {
+              const isConflicting = (d: HistogramDatum) =>
+                this.controlSeries(d, opts) === 'conflicting' && this.filterControlVariantByEffect(d)
               series.push({
-                classifier: (d: HistogramDatum) =>
-                  this.controlSeries(d, opts) === 'conflicting' && this.filterControlVariantByEffect(d),
+                classifier: isConflicting,
                 options: {
                   color: '#984ea3',
-                  title: conflictingClinicalSignificanceSeriesLabelForVersion(this.clinical.controlVersion)
+                  title: this.seriesTitle(
+                    conflictingClinicalSignificanceSeriesLabelForVersion(this.clinical.controlVersion),
+                    isConflicting
+                  )
                 }
               })
             }
@@ -987,16 +984,17 @@ export default defineComponent({
       // A projected placement: the measured allele has no ClinVar record, so this call
       // is about a related variant at a different level. Say so — otherwise the histogram appears to
       // contradict the assay-facts card, which shows this variant's own (empty) measured-level ClinVar.
-      const projectedAsterisk = control.projected ? '*' : ''
+      // "Inferred" is the app-wide word for this (matches VariantClinvarStat's "inferred from N related
+      // variants"), rather than a bare asterisk that needs its own legend to decode.
       const projectedNote = control.projected
         ? tooltipFootnote(
-            'For a related variant with the same protein consequence — the measured variant has no ClinVar record.'
+            'This classification is inferred from a related variant with the same protein consequence. The measured variant has no ClinVar record of its own.'
           )
         : null
 
       return tooltipSection([
         tooltipSectionLabel('ClinVar'),
-        tooltipText(`${description}${stars}${projectedAsterisk}`),
+        tooltipText(`${description}${stars}`),
         hasReviewStatus
           ? tooltipLink(
               `http://www.ncbi.nlm.nih.gov/clinvar/?term=${control.dbIdentifier}[alleleid]`,
@@ -1059,10 +1057,13 @@ export default defineComponent({
 
       bin.seriesBins.forEach((serieBin, i) => {
         const series = allSeries[i]
+        // The legend can wrap a series title across lines to stay narrow; this row has its own wrapping
+        // (it's inside a tooltip, not fixed-width SVG text), so it always reads as one flat line.
+        const title = Array.isArray(series?.title) ? series.title.join(' ') : series?.title
         rows.push(
           tooltipCountRow({
             color: series?.color || DEFAULT_SERIES_COLOR,
-            label: series?.title || (allSeries.length > 1 ? `Series ${i + 1}` : ''),
+            label: title || (allSeries.length > 1 ? `Series ${i + 1}` : ''),
             count: serieBin.length,
             active: seriesContainingVariant.includes(series)
           })
@@ -1125,6 +1126,14 @@ export default defineComponent({
     controlSeries(variant: DisplayVariant, opts: ControlSeriesOptions): ClinvarControlSeriesKey | null {
       return resolveControlSeries(variant.control, opts)
     },
+    // A series's calls can be a mix of direct ClinVar records and ones inferred from a related allele at
+    // the same protein consequence — flag it right on the series that actually has them, rather than a
+    // single blanket note for the whole chart. Returned as two lines (the legend wraps a `string[]` title)
+    // rather than one long line, which would widen the legend enough to cover plotted data.
+    seriesTitle(baseTitle: string, classifier: (d: HistogramDatum) => boolean): string | string[] {
+      const hasInferred = (this.variants as DisplayVariant[]).some((v) => classifier(v) && v.control?.projected)
+      return hasInferred ? [baseTitle, '(includes inferred calls)'] : baseTitle
+    },
     /** Whether a significance string is an uncertain call — used to gate the mutually-exclusive filters. */
     isUncertainSignificance,
     filterControlVariantByEffect(variant: DisplayVariant) {
diff --git a/src/components/variant/VariantClinvarStat.vue b/src/components/variant/VariantClinvarStat.vue
index a07f8511..9142a0fe 100644
--- a/src/components/variant/VariantClinvarStat.vue
+++ b/src/components/variant/VariantClinvarStat.vue
@@ -182,7 +182,7 @@ export default defineComponent({
     },
     underlyingClinvarNote(): string {
       return this.isProjectedHeadline
-        ? 'This variant has no ClinVar record. The classification above is pooled from these nucleotide variants that encode the same protein change and does not represent a ClinVar assertion for this variant.'
+        ? 'This variant has no ClinVar record. The classification above is inferred from these nucleotide variants that encode the same protein change and does not represent a ClinVar assertion for this variant.'
         : 'Other variants with the same protein consequence that also carry ClinVar records.'
     }
   },
diff --git a/src/glossary.ts b/src/glossary.ts
index ae837874..358cf107 100644
--- a/src/glossary.ts
+++ b/src/glossary.ts
@@ -3,7 +3,7 @@ import type {KeySection} from '@/composables/use-key-drawer'
 import {COORDINATE_FRAME_KEY_SECTION} from '@/composables/use-variant-coordinates'
 import {ACMG_KEY_SECTION} from '@/lib/acmg'
 import {CONFIDENCE_KEY_SECTION} from '@/lib/allele-grouping'
-import {CLINICAL_SIGNIFICANCE_KEY_SECTION, SIBLING_CONTROL_KEY_SECTION} from '@/lib/clinvar-controls'
+import {CLINICAL_SIGNIFICANCE_KEY_SECTION, INFERRED_CONTROL_KEY_SECTION} from '@/lib/clinvar-controls'
 import {FUNCTIONAL_IMPACT_KEY_SECTION} from '@/lib/functional-impact'
 import {AS_OF_KEY_SECTION, CONSEQUENCE_KEY_SECTION, THIS_VARIANT_KEY_SECTION, SUPERSEDED_KEY_SECTION} from '@/lib/glossary-prose'
 import {POPULATION_KEY_SECTION} from '@/lib/gnomad'
@@ -22,7 +22,7 @@ export const GLOSSARY_SECTIONS: KeySection[] = [
   ACMG_KEY_SECTION,
   POPULATION_KEY_SECTION,
   CLINICAL_SIGNIFICANCE_KEY_SECTION,
-  SIBLING_CONTROL_KEY_SECTION,
+  INFERRED_CONTROL_KEY_SECTION,
   AS_OF_KEY_SECTION,
   SUPERSEDED_KEY_SECTION
 ]
diff --git a/src/lib/clinvar-controls.ts b/src/lib/clinvar-controls.ts
index e61b3c98..12b45a5d 100644
--- a/src/lib/clinvar-controls.ts
+++ b/src/lib/clinvar-controls.ts
@@ -20,15 +20,15 @@ export const CLINICAL_SIGNIFICANCE_KEY_SECTION: KeySection = {
   ]
 }
 
-/** Key-drawer glossary for sibling-allele ClinVar controls (calls carried over from a sibling allele). */
-export const SIBLING_CONTROL_KEY_SECTION: KeySection = {
-  id: 'passthrough',
-  title: 'Sibling-allele controls',
+/** Key-drawer glossary for inferred ClinVar controls (calls carried over from a related allele). */
+export const INFERRED_CONTROL_KEY_SECTION: KeySection = {
+  id: 'inferred',
+  title: 'Inferred controls',
   terms: [
     {
-      label: 'From a sibling allele',
+      label: 'Inferred call',
       definition:
-        'A ClinVar call carried over from a sibling allele that shares the protein consequence, shown when the assayed variant itself has no ClinVar record. Marked with *.'
+        'A ClinVar call inferred from a related allele with the same protein consequence — shown only when the assayed variant has no ClinVar record of its own.'
     }
   ]
 }
diff --git a/src/lib/histogram.ts b/src/lib/histogram.ts
index a6300930..a05db33c 100644
--- a/src/lib/histogram.ts
+++ b/src/lib/histogram.ts
@@ -39,7 +39,9 @@ export interface HistogramMargins {
 }
 
 export interface HistogramSerieOptions {
-  title?: string
+  // A plain title renders as one legend line. An array wraps it across multiple lines instead of
+  // widening the legend indefinitely — e.g. a base label plus a caveat that doesn't fit alongside it.
+  title?: string | string[]
   color: string // TODO Make this optional by providing default colors.
 }
 
@@ -908,24 +910,31 @@ export default function makeHistogram(): Histogram {
         const legendX = 32
         const legendY = 12
         const legendItemHeight = 22
+        const legendWrappedLineHeight = 15 // extra vertical space per title line beyond the first
         const legendFontSize = '13px'
         const legendCircleWidth = 7
         const legendSpacing = 5
         const legend = svg.select('g.histogram-legend')
+        const legendItemsShown = chartHasContent && series.length > 1
+        const legendSeries = legendItemsShown ? series : []
+        const legendTitleLines = (d: HistogramSerie): string[] =>
+          Array.isArray(d.options.title) ? d.options.title : [d.options.title || '']
+        // Cumulative Y offset per item — an item's own title may wrap across more than one line, which
+        // pushes every item after it further down than a flat `index * legendItemHeight` would.
+        const legendItemOffsets: number[] = []
+        let legendCumulativeHeight = 0
+        for (const d of legendSeries) {
+          legendItemOffsets.push(legendCumulativeHeight)
+          legendCumulativeHeight += legendItemHeight + (legendTitleLines(d).length - 1) * legendWrappedLineHeight
+        }
         const legendItem = legend
           .selectAll('g.histogram-legend-item')
-          .data(chartHasContent && series.length > 1 ? series : [])
+          .data(legendSeries)
           .join(
             (enter) => {
               const g = enter.append('g').attr('class', 'histogram-legend-item')
               g.append('circle').attr('r', legendCircleWidth).attr('cx', legendX)
-              //.attr('cy', (d, i) => legendY + i * legendItemHeight)
-              //.style('fill', (d) => d.options.color)
-              g.append('text')
-                .attr('x', legendX + legendCircleWidth + legendSpacing)
-                .attr('y', (_d: HistogramSerie, i) => legendY + i * legendItemHeight + legendSpacing)
-                .style('font-size', legendFontSize)
-              //.text((d, i) => d.options.title || `Series ${i + 1}`)
+              g.append('text').attr('x', legendX + legendCircleWidth + legendSpacing).style('font-size', legendFontSize)
               return g
             },
             (update) => update,
@@ -934,13 +943,23 @@ export default function makeHistogram(): Histogram {
         legendItem
           .select('circle')
           // @ts-ignore
-          .attr('cy', (_d: HistogramSerie, i) => legendY + i * legendItemHeight)
+          .attr('cy', (_d: HistogramSerie, i) => legendY + legendItemOffsets[i])
           // @ts-ignore
           .style('fill', (d: HistogramSerie) => d.options.color)
         legendItem
           .select('text')
           // @ts-ignore
-          .text((d: HistogramSerie, i) => d.options.title || `Series ${i + 1}`)
+          .attr('y', (_d: HistogramSerie, i) => legendY + legendItemOffsets[i] + legendSpacing)
+          .each(function (d: unknown, i: number) {
+            const lines = legendTitleLines(d as HistogramSerie)
+            d3.select(this)
+              .selectAll('tspan')
+              .data(lines.length ? lines : [`Series ${i + 1}`])
+              .join('tspan')
+              .attr('x', legendX + legendCircleWidth + legendSpacing)
+              .attr('dy', (_line: string, lineIndex: number) => (lineIndex === 0 ? 0 : legendWrappedLineHeight))
+              .text((line: string) => line)
+          })
 
         // The client may have specified a line of text to display below the legend.
         legend
@@ -950,7 +969,7 @@ export default function makeHistogram(): Histogram {
           .attr('class', 'histogram-legend-note')
           .attr('font-size', legendFontSize)
           .attr('x', legendX - legendCircleWidth)
-          .attr('y', legendY + (series.length == 1 ? 0 : series.length) * legendItemHeight + legendSpacing - 1)
+          .attr('y', legendY + (legendItemsShown ? legendCumulativeHeight : 0) + legendSpacing - 1)
           .text((d) => d)
 
         // Add a background for the legend, for visibility.

From 5abe8377b41b0d6d6db5d8291db19951a8d07ff3 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 23 Jul 2026 20:24:52 -0700
Subject: [PATCH 73/84] chore(variant): drop unused prop, clarify allele-ledger
 subtitle

MvAlleleLedger never declared an "identify" prop, so ScoreSetView's
:identify="false" was dead markup. Also reworks the ledger's subtitle
for clarity.
---
 src/components/screens/ScoreSetView.vue   | 1 -
 src/components/variant/MvAlleleLedger.vue | 2 +-
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/components/screens/ScoreSetView.vue b/src/components/screens/ScoreSetView.vue
index cd095930..e35821a0 100644
--- a/src/components/screens/ScoreSetView.vue
+++ b/src/components/screens/ScoreSetView.vue
@@ -124,7 +124,6 @@
             :clinvar-version="clinvarControls.controlVersion"
             :coordinate="variantOptionLabel(variantToVisualize)"
             :flush="true"
-            :identify="false"
             :selected-calibration-id="selectedCalibrationObjects[0]?.id ?? null"
             :underlying-coordinate="variantUnderlyingLabel(variantToVisualize) ?? ''"
             :urn="variantToVisualize.variantUrn"
diff --git a/src/components/variant/MvAlleleLedger.vue b/src/components/variant/MvAlleleLedger.vue
index 766e7499..d0e30503 100644
--- a/src/components/variant/MvAlleleLedger.vue
+++ b/src/components/variant/MvAlleleLedger.vue
@@ -2,7 +2,7 @@
   <div>
     <div class="mb-3 flex flex-wrap items-baseline gap-x-2">
       <h3 class="mave-section-title !mb-0">Clinical &amp; population data</h3>
-      <span class="text-xs-minus text-text-muted">a property of the exact allele, shown at every level</span>
+      <span class="text-xs-minus text-text-muted">reference data for all alleles related to this variant</span>
     </div>
 
     <!-- One uniform card per allele group. This variant (X) leads; the measured allele (Y) follows when the

From 20ac9a0d8b402affa63d56deb82d3e5b929920e6 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 23 Jul 2026 22:21:45 -0700
Subject: [PATCH 74/84] refactor(ui): centralize functional-score display
 precision

Introduce formatScore() + SCORE_DISPLAY_PRECISION in lib/scores.ts as the single source of truth for rendering a variant's functional score (4 significant figures; null for NA/absent, so callers own the empty case). Route the histogram tooltip, variant-page score, and both measurement components through it, replacing scattered toPrecision(4) literals.
---
 src/components/score-set/ScoreSetHistogram.vue |  3 ++-
 src/components/screens/VariantScreen.vue       |  5 ++++-
 src/components/search/MvMeasurementRow.vue     |  6 ++++--
 src/components/variant/MvMeasurementCard.vue   |  6 ++++--
 src/lib/scores.test.ts                         | 18 ++++++++++++++++++
 src/lib/scores.ts                              | 13 +++++++++++++
 6 files changed, 45 insertions(+), 6 deletions(-)
 create mode 100644 src/lib/scores.test.ts

diff --git a/src/components/score-set/ScoreSetHistogram.vue b/src/components/score-set/ScoreSetHistogram.vue
index 85908435..c3835d66 100644
--- a/src/components/score-set/ScoreSetHistogram.vue
+++ b/src/components/score-set/ScoreSetHistogram.vue
@@ -257,6 +257,7 @@ import {
   tooltipVariantDetailsLink
 } from '@/lib/tooltips'
 import {DisplayVariant} from '@/lib/variants'
+import {formatScore} from '@/lib/scores'
 import {
   consequenceBucket,
   EFFECT_BUCKETS,
@@ -915,7 +916,7 @@ export default defineComponent({
       }
 
       if (variant.score != null) {
-        identity.push(tooltipText(`Score ${variant.score.toPrecision(4)}`))
+        identity.push(tooltipText(`Score ${formatScore(variant.score)}`))
         const classification = this.matchVariantClassification(variant)
         if (classification) {
           identity.push(tooltipBadgeBlock(getClassificationColor(classification), classification.label))
diff --git a/src/components/screens/VariantScreen.vue b/src/components/screens/VariantScreen.vue
index 197dab36..da5e6628 100644
--- a/src/components/screens/VariantScreen.vue
+++ b/src/components/screens/VariantScreen.vue
@@ -224,7 +224,7 @@
             <div class="flex flex-col gap-0.5">
               <span class="text-[10px] font-semibold uppercase tracking-[0.3px] text-[#aaa]">Functional score</span>
               <span class="text-sm font-semibold text-text-primary">{{
-                lookup.selectedVariantScore.value?.toPrecision(4)
+                formatScore(lookup.selectedVariantScore.value)
               }}</span>
             </div>
             <div class="flex flex-col gap-0.5">
@@ -381,6 +381,7 @@ import MvMeasurementCard from '@/components/variant/MvMeasurementCard.vue'
 import MvRowActionMenu, {type RowAction} from '@/components/common/MvRowActionMenu.vue'
 import {useVariantLookup} from '@/composables/use-variant-lookup'
 import {assayLevelDisplay} from '@/lib/measurement-types'
+import {formatScore} from '@/lib/scores'
 import {hasFunctionalCalibrations, hasPathogenicityCalibrations} from '@/lib/calibrations'
 import {confidenceBadge, groupAlleles, type AlleleGroup, type ConfidenceBadge} from '@/lib/allele-grouping'
 import type {components} from '@/schema/openapi'
@@ -610,6 +611,8 @@ export default defineComponent({
   },
 
   methods: {
+    formatScore,
+
     toIsoDate(date: Date): string {
       const year = date.getFullYear()
       const month = String(date.getMonth() + 1).padStart(2, '0')
diff --git a/src/components/search/MvMeasurementRow.vue b/src/components/search/MvMeasurementRow.vue
index 56f04115..8c68efaf 100644
--- a/src/components/search/MvMeasurementRow.vue
+++ b/src/components/search/MvMeasurementRow.vue
@@ -8,7 +8,7 @@
     >
     <span class="font-mono text-xs-plus font-semibold text-gray-700">{{ hgvs }}</span>
     <span v-if="measurement.score != null" class="text-xs-minus text-gray-500"
-      >score <strong class="font-mono text-gray-700">{{ measurement.score.toPrecision(4) }}</strong></span
+      >score <strong class="font-mono text-gray-700">{{ formatScore(measurement.score) }}</strong></span
     >
     <MvClassificationTag v-if="classification" :classification="classification" />
     <router-link
@@ -26,6 +26,7 @@ import {defineComponent, type PropType} from 'vue'
 
 import MvClassificationTag from '@/components/common/MvClassificationTag.vue'
 import {assayLevelDisplay} from '@/lib/measurement-types'
+import {formatScore} from '@/lib/scores'
 import type {components} from '@/schema/openapi'
 
 type AlleleMeasurement = components['schemas']['AlleleMeasurement']
@@ -53,6 +54,7 @@ export default defineComponent({
     classification(): string | null {
       return this.measurement.preferredClassification?.functionalClassification ?? null
     }
-  }
+  },
+  methods: {formatScore}
 })
 </script>
diff --git a/src/components/variant/MvMeasurementCard.vue b/src/components/variant/MvMeasurementCard.vue
index d21bd17f..fa2c6b1f 100644
--- a/src/components/variant/MvMeasurementCard.vue
+++ b/src/components/variant/MvMeasurementCard.vue
@@ -50,7 +50,7 @@
     <div class="mt-auto border-t border-border-light pt-3">
       <div v-if="score != null" class="mb-2 flex items-center gap-2.5 text-xs-minus text-text-muted">
         <span class="text-[10px] font-bold uppercase tracking-[0.3px] text-[#aaa]">Functional score</span>
-        <strong class="font-mono font-bold text-text-secondary">{{ score.toPrecision(4) }}</strong>
+        <strong class="font-mono font-bold text-text-secondary">{{ formatScore(score) }}</strong>
       </div>
       <div v-if="classification || evidenceCode" class="mt-1.5">
         <span class="mb-1 block text-[10px] font-bold uppercase tracking-[0.3px] text-[#aaa]">Classified as</span>
@@ -75,6 +75,7 @@ import {defineComponent, type PropType} from 'vue'
 import MvClassificationTag from '@/components/common/MvClassificationTag.vue'
 import MvEvidenceTag from '@/components/common/MvEvidenceTag.vue'
 import {assayLevelDisplay, RELATIONSHIPS, type MeasurementRelationship} from '@/lib/measurement-types'
+import {formatScore} from '@/lib/scores'
 import type {components} from '@/schema/openapi'
 
 type SavedFunctionalClassification = components['schemas']['SavedFunctionalClassification']
@@ -135,7 +136,8 @@ export default defineComponent({
     oddspathsRatio(): number | null {
       return this.preferredClassification?.oddspathsRatio ?? null
     }
-  }
+  },
+  methods: {formatScore}
 })
 </script>
 
diff --git a/src/lib/scores.test.ts b/src/lib/scores.test.ts
new file mode 100644
index 00000000..e64dc44e
--- /dev/null
+++ b/src/lib/scores.test.ts
@@ -0,0 +1,18 @@
+import {describe, expect, it} from 'vitest'
+
+import {formatScore, SCORE_DISPLAY_PRECISION} from './scores'
+
+describe('formatScore', () => {
+  it('renders a numeric score to the app-wide significant-figure precision', () => {
+    expect(formatScore(1.23456)).toBe((1.23456).toPrecision(SCORE_DISPLAY_PRECISION))
+    expect(formatScore(1.23456)).toBe('1.235')
+    // Trailing zeros are kept — sig figs, not decimal places.
+    expect(formatScore(-2)).toBe('-2.000')
+    expect(formatScore(0)).toBe('0.000')
+  })
+
+  it('returns null for a non-numeric (NA/absent) score, so callers own the empty rendering', () => {
+    expect(formatScore(null)).toBeNull()
+    expect(formatScore(undefined)).toBeNull()
+  })
+})
diff --git a/src/lib/scores.ts b/src/lib/scores.ts
index 6fba1e95..dac81760 100644
--- a/src/lib/scores.ts
+++ b/src/lib/scores.ts
@@ -5,6 +5,19 @@ export interface ScoresOrCountsRow {
   [key: string]: any
 }
 
+/** Significant figures used to display a functional score, app-wide. */
+export const SCORE_DISPLAY_PRECISION = 4
+
+/**
+ * Format a functional score for display — the single source of truth for the score's significant-figure
+ * precision, so every surface (search rows, histogram/heatmap tooltips, the detail panel, the variant
+ * page) reads it the same way. Returns null for a non-numeric (NA/absent) score, leaving each caller to
+ * decide how to render its absence (hide the field, "Not scored", a dash, …).
+ */
+export function formatScore(score: number | null | undefined): string | null {
+  return typeof score === 'number' ? score.toPrecision(SCORE_DISPLAY_PRECISION) : null
+}
+
 /**
  * Transform flat namespaced columns into nested objects.
  * Converts columns like "namespace.colname" into nested structure { namespace: { colname: value } }

From 35cfa92fd8e9445bd4be1470517e0feecf5b4930 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 23 Jul 2026 22:21:45 -0700
Subject: [PATCH 75/84] fix(score-set): find unscored variants, surface score
 in detail panel
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Search indexed only scored variants, so a coordinate query for an in-set variant with an NA score returned "No matching variants" — a false negative on the page's only directory surface. Index the whole set instead; unscored matches select normally.

Since the histogram can't jump to a scoreless variant, the detail panel now carries a Score headline (4 sig figs, or "Not scored") so a selection always reports its measurement.

Also unify the search dropdown's leading dot to one meaning everywhere — a ClinVar control colored by classification — instead of overloading it with consequence-palette and score colors in the empty state.
---
 .../score-set/ScoreSetVariantSearch.vue       | 52 ++++++++++---------
 src/components/screens/ScoreSetView.vue       |  1 +
 src/components/variant/VariantDetailPanel.vue | 30 ++++++++---
 3 files changed, 52 insertions(+), 31 deletions(-)

diff --git a/src/components/score-set/ScoreSetVariantSearch.vue b/src/components/score-set/ScoreSetVariantSearch.vue
index 0e51e1d9..d17496cb 100644
--- a/src/components/score-set/ScoreSetVariantSearch.vue
+++ b/src/components/score-set/ScoreSetVariantSearch.vue
@@ -28,7 +28,7 @@
               v-if="!variantSearchQuery && variantSearchSuggestions.length"
               class="border-b border-border-light px-3 py-1.5 text-xs text-text-muted"
             >
-              Showing sample variants — type to search all {{ scoredVariants.length.toLocaleString() }}.
+              Showing sample variants — type to search all {{ variants.length.toLocaleString() }}.
             </div>
           </template>
           <template #optiongroup="{option}">
@@ -42,14 +42,13 @@
           <template #option="{option}">
             <div class="flex w-full items-center justify-between gap-2">
               <div class="flex min-w-0 items-center gap-2">
-                <!-- Leading dot. On the empty box it's the notable caption's (consequence palette or red/
-                     blue clinical call). While searching it flags the "interesting" hits — ClinVar controls,
-                     colored by classification — and is transparent (but reserves its width, so labels stay
-                     aligned) for everything else. -->
+                <!-- Leading dot — one meaning everywhere: a ClinVar control, colored by its classification
+                     (red pathogenic, blue benign, grey otherwise). Transparent (but width-reserved, so
+                     labels stay aligned) for every non-control row, in both the empty and typing states. -->
                 <span
                   class="size-2 shrink-0 rounded-full"
                   :style="{backgroundColor: optionDotColor(option) || 'transparent'}"
-                  :title="variantSearchQuery ? (clinicalTag(option) ?? undefined) : undefined"
+                  :title="clinicalTag(option) ?? undefined"
                 />
                 <div class="flex min-w-0 flex-col justify-center leading-tight">
                   <span class="truncate">{{ variantOptionLabel(option) }}</span>
@@ -73,7 +72,7 @@
                 </div>
               </div>
               <span v-if="typeof option.score === 'number'" class="shrink-0 text-xs text-text-muted">
-                {{ option.score.toFixed(2) }}
+                {{ formatScore(option.score) }}
               </span>
             </div>
           </template>
@@ -112,7 +111,8 @@ import {
   DEFAULT_MIN_STAR_RATING,
   PATHOGENIC_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS
 } from '@/lib/clinvar-controls'
-import {consequenceBucket, EFFECT_BUCKETS} from '@/lib/consequences'
+import {consequenceBucket} from '@/lib/consequences'
+import {formatScore} from '@/lib/scores'
 import {
   clinicalExtremesPerClass,
   consequenceExemplars,
@@ -131,10 +131,9 @@ interface VariantGroup {
 }
 
 // The secondary line rendered under a notable row, framed for its group (a consequence name, a ClinVar
-// call, or a deviations-from-median readout). `color` drives the leading dot when present.
+// call, or a deviations-from-median readout).
 interface NotableCaption {
   label: string
-  color?: string
 }
 
 // How many most-extreme-score rows to sample on the empty state.
@@ -201,16 +200,20 @@ export default defineComponent({
     hasSelection(): boolean {
       return typeof this.localSelection === 'object' && this.localSelection !== null
     },
-    // Only scored variants are selectable — the visualizations plot a score, so a variant without one has
-    // nothing to jump to.
+    // The scored subset — the pool the empty-state notables (clinical extremes, consequence exemplars,
+    // score extremes) sample from, since a notable is a jump-to-position suggestion and needs a score to
+    // land on. Search itself spans the whole set (see `variantSearchIndex`), scored or not.
     scoredVariants(): DisplayVariant[] {
       return this.variants.filter((v) => typeof v.score === 'number')
     },
-    // Search index built once per loaded set: each scored variant paired with a lowercased haystack of all
-    // its coordinate strings (both frames) plus its URN. Filtering a keystroke is then one `includes` per
-    // variant instead of re-resolving ~7 coordinates and re-lowercasing them on every keypress.
+    // Search index built once per loaded set: every variant — scored or not — paired with a lowercased
+    // haystack of all its coordinate strings (both frames) plus its URN. Unscored variants stay findable:
+    // they're real members of the set (a coordinate the depositor submitted that carries an NA score), so a
+    // coordinate query must still reach them even though the histogram has no bar to jump to — the detail
+    // panel reports the missing score instead. Filtering a keystroke is then one `includes` per variant
+    // instead of re-resolving ~7 coordinates and re-lowercasing them on every keypress.
     variantSearchIndex(): {variant: DisplayVariant; haystack: string}[] {
-      return this.scoredVariants.map((v) => ({
+      return this.variants.map((v) => ({
         variant: v,
         haystack: [
           v.hgvsNt?.hgvs,
@@ -253,8 +256,7 @@ export default defineComponent({
       const consequence = consequenceExemplars(scored).filter((v) => !seen.has(v.variantUrn))
       for (const v of consequence) {
         seen.add(v.variantUrn)
-        const bucket = consequenceBucket(v.consequence)
-        captions.set(v.variantUrn, {label: bucket, color: EFFECT_BUCKETS.find((b) => b.name === bucket)?.color})
+        captions.set(v.variantUrn, {label: consequenceBucket(v.consequence)})
       }
       if (consequence.length) groups.push({label: 'By consequence', items: consequence})
 
@@ -323,16 +325,18 @@ export default defineComponent({
   },
 
   methods: {
+    formatScore,
+
     // The precomputed caption for a notable row (empty-box state), keyed by URN; null for search-result
     // rows, which show the variant's annotation instead.
     notableCaption(variant: DisplayVariant): NotableCaption | null {
       return this.notableData.captions.get(variant.variantUrn) ?? null
     },
 
-    // The leading dot color. On the empty box it's the notable caption's; while searching it's the
-    // ClinVar classification color for control hits (the "interesting" flag) and undefined otherwise.
+    // The leading dot color: the ClinVar classification color when the variant is a control, undefined
+    // otherwise — the same rule in both the empty (notables) and typing states.
     optionDotColor(variant: DisplayVariant): string | undefined {
-      return this.variantSearchQuery ? this.clinicalColor(variant) : this.notableCaption(variant)?.color
+      return this.clinicalColor(variant)
     },
 
     // Classification color for a ClinVar control (red pathogenic, blue benign, grey otherwise), echoing
@@ -359,9 +363,9 @@ export default defineComponent({
       return stars ? `${significance} · ${stars}★` : significance
     },
 
-    // Caption for a clinical-control notable row: the ClinVar call and star rating, dotted by class.
+    // Caption for a clinical-control notable row: the ClinVar call and star rating.
     clinicalCaption(variant: DisplayVariant): NotableCaption {
-      return {label: this.clinicalTag(variant) ?? '', color: this.clinicalColor(variant)}
+      return {label: this.clinicalTag(variant) ?? ''}
     },
 
     // Caption for a most-extreme-scores row: distance from the median in robust (MAD) units. Falls back to
@@ -391,7 +395,7 @@ export default defineComponent({
       this.variantSearchSuggestions = matches.length
         ? [
             {
-              label: `${matches.length.toLocaleString()} of ${this.scoredVariants.length.toLocaleString()} variants match`,
+              label: `${matches.length.toLocaleString()} of ${this.variants.length.toLocaleString()} variants match`,
               items: matches
             }
           ]
diff --git a/src/components/screens/ScoreSetView.vue b/src/components/screens/ScoreSetView.vue
index e35821a0..19c43175 100644
--- a/src/components/screens/ScoreSetView.vue
+++ b/src/components/screens/ScoreSetView.vue
@@ -124,6 +124,7 @@
             :clinvar-version="clinvarControls.controlVersion"
             :coordinate="variantOptionLabel(variantToVisualize)"
             :flush="true"
+            :score="variantToVisualize.score ?? null"
             :selected-calibration-id="selectedCalibrationObjects[0]?.id ?? null"
             :underlying-coordinate="variantUnderlyingLabel(variantToVisualize) ?? ''"
             :urn="variantToVisualize.variantUrn"
diff --git a/src/components/variant/VariantDetailPanel.vue b/src/components/variant/VariantDetailPanel.vue
index 21219c5c..154d56a4 100644
--- a/src/components/variant/VariantDetailPanel.vue
+++ b/src/components/variant/VariantDetailPanel.vue
@@ -16,12 +16,11 @@
     </div>
 
     <template v-else-if="detail">
-      <!-- Identity: shown with the facts grid, and in the empty state only when an alternate spelling
-           (a distinct underlying nucleotide coordinate) disambiguates the selection. -->
-      <div
-        v-if="anyAnnotationsAvailable || hasAlternateSpelling"
-        class="flex flex-wrap items-baseline gap-x-2.5 gap-y-1 px-4 pb-3 pt-3.5 tablet:px-5"
-      >
+      <!-- Identity + score headline: the coordinate, its alternate nucleotide spelling when one
+           disambiguates, and the functional score (or "Not scored") pushed to the right. Always shown —
+           the score is the headline fact, and reporting it here is what keeps an unscored selection from
+           reading as a dead end when the histogram has no bar to jump to. -->
+      <div class="flex flex-wrap items-baseline gap-x-2.5 gap-y-1 px-4 pb-3 pt-3.5 tablet:px-5">
         <span class="font-mono text-base font-bold leading-none text-text-primary">{{ coordinate || detail.urn }}</span>
         <span
           v-if="hasAlternateSpelling"
@@ -30,6 +29,13 @@
         >
           {{ underlyingCoordinate }}
         </span>
+        <span class="ml-auto flex items-baseline gap-1.5 leading-none">
+          <span class="text-[10px] font-bold uppercase tracking-wide text-text-muted">Score</span>
+          <span v-if="score != null" class="font-mono text-base font-bold text-text-primary">{{
+            formatScore(score)
+          }}</span>
+          <span v-else class="text-xs font-semibold italic text-text-muted">Not scored</span>
+        </span>
       </div>
 
       <!-- Facts -->
@@ -41,7 +47,11 @@
         <div class="stat">
           <span v-key-term="'functional-impact'" class="stat-label">Classification</span>
           <span v-if="selectedClassification" class="flex flex-wrap items-center gap-1.5">
-            <span class="rounded px-1.5 py-0.5 text-xs-plus" :class="classificationClass">
+            <span
+              v-key-term="'functional-impact'"
+              class="rounded px-1.5 py-0.5 text-xs-plus"
+              :class="classificationClass"
+            >
               {{ formatToken(selectedClassification.classification.functionalClassification) }}
             </span>
             <MvEvidenceTag v-if="acmgCode" :code="acmgCode" />
@@ -111,6 +121,7 @@ import VariantGnomadStat from '@/components/variant/VariantGnomadStat.vue'
 import VariantClinvarStat from '@/components/variant/VariantClinvarStat.vue'
 import {getVariantDetail} from '@/api/mavedb/variants'
 import {collectGnomadFrequencies} from '@/lib/gnomad'
+import {formatScore} from '@/lib/scores'
 import {enumerateUnderlyingClinvar, resolveClinvarRecords} from '@/lib/clinvar-controls'
 import {resolveClinvarHeadline} from '@/lib/clinvar-control-placement'
 import type {components} from '@/schema/openapi'
@@ -143,6 +154,9 @@ export default defineComponent({
     // primary label to disambiguate distinct coding variants that collapse to the same protein change.
     // Empty when there is no underlying nucleotide coordinate.
     underlyingCoordinate: {type: String as PropType<string | null>, default: null},
+    // The variant's functional score, or null for an NA/absent score. Rendered in the headline so a
+    // selection still reports its measurement even when the histogram has no bar to jump to.
+    score: {type: Number as PropType<number | null>, default: null},
     // The calibration selected on the page (its numeric id); its classification is the one shown.
     selectedCalibrationId: {type: Number as PropType<number | null>, default: null},
     // The ClinVar release the page's clinical-controls store has selected (raw `MM_YYYY`), passed through to
@@ -228,6 +242,8 @@ export default defineComponent({
   },
 
   methods: {
+    formatScore,
+
     async fetchDetail(urn: string) {
       if (!urn) return
       this.status = 'loading'

From f3fa94f9ed9dd7207ceac652f0f39429857b7257 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Thu, 23 Jul 2026 22:24:04 -0700
Subject: [PATCH 76/84] refactor(search): drop the retired
 include_nucleotide_siblings flag

The API now reaches a CA's protein consequence and sibling nt encodings unconditionally (one behavior on every surface), so the client flag no longer gates anything. Remove includeNucleotideSiblings from the getAlleleMeasurements wrapper (and its memo key) and from the variant search's only call site, which now requests the full equivalence class like the variant page.
---
 src/api/mavedb/variants.ts                      | 9 ++++-----
 src/components/screens/SearchVariantsScreen.vue | 6 +++---
 2 files changed, 7 insertions(+), 8 deletions(-)

diff --git a/src/api/mavedb/variants.ts b/src/api/mavedb/variants.ts
index eec3a2b2..6c1d1310 100644
--- a/src/api/mavedb/variants.ts
+++ b/src/api/mavedb/variants.ts
@@ -10,16 +10,15 @@ type VariantVrsMatch = components['schemas']['VariantVrsMatch']
 
 // The ClinGen-allele-centric variant page's entrypoint: every measurement whose cross-layer
 // equivalence class touches this CAID/PAID, in the API's default order (direct-first). `includeSuperseded`
-// opts in to superseded score-set versions; `includeNucleotideSiblings` (CA only) widens a nucleotide
-// query through its protein consequence to the sibling nt changes — the search discovery path.
+// opts in to superseded score-set versions. A CA query always includes its protein consequence and the
+// sibling nt changes; a PA query, its nt encodings — the same on every surface.
 export const getAlleleMeasurements = memoizeRead(
   async (
     clingenAlleleId: string,
-    options?: {includeSuperseded?: boolean; includeNucleotideSiblings?: boolean; asOf?: string}
+    options?: {includeSuperseded?: boolean; asOf?: string}
   ): Promise<AlleleMeasurement[]> => {
     const params: Record<string, string | boolean> = {}
     if (options?.includeSuperseded) params.include_superseded = true
-    if (options?.includeNucleotideSiblings) params.include_nucleotide_siblings = true
     if (options?.asOf) params.as_of = options.asOf
     const response = await axios.get(
       `${config.apiBaseUrl}/clingen-alleles/${encodeURIComponent(clingenAlleleId)}/measurements`,
@@ -28,7 +27,7 @@ export const getAlleleMeasurements = memoizeRead(
     return response.data
   },
   (clingenAlleleId, options) =>
-    `${clingenAlleleId}|${options?.includeSuperseded ?? false}|${options?.includeNucleotideSiblings ?? false}|${options?.asOf ?? ''}`
+    `${clingenAlleleId}|${options?.includeSuperseded ?? false}|${options?.asOf ?? ''}`
 )
 
 export async function lookupVariantsByVrsDigest(identifier: string): Promise<VariantVrsMatch[]> {
diff --git a/src/components/screens/SearchVariantsScreen.vue b/src/components/screens/SearchVariantsScreen.vue
index 44abbbd4..4b62c582 100644
--- a/src/components/screens/SearchVariantsScreen.vue
+++ b/src/components/screens/SearchVariantsScreen.vue
@@ -1159,9 +1159,9 @@ export default defineComponent({
         if (!caId) continue
         allele.variantsStatus = 'Loading'
         try {
-          // A nucleotide query widens to its protein consequence's sibling nt changes (search discovery);
-          // a protein query already returns every encoding, so the flag is a no-op there.
-          const measurements = await getAlleleMeasurements(caId, {includeNucleotideSiblings: !caId.startsWith('PA')})
+          // The full equivalence class: a CA query returns its protein consequence and sibling nt changes,
+          // a PA query its nt encodings — the same set the variant page shows.
+          const measurements = await getAlleleMeasurements(caId)
 
           // Bucket each measurement by the API's relationship directly — the display labels (below) interpret
           // each bucket for the searched level. Variant-level: every measurement is its own row (no score-set

From d48da5e228a9b1dd98cf032ba197940b4de00c80 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Fri, 24 Jul 2026 08:00:43 -0700
Subject: [PATCH 77/84] fix(download-buttons): update download buttons image in
 docs

---
 docs/content/images/download_buttons.png | Bin 265746 -> 37205 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs/content/images/download_buttons.png b/docs/content/images/download_buttons.png
index d2c7512a53d514f5e367d61d65b8ff6a6dc56211..45b8cb456f7900047f2dfeb0b22e81e10c78e72b 100644
GIT binary patch
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From 490d9a174bcd1eb4a3e1ac789d07a1ede5ad197a Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Fri, 24 Jul 2026 08:54:38 -0700
Subject: [PATCH 78/84] fix(variant): show each allele's own gnomAD frequency
 in the ledger

MvAlleleLedger never passed assay-gnomad to VariantGnomadStat, so an
allele's own direct frequency was neither promoted to the headline nor
included in the pooled/related list (its digests are in the subject
exclusion set). Only pooled protein-change frequencies from other
alleles survived, leaving the actual allele's cell blank.

Pass the group's coalesced gnomAD annotation, mirroring the existing
vep wiring on the sibling consequence stat, so the allele's own
frequency renders as the direct headline.
---
 src/components/variant/MvAlleleLedger.vue | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/components/variant/MvAlleleLedger.vue b/src/components/variant/MvAlleleLedger.vue
index d0e30503..314472f8 100644
--- a/src/components/variant/MvAlleleLedger.vue
+++ b/src/components/variant/MvAlleleLedger.vue
@@ -58,6 +58,7 @@
           <VariantGnomadStat
             :alleles="alleles"
             :annotations="annotations"
+            :assay-gnomad="entry.group.coalescedAnnotations?.gnomad ?? null"
             :assay-level="groupLevel(entry.group)"
             :assay-level-digest="digestsOf(entry.group)"
             plain

From b6a1c4f0986746c260b2fe18a8e07c21c417f2e0 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Tue, 18 Aug 2026 10:55:20 -0700
Subject: [PATCH 79/84] refactor(variant): rename allele projection terminology
 and relation enum values

Renames "twin"/"sibling" to "projection"/"encodings" in the ClinVar/gnomAD
library comments, updates the Cat-VRS `relation` test fixtures from
`is_genomic_of` to `coordinate_representation_of`, and adds the confidence-
badge color tokens (measured/resolved/convergent/candidate) to app.css.
---
 src/assets/app.css                        | 28 ++++++++++++----
 src/lib/allele-grouping.test.ts           | 10 +++---
 src/lib/annotation-subject.ts             |  2 +-
 src/lib/clinvar-control-placement.test.ts | 40 +++++++++++------------
 src/lib/clinvar-controls.test.ts          | 14 ++++----
 src/lib/gnomad.test.ts                    |  6 ++--
 src/lib/gnomad.ts                         |  4 +--
 7 files changed, 60 insertions(+), 44 deletions(-)

diff --git a/src/assets/app.css b/src/assets/app.css
index aa7d99f4..40e10b8a 100644
--- a/src/assets/app.css
+++ b/src/assets/app.css
@@ -120,16 +120,32 @@
   --color-ga4gh: #0f6ca4;
   --color-ga4gh-light: #e3f0f9;
 
-  /* ── Measurement Types (variant screen) ────────────────────── */
+  /* ── Assay Level (variant screen) ──────────────────────────── */
+  /* The level a result measured the change at — see LEVEL_BUCKETS in lib/measurement-types.ts. */
   --color-nucleotide: #a8247c;
   --color-nucleotide-light: #fce8f4;
   --color-nucleotide-border: #eec3e0;
   --color-amino-acid: #7e5daf;
   --color-amino-acid-light: #f1ecf8;
   --color-amino-acid-border: #b5a0d0;
-  --color-synonymous-nucleotide: #8a5700;
-  --color-synonymous-nucleotide-light: #fef8e1;
-  --color-synonymous-nucleotide-border: #f5c97a;
+
+  /* ── Allele relationship axis (variant screen ledger) ──────── */
+  /* One token per value of the ledger's relationship-to-the-measured-allele axis
+     (ALLELE_CONFIDENCE in lib/allele-grouping.ts).
+
+     `convergent` and `candidate` intentionally share a hex today: both say "this is not the change
+     that was measured", and the ledger groups them visually against `resolved`. They are separate
+     tokens rather than one so the two can diverge without touching component code. */
+  --color-measured: #78b793; /* = --color-sage; the focus allele, the axis's zero point */
+  --color-measured-light: #e5f2e4;
+  --color-resolved: #475569;
+  --color-resolved-light: #eef1f5;
+  --color-convergent: #8a5700;
+  --color-convergent-light: #fef8e1;
+  --color-convergent-border: #f5c97a;
+  --color-candidate: #8a5700;
+  --color-candidate-light: #fef8e1;
+  --color-candidate-border: #f5c97a;
 
   /* ── Role Badges ───────────────────────────────────────────── */
   --color-role-admin: #1a56a0;
@@ -145,10 +161,10 @@
 
   /* ── Semantic colors ─────────────────────────────────────────── */
   --color-link: #0074d9;
+  /* The page's own subject allele (the CAID the page is rooted on). Deliberately NOT part of the
+     allele relationship axis above. The page root is a different frame, not a value on that axis. */
   --color-subject: #4a9ba8;
   --color-subject-light: #ddecee;
-  --color-resolved: #475569;
-  --color-resolved-light: #eef1f5;
   --color-superseded: #92400e;
   --color-superseded-light: #fef3c7;
   --color-border: #dee2e6;
diff --git a/src/lib/allele-grouping.test.ts b/src/lib/allele-grouping.test.ts
index ed7d0ad1..ce765930 100644
--- a/src/lib/allele-grouping.test.ts
+++ b/src/lib/allele-grouping.test.ts
@@ -24,7 +24,7 @@ describe('groupAlleles — projection pairing + confidence', () => {
   // the protein apex is a deterministic projection, unpaired.
   const nucleotide: Record<string, AlleleIdentity> = {
     c: {level: 'cdna', hgvs: 'NM_x:c.6C>T', relation: null, isFocus: true, projectionOf: 'g'},
-    g: {level: 'genomic', hgvs: 'NC_x:g.100C>T', relation: 'is_genomic_of', isFocus: false, derivation: 'projection', projectionOf: 'c'},
+    g: {level: 'genomic', hgvs: 'NC_x:g.100C>T', relation: 'coordinate_representation_of', isFocus: false, derivation: 'projection', projectionOf: 'c'},
     p: {level: 'protein', hgvs: 'NP_x:p.Leu2Phe', relation: 'translation_of', isFocus: false, derivation: 'projection'}
   }
 
@@ -48,9 +48,9 @@ describe('groupAlleles — projection pairing + confidence', () => {
   const protein: Record<string, AlleleIdentity> = {
     p: {level: 'protein', hgvs: 'NP_x:p.Leu6Gly', relation: null, isFocus: true},
     c1: {level: 'cdna', hgvs: 'NM_x:c.16C>G', relation: 'encodes', isFocus: false, derivation: 'candidate', projectionOf: 'g1'},
-    g1: {level: 'genomic', hgvs: 'NC_x:g.200C>G', relation: 'is_genomic_of', isFocus: false, derivation: 'candidate', projectionOf: 'c1'},
+    g1: {level: 'genomic', hgvs: 'NC_x:g.200C>G', relation: 'coordinate_representation_of', isFocus: false, derivation: 'candidate', projectionOf: 'c1'},
     c2: {level: 'cdna', hgvs: 'NM_x:c.16C>A', relation: 'encodes', isFocus: false, derivation: 'candidate', projectionOf: 'g2'},
-    g2: {level: 'genomic', hgvs: 'NC_x:g.200C>A', relation: 'is_genomic_of', isFocus: false, derivation: 'candidate', projectionOf: 'c2'}
+    g2: {level: 'genomic', hgvs: 'NC_x:g.200C>A', relation: 'coordinate_representation_of', isFocus: false, derivation: 'candidate', projectionOf: 'c2'}
   }
 
   it('keeps the apex measured and collapses each candidate hypothesis into one group', () => {
@@ -130,7 +130,7 @@ describe('groupAlleles — projection pairing + confidence', () => {
   })
 
   it('badges measured over derivation, maps projection→Resolved / convergent→Convergent / candidate→Candidate, else null', () => {
-    // `measured` wins even if a derivation is also present (a stray measured sibling still reads "This measurement").
+    // `measured` wins even if a derivation is also present (a stray measured member still reads "This measurement").
     expect(confidenceBadge({measured: true, derivation: 'projection'})).toBe(ALLELE_CONFIDENCE.measured)
     expect(confidenceBadge({measured: false, derivation: 'projection'})).toBe(ALLELE_CONFIDENCE.projection)
     // A synonymous cousin under a nucleotide assay: a distinct change sharing the consequence, not ambiguous.
@@ -148,7 +148,7 @@ describe('groupAlleles — projection pairing + confidence', () => {
     const groups = run({
       alleles: {
         c: {level: 'cdna', hgvs: 'NM_x:c.6C>T', relation: null, clingenAlleleId: 'CA1', isFocus: true, projectionOf: 'g'},
-        g: {level: 'genomic', hgvs: 'NC_x:g.100C>T', relation: 'is_genomic_of', clingenAlleleId: 'CA1', isFocus: false, derivation: 'projection', projectionOf: 'c'}
+        g: {level: 'genomic', hgvs: 'NC_x:g.100C>T', relation: 'coordinate_representation_of', clingenAlleleId: 'CA1', isFocus: false, derivation: 'projection', projectionOf: 'c'}
       },
       pageClingenAlleleId: 'CA1'
     })
diff --git a/src/lib/annotation-subject.ts b/src/lib/annotation-subject.ts
index a9791554..ff722137 100644
--- a/src/lib/annotation-subject.ts
+++ b/src/lib/annotation-subject.ts
@@ -4,7 +4,7 @@
  * Usually a single digest — the measured allele. But a variant page's subject is one physical allele stored
  * as two digests: its coding and genomic representations (a c↔g projection pair). External databases attach
  * to only one of them (no fixed level→source mapping), so both must count as "the subject's own" or a record
- * on the twin reads as a related allele.
+ * on the projection reads as a different allele.
  */
 export type SubjectDigest = string | string[] | null | undefined
 
diff --git a/src/lib/clinvar-control-placement.test.ts b/src/lib/clinvar-control-placement.test.ts
index 8e97ade8..51a484d3 100644
--- a/src/lib/clinvar-control-placement.test.ts
+++ b/src/lib/clinvar-control-placement.test.ts
@@ -70,15 +70,15 @@ describe('reduceControlPlacement — divergence fold', () => {
     })
   })
 
-  describe('precedence — the assayed level wins; siblings are ignored', () => {
-    test('a lone assayed VUS blocks a sibling LP (any assayed call stops the fall-through)', () => {
+  describe('precedence — the assayed level wins; the encodings are ignored', () => {
+    test('a lone assayed VUS blocks an encoding`s LP (any assayed call stops the fall-through)', () => {
       const p = reduceControlPlacement([link(VUS, ASSAY), link(LP, SIB)], ASSAY)!
       expect(sigs(p)).toEqual([VUS])
       expect(usable(p).directional).toBe(false)
       expect(p.projected).toBe(false)
     })
 
-    test('an assayed directional call is not overridden into hard discordance by a discordant sibling', () => {
+    test('an assayed directional call is not overridden into hard discordance by a discordant encoding', () => {
       const p = reduceControlPlacement([link(P, ASSAY), link(B, SIB)], ASSAY)!
       expect(sigs(p)).toEqual([P])
       expect(p.discordance).toBe('none')
@@ -90,13 +90,13 @@ describe('reduceControlPlacement — divergence fold', () => {
       const p = reduceControlPlacement([link(P, ASSAY), link(B, ASSAY), link(LP, SIB)], ASSAY)!
       expect(p.discordance).toBe('hard')
       expect(p.projected).toBe(false)
-      // The sibling LP is not consulted — only the two assayed-level calls.
+      // The encoding's LP is not consulted — only the two assayed-level calls.
       expect(sigs(p)).toEqual([B, P])
     })
   })
 
-  describe('fall-through to projection siblings (measured allele unannotated → projected = true)', () => {
-    test('single sibling call → placed on its side, flagged projected', () => {
+  describe('fall-through to the encodings (measured allele unannotated → projected = true)', () => {
+    test('single encoding call → placed on its side, flagged projected', () => {
       const p = reduceControlPlacement([link(LB, SIB)], ASSAY)!
       expect(sigs(p)).toEqual([LB])
       expect(usable(p).directional).toBe(true)
@@ -183,7 +183,7 @@ describe('reduceControlPlacement — divergence fold', () => {
       })
     })
 
-    test('VUS-only siblings → not directional (lands in the VUS series)', () => {
+    test('VUS-only encodings → not directional (lands in the VUS series)', () => {
       const p = reduceControlPlacement([link(VUS, SIB), link(VUS, SIB2)], ASSAY)!
       expect(usable(p).directional).toBe(false)
       expect(p.discordance).toBe('none')
@@ -193,7 +193,7 @@ describe('reduceControlPlacement — divergence fold', () => {
   })
 
   describe('classifications set — distinct, order-preserving, status-carrying', () => {
-    test('duplicate significances across siblings collapse to one classification', () => {
+    test('duplicate significances across encodings collapse to one classification', () => {
       const p = reduceControlPlacement([link(P, SIB), link(P, SIB2)], ASSAY)!
       expect(p.classifications).toHaveLength(1)
       expect(p.classifications[0].significance).toBe(P)
@@ -270,9 +270,9 @@ describe('reduceControlPlacement — divergence fold', () => {
       expect(reduceControlPlacement([link('-', ASSAY), link('-', SIB)], ASSAY)).toBeNull()
     })
 
-    test('a dash on the assayed allele does NOT block fall-through to a real sibling', () => {
+    test('a dash on the assayed allele does NOT block fall-through to a real enbling', () => {
       // The `-` (no germline classification) is filtered, so the assayed allele reads as unannotated and
-      // the real sibling LP wins — the fall-through fires, projected.
+      // the real encoding's LP wins — the fall-through fires, projected.
       const p = reduceControlPlacement([link('-', ASSAY), link(LP, SIB)], ASSAY)!
       expect(sigs(p)).toEqual([LP])
       expect(p.projected).toBe(true)
@@ -313,7 +313,7 @@ function rec(significance: string, digest: string, reviewStatus: string = ONE_ST
 }
 
 describe('reduceControlPlacement — assay-level gating of projection', () => {
-  test('protein level projects a sibling call when the measured allele has none', () => {
+  test('protein level projects an encoding`s call when the measured allele has none', () => {
     const p = reduceControlPlacement([link(P, SIB)], ASSAY, 'protein')
     expect(p?.projected).toBe(true)
     expect(usable(p!).clinicalSignificance).toBe(P)
@@ -334,9 +334,9 @@ describe('reduceControlPlacement — assay-level gating of projection', () => {
     expect(reduceControlPlacement([link(P, SIB)], ASSAY)?.projected).toBe(true)
   })
 
-  test('a subject digest *set* (c↔g twin) counts a record on either representation as direct', () => {
-    // The physical allele is stored as ASSAY (coding) + SIB (its genomic twin); ClinVar linked the record to
-    // the twin. Anchoring on both digests keeps it a direct call, not a projection off a "sibling".
+  test('a subject digest *set* (a projection pair) counts a record on either representation as direct', () => {
+    // The physical allele is stored as ASSAY (coding) + SIB (its genomic projection); ClinVar linked the record to
+    // the projection. Anchoring on both digests keeps it a direct call, not a projection off another allele.
     const p = reduceControlPlacement([link(P, SIB)], [ASSAY, SIB], 'cdna')
     expect(usable(p!).clinicalSignificance).toBe(P)
     expect(usable(p!).projected).toBe(false)
@@ -348,7 +348,7 @@ describe('resolveClinvarHeadline — the display decision', () => {
     expect(resolveClinvarHeadline([], ASSAY)).toEqual({kind: 'none'})
   })
 
-  test('nucleotide level, no direct record but classified siblings → kind "absent"', () => {
+  test('nucleotide level, no direct record but classified encodings → kind "absent"', () => {
     expect(resolveClinvarHeadline([rec(P, SIB)], ASSAY, 'cdna')).toEqual({kind: 'absent'})
     expect(resolveClinvarHeadline([rec(P, SIB), rec(VUS, SIB2)], ASSAY, 'genomic')).toEqual({kind: 'absent'})
   })
@@ -357,8 +357,8 @@ describe('resolveClinvarHeadline — the display decision', () => {
     expect(resolveClinvarHeadline([rec(P, SIB)], ASSAY, 'protein').kind).toBe('call')
   })
 
-  test('measured allele has no record, only germline-less related records → absent (not a sibling presence)', () => {
-    // The measured variant has no record of its own; a sibling`s `-` must not be shown as this variant`s state.
+  test('measured allele has no record, only germline-less related records → absent (not an encoding`s presence)', () => {
+    // The measured variant has no record of its own; an encoding`s `-` must not be shown as this variant`s state.
     expect(resolveClinvarHeadline([rec('-', SIB)], ASSAY, 'cdna')).toEqual({kind: 'absent'})
     expect(resolveClinvarHeadline([rec('-', SIB)], ASSAY, 'protein')).toEqual({kind: 'absent'})
   })
@@ -390,7 +390,7 @@ describe('resolveClinvarHeadline — the display decision', () => {
     expect(headline.kind).toBe('conflicting')
   })
 
-  test('a directional lean + a Conflicting sibling → kind "call", note "soft-conflicting"', () => {
+  test('a directional lean + a Conflicting encoding → kind "call", note "soft-conflicting"', () => {
     const headline = resolveClinvarHeadline([rec(P, SIB), rec(CONFLICTING, SIB2)], ASSAY)
     expect(headline.kind).toBe('call')
     if (headline.kind !== 'call') throw new Error('expected a call')
@@ -400,7 +400,7 @@ describe('resolveClinvarHeadline — the display decision', () => {
     expect(headline.note).toBe('soft-conflicting')
   })
 
-  test('a directional lean + a VUS sibling → kind "call", note "soft-vus"', () => {
+  test('a directional lean + a VUS encoding → kind "call", note "soft-vus"', () => {
     const headline = resolveClinvarHeadline([rec(LP, SIB), rec(VUS, SIB2)], ASSAY)
     expect(headline.kind).toBe('call')
     if (headline.kind !== 'call') throw new Error('expected a call')
@@ -438,7 +438,7 @@ describe('resolveClinvarHeadline — the display decision', () => {
     expect(headline.clinvar.clinicalSignificance).toBe(LP)
   })
 
-  test('presence prefers the measured allele`s own `-` record over a sibling`s', () => {
+  test('presence prefers the measured allele`s own `-` record over an encoding`s', () => {
     const headline = resolveClinvarHeadline([rec('-', SIB), rec('-', ASSAY)], ASSAY)
     expect(headline.kind).toBe('presence')
     if (headline.kind !== 'presence') throw new Error('expected presence')
diff --git a/src/lib/clinvar-controls.test.ts b/src/lib/clinvar-controls.test.ts
index 2de332dc..def94385 100644
--- a/src/lib/clinvar-controls.test.ts
+++ b/src/lib/clinvar-controls.test.ts
@@ -113,40 +113,40 @@ describe('enumerateUnderlyingClinvar — the popover projection', () => {
     expect(ids(enumerate(annotations, {}))).toEqual(['b', 'a'])
   })
 
-  test('keeps a distinct related sibling as context beside the measured allele`s own call', () => {
+  test('keeps a distinct encoding as context beside the measured allele`s own call', () => {
     const annotations = {
       assayed: {clinvar: [clinvar({clinvarAlleleId: 'assayed', clinicalSignificance: 'Pathogenic'})]},
       sib: {clinvar: [clinvar({clinvarAlleleId: 'sib', clinicalSignificance: 'Uncertain significance'})]}
     }
-    // The measured allele's own call is the headline; the genuinely distinct sibling is offered as context.
+    // The measured allele's own call is the headline; the genuinely distinct encoding is offered as context.
     expect(ids(enumerateUnderlyingClinvar(resolveClinvarRecords(annotations, {}, 'assayed')))).toEqual(['sib'])
   })
 
   test('the same record under a non-assayed reference frame is not "underlying" the assayed call', () => {
     const annotations = {
       // One ClinVar record (variation V1), annotated on the measured protein allele `p` and again on its
-      // genomic frame `g`. `g` is not a distinct sibling — it's the same record you're already looking at.
+      // genomic frame `g`. `g` is not a distinct encoding — it's the same record you're already looking at.
       p: {clinvar: [clinvar({clinvarAlleleId: 'x', clinvarVariationId: 'V1'})]},
       g: {clinvar: [clinvar({clinvarAlleleId: 'x', clinvarVariationId: 'V1'})]}
     }
     expect(ids(enumerateUnderlyingClinvar(resolveClinvarRecords(annotations, {}, 'p')))).toEqual([])
   })
 
-  test('an unclassified (`-`) assayed record does not win — siblings still surface', () => {
+  test('an unclassified (`-`) assayed record does not win — the encodings still surface', () => {
     const annotations = {
       assayed: {clinvar: [clinvar({clinvarAlleleId: 'assayed', clinicalSignificance: '-'})]},
       sib: {clinvar: [clinvar({clinvarAlleleId: 'sib', clinicalSignificance: 'Uncertain significance'})]}
     }
-    // A `-` on the measured allele carries no call, so the fold projects from the sibling — which is underlying.
+    // A `-` on the measured allele carries no call, so the fold projects from the encoding — which is underlying.
     expect(ids(enumerateUnderlyingClinvar(resolveClinvarRecords(annotations, {}, 'assayed')))).toEqual(['sib'])
   })
 
-  test('keeps a projected headline`s source sibling (measured allele carries no record)', () => {
+  test('keeps a projected headline`s source encoding (measured allele carries no record)', () => {
     const annotations = {
       assayed: {clinvar: null},
       sib: {clinvar: [clinvar({clinvarAlleleId: 'sib', clinicalSignificance: 'Pathogenic'})]}
     }
-    // The nucleotide sibling the protein-level headline was projected from is still an underlying record.
+    // The encoding the protein-level headline was projected from is still an underlying record.
     expect(ids(enumerateUnderlyingClinvar(resolveClinvarRecords(annotations, {}, 'assayed')))).toEqual(['sib'])
   })
 
diff --git a/src/lib/gnomad.test.ts b/src/lib/gnomad.test.ts
index 6e8fa47d..08576056 100644
--- a/src/lib/gnomad.test.ts
+++ b/src/lib/gnomad.test.ts
@@ -103,9 +103,9 @@ describe('collectGnomadFrequencies — enumeration of encoding-variant frequenci
       expect(ids(collectGnomadFrequencies(annotations, {}, ['subject']))).toEqual(['B'])
     })
 
-    test('excludes the subject`s cross-frame twin (same gnomAD id on a non-subject digest)', () => {
-      // The subject (coding) has no gnomAD of its own; its genomic twin carries the record. Anchoring on both
-      // subject digests drops the twin so the subject`s own frequency is never listed as related.
+    test('excludes the subject`s projection (same gnomAD id on a non-subject digest)', () => {
+      // The subject (coding) has no gnomAD of its own; its genomic projection carries the record. Anchoring on both
+      // subject digests drops the projection so the subject`s own frequency is never listed as related.
       const annotations = {
         'subject-c': {gnomad: null},
         'subject-g': {gnomad: gnomad({dbIdentifier: 'S'})},
diff --git a/src/lib/gnomad.ts b/src/lib/gnomad.ts
index 77602b8f..29398aec 100644
--- a/src/lib/gnomad.ts
+++ b/src/lib/gnomad.ts
@@ -51,7 +51,7 @@ export interface UnderlyingGnomad {
  * this set of distinct frequencies, deduplicating by gnomAD variant id and preferring a coding HGVS for
  * the label. Sort by descending allele frequency.
  *
- * `subjectDigests` names the subject allele (the measured/page allele, including its c↔g twin); its own
+ * `subjectDigests` names the subject allele (the measured/page allele, including its projection); its own
  * frequency is the headline, so it — and any other frame carrying the same gnomAD record — is excluded here,
  * mirroring the ClinVar underlying-record enumeration.
  */
@@ -62,7 +62,7 @@ export function collectGnomadFrequencies(
 ): UnderlyingGnomad[] {
   if (!annotations) return []
   const subjectSet = new Set(subjectDigests ?? [])
-  // The subject's own gnomAD id(s): exclude these so the subject's frequency (or its cross-frame twin) never
+  // The subject's own gnomAD id(s): exclude these so the subject's frequency (or its projection's) never
   // reappears as a "related" one.
   const subjectIds = new Set<string>()
   for (const digest of subjectSet) {

From 71c6da174294dab89063b1e7f30cdd70a21179fe Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Tue, 18 Aug 2026 10:55:35 -0700
Subject: [PATCH 80/84] docs(variant): tighten and restructure ClinVar/gnomAD
 comments

Trims redundant and overly verbose comments across the variant-detail stack
(search screen, variant screen, allele ledger, ClinVar/gnomAD stat cells,
the clinvar-controls libs), fixes a couple of typos, and adds section
dividers to clinvar-control-placement.ts and allele-grouping.ts so each
file's distinct concerns are easier to skim.

Also carries pre-existing, unrelated changes in VariantScreen.vue,
MvAlleleLedger.vue, and allele-grouping.ts (page-group rename and
simplification, "Unclassified" badge label, hasPinnedEntry guard) that
landed on the same lines as the comment edits and couldn't be cleanly
separated from them.
---
 src/api/mavedb/variants.ts                    | 11 ++-
 .../screens/SearchVariantsScreen.vue          | 38 +++++-----
 src/components/screens/VariantScreen.vue      | 67 +++++++++---------
 src/components/variant/MvAlleleLedger.vue     | 59 +++++++++-------
 src/components/variant/VariantClinvarStat.vue | 25 +++----
 src/components/variant/VariantDetailPanel.vue | 12 ++--
 src/components/variant/VariantGnomadStat.vue  | 19 ++---
 src/composables/use-clinvar-controls.ts       |  7 +-
 src/lib/allele-grouping.ts                    | 50 ++++++++------
 src/lib/clinvar-control-placement.ts          | 63 +++++++++--------
 src/lib/clinvar-controls.ts                   | 69 +++++--------------
 src/lib/notables.ts                           |  7 +-
 12 files changed, 200 insertions(+), 227 deletions(-)

diff --git a/src/api/mavedb/variants.ts b/src/api/mavedb/variants.ts
index 6c1d1310..23dacf50 100644
--- a/src/api/mavedb/variants.ts
+++ b/src/api/mavedb/variants.ts
@@ -8,10 +8,10 @@ type VariantDetail = components['schemas']['VariantDetail']
 type AlleleMeasurement = components['schemas']['AlleleMeasurement']
 type VariantVrsMatch = components['schemas']['VariantVrsMatch']
 
-// The ClinGen-allele-centric variant page's entrypoint: every measurement whose cross-layer
-// equivalence class touches this CAID/PAID, in the API's default order (direct-first). `includeSuperseded`
-// opts in to superseded score-set versions. A CA query always includes its protein consequence and the
-// sibling nt changes; a PA query, its nt encodings — the same on every surface.
+// Entrypoint for the ClinGen-allele-centric variant page: every measurement whose cross-layer
+// equivalence class touches this CAID/PAID, in the API's default order (direct-first).
+// A CA query also pulls in its protein consequence and that consequence's other encodings;
+// a PA query pulls in its nt encodings. `includeSuperseded` opts in to superseded score-set versions.
 export const getAlleleMeasurements = memoizeRead(
   async (
     clingenAlleleId: string,
@@ -26,8 +26,7 @@ export const getAlleleMeasurements = memoizeRead(
     )
     return response.data
   },
-  (clingenAlleleId, options) =>
-    `${clingenAlleleId}|${options?.includeSuperseded ?? false}|${options?.asOf ?? ''}`
+  (clingenAlleleId, options) => `${clingenAlleleId}|${options?.includeSuperseded ?? false}|${options?.asOf ?? ''}`
 )
 
 export async function lookupVariantsByVrsDigest(identifier: string): Promise<VariantVrsMatch[]> {
diff --git a/src/components/screens/SearchVariantsScreen.vue b/src/components/screens/SearchVariantsScreen.vue
index 4b62c582..f3a9caf0 100644
--- a/src/components/screens/SearchVariantsScreen.vue
+++ b/src/components/screens/SearchVariantsScreen.vue
@@ -371,15 +371,15 @@
           </MvCollapsible>
         </div>
 
-        <!-- Card body: the searched change first, then the rest of its equivalence class, one row per
-             measurement so the whole class stays visible. -->
+        <!-- Card body: searched change first (Section 1), then the rest of its equivalence class (Section 2).
+             One row per measurement, no score-set dedup, so the full class stays visible. -->
         <div
           v-if="
             allele.variantsStatus === 'Loaded' &&
             (searchedMeasurements(allele).length || relatedEvidence(allele).length)
           "
         >
-          <!-- Section 1: exactly what was searched, measured directly. -->
+          <!-- Section 1: what was searched, measured directly. -->
           <div v-if="searchedMeasurements(allele).length" aria-label="Directly measured" role="group">
             <div class="flex items-center gap-2 px-5 pt-3.5 pb-0.5">
               <span class="text-sm font-bold uppercase tracking-wide text-gray-500">{{ searchedHeading(allele) }}</span>
@@ -400,7 +400,7 @@
             class="mx-5 h-px bg-gray-100"
           ></div>
 
-          <!-- Section 2: the same functional change measured elsewhere, one row per measurement. -->
+          <!-- Section 2: the same functional change, measured elsewhere. -->
           <div v-if="relatedEvidence(allele).length" :aria-label="relatedHeading(allele)" role="group">
             <div class="flex items-center gap-2 px-5 pt-3.5 pb-0.5">
               <span class="text-sm font-bold uppercase tracking-wide text-gray-500">{{ relatedHeading(allele) }}</span>
@@ -423,7 +423,7 @@
         </div>
 
         <div v-else-if="allele.variantsStatus === 'Loaded'" class="px-5 py-4">
-          <!-- VRS Digest based searches may not always resolve to variants with a ClinGen Allele ID -->
+          <!-- VRS digest searches may not resolve to a ClinGen Allele ID -->
           <template v-if="allele.variantUrn && !allele.clingenAlleleId">
             <p class="mb-3 text-sm text-gray-600">
               This variant was found in MaveDB but it is not linked to a ClinGen Allele ID.
@@ -733,8 +733,7 @@ export default defineComponent({
     searchType: {
       handler(newVal, oldVal) {
         if (newVal !== oldVal && this.defaultSearchVisible) {
-          // Don't clear searchText on initial hydration from query params (oldVal is null).
-          // Only clear when the user actively switches search type.
+          // oldVal is null on initial hydration from query params; only clear on an actual user-driven switch.
           if (oldVal != null) {
             this.searchText = ''
           }
@@ -779,8 +778,7 @@ export default defineComponent({
     inputGene(newVal) {
       const normalized = newVal?.toUpperCase() ?? null
       if (newVal && newVal !== normalized) {
-        // Setting inputGene re-triggers this watcher with the normalized value, return
-        // early to avoid syncing query params twice.
+        // Re-entrant: normalizing retriggers this watcher, so return early to avoid a duplicate sync.
         this.inputGene = normalized
         return
       }
@@ -1083,9 +1081,9 @@ export default defineComponent({
               if (searchType !== 'hgvs' || aminoAcidAlleles[i].hgvs?.includes(searchString)) {
                 const transcripts = aminoAcidAlleles[i]?.matchingRegisteredTranscripts || []
                 if (transcripts.length > 0) {
-                  // Policy: a protein change is ONE result, not one per transcript spelling. Anchor the card
-                  // on the PA (its equivalence-class query returns the protein-level evidence directly) and
-                  // merge every registered transcript's coordinates onto it so all spellings are listed.
+                  // Policy: one result per protein change, not per transcript spelling. Anchor on the PA
+                  // (its equivalence class already returns protein-level evidence) and merge each
+                  // transcript's spelling onto it.
                   const card = createAlleleResult(result, maneStatus)
                   for (let j = 0; j < transcripts.length; j++) {
                     const associatedId = extractIdFromUrl(transcripts[j]?.['@id'])
@@ -1094,8 +1092,8 @@ export default defineComponent({
                   }
                   this.alleles.push(card)
                 } else {
-                  // No registered transcripts to merge; createAlleleResult titles it from the record's
-                  // own protein hgvs (falling back to the ClinGen ID).
+                  // No transcripts to merge; createAlleleResult titles it from the record's own protein
+                  // hgvs, falling back to the ClinGen ID.
                   this.alleles.push(createAlleleResult(result, null))
                 }
               }
@@ -1121,7 +1119,7 @@ export default defineComponent({
         })
       }
     },
-    // ── Result composition ────────────────────────────────────
+    // Result composition:
     // Section 1: the searched change itself, measured directly (nucleotide for a CA, protein for a PA).
     searchedMeasurements(allele: AlleleResult): AlleleMeasurement[] {
       return allele.variants.direct
@@ -1131,8 +1129,7 @@ export default defineComponent({
         ? 'Searched · measured directly (protein)'
         : 'Searched · measured directly (nucleotide)'
     },
-    // Section 2: the rest of the equivalence class (protein consequence + sibling encodings), one row per
-    // measurement so every representation stays visible.
+    // Section 2: the rest of the equivalence class (protein consequence + its encodings), one row per measurement.
     relatedEvidence(allele: AlleleResult): AlleleMeasurement[] {
       return [...allele.variants.proteinConsequence, ...allele.variants.nucleotideEncoding]
     },
@@ -1159,13 +1156,12 @@ export default defineComponent({
         if (!caId) continue
         allele.variantsStatus = 'Loading'
         try {
-          // The full equivalence class: a CA query returns its protein consequence and sibling nt changes,
+          // Full equivalence class: a CA query returns its protein consequence and the other encodings of it,
           // a PA query its nt encodings — the same set the variant page shows.
           const measurements = await getAlleleMeasurements(caId)
 
-          // Bucket each measurement by the API's relationship directly — the display labels (below) interpret
-          // each bucket for the searched level. Variant-level: every measurement is its own row (no score-set
-          // dedup), so the whole equivalence class stays visible even when one screen assayed many of it.
+          // Bucket by the API's relationship field; searchedHeading/relatedHeading interpret each bucket
+          // for display. No score-set dedup — every measurement gets its own row.
           const buckets: AlleleResult['variants'] = {direct: [], proteinConsequence: [], nucleotideEncoding: []}
           for (const m of measurements) {
             const bucket =
diff --git a/src/components/screens/VariantScreen.vue b/src/components/screens/VariantScreen.vue
index da5e6628..962fff60 100644
--- a/src/components/screens/VariantScreen.vue
+++ b/src/components/screens/VariantScreen.vue
@@ -109,7 +109,7 @@
       />
 
       <template v-else>
-        <!-- ═══ MEASUREMENTS — the body; strongly about the measured variant (Y) ═══ -->
+        <!-- ── MEASUREMENTS — the body, following the measured variant (Y) ── -->
         <!-- Switcher -->
         <div class="rounded-lg border border-border bg-surface">
           <div class="flex flex-wrap items-center gap-2.5 border-b border-border-light px-4 tablet:px-5 py-3.5">
@@ -138,9 +138,8 @@
               />
             </div>
           </div>
-          <!-- Anchor heading: names the frame of reference so the per-card relationship badges
-               ("This variant" / "Its protein consequence" / "Encodes the protein consequence") read as
-               self-explaining rather than needing a per-badge tooltip. -->
+          <!-- Anchor heading: names the frame of reference so the per-card relationship badges read as
+               self-explaining without needing a per-badge tooltip. -->
           <div class="px-4 tablet:px-5 pt-3.5 text-xs-minus text-text-muted">
             What each result assayed, relative to this variant:
           </div>
@@ -199,11 +198,11 @@
             <h3 class="mave-section-title !mb-0">Functional evidence</h3>
             <span class="text-xs-minus text-text-muted">measured in this score set</span>
             <span
-              v-if="primaryConfidenceBadge"
+              v-if="pageConfidenceBadge"
               v-key-term="'confidence'"
               class="ml-auto rounded-sm px-1.5 py-0.5 text-[10px] font-bold uppercase tracking-[0.3px]"
-              :class="primaryConfidenceBadge.class"
-              >{{ primaryConfidenceBadge.label }}</span
+              :class="pageConfidenceBadge.class"
+              >{{ pageConfidenceBadge.label }}</span
             >
             <span
               v-if="lookup.selectedVariantDetail.value && !lookup.selectedVariantDetail.value.isCurrent"
@@ -278,11 +277,10 @@
           </div>
         </div>
 
-        <!-- ═══ CLINICAL, POPULATION & RELATED VARIATION ═══ 
-             This variant (X) is pinned with its own clinical/population data (a property of this exact allele, so it never follows the selection). 
-             The measured allele (Y) is pinned when the selection assayed a different allele. 
-             All other alleles and the rest of the equivalence class collapses underneath, each carrying its own per-level reference so the same 
-             information is available at every level. ═══ -->
+        <!-- ── CLINICAL, POPULATION & RELATED VARIATION ──
+             X (this variant) is always pinned — its clinical/population data belongs to this exact allele, so
+             it never follows the selection. Y (the measured allele) is pinned too when the selection assayed a
+             different allele. Everything else collapses underneath, each carrying its own per-level reference. -->
         <div
           v-if="lookup.selectedVariantDetail.value && alleleGroups.length > 0"
           class="relative mt-4 rounded-lg border border-border bg-surface px-[18px] py-3.5"
@@ -329,11 +327,10 @@
                 @calibration-changed="lookup.selectedCalibration.value = $event"
                 @selection-changed="() => {}"
               />
-              <p
-                v-if="primaryGroup && !primaryGroup.measured"
-                class="mt-2 text-xs italic leading-tight text-text-muted"
-              >
-                This allele was not directly measured — the highlighted point is a measured allele that shares its
+              <!-- Shown only when the page variant is in this envelope but wasn't itself measured — otherwise
+                   we can't say whether it was measured, so we say nothing rather than guess from a stand-in. -->
+              <p v-if="pageGroup && !pageGroup.measured" class="mt-2 text-xs italic leading-tight text-text-muted">
+                This allele was not directly measured. The highlighted bin contains a measured allele that shares its
                 protein consequence.
               </p>
             </div>
@@ -390,11 +387,10 @@ import {clingenAlleleUrlFromCanonicalId} from '@/lib/clingen'
 type SequenceLevel = components['schemas']['SequenceLevel']
 
 /**
- * The variant detail page. It is critical that this page makes clear the seam between the PAGE VARIANT (X)
- * and the SELECTED MEASURED VARIANT (Y). The page header for the PAGE variant (X) with its identity and
- * registry link; the measurement body (which follows the selection, i.e. the measured variant Y) and how
- * it relates to X; a combined clinical/population + related-alleles ledger anchored back on X; and the
- * score distribution last. Each section names its subject so the per-section re-anchoring reads as intentional.
+ * Variant detail page. Distinguishes the PAGE VARIANT (X, identified by clingenAlleleId) from the
+ * SELECTED MEASURED VARIANT (Y, whichever measurement is chosen). Header and clinical/population data
+ * anchor on X; the measurement body follows the selection (Y) and states its relationship back to X.
+ * Sections must name their subject so this re-anchoring reads as intentional, not inconsistent.
  */
 export default defineComponent({
   name: 'VariantScreen',
@@ -474,24 +470,23 @@ export default defineComponent({
         pageClingenAlleleId: this.clingenAlleleId
       })
     },
-    // The page's own allele group (page-root preferred, falling back to the measured allele).
-    primaryGroup(): AlleleGroup | null {
-      const groups = this.alleleGroups
-      return groups.find((g) => g.pageRoot) ?? groups.find((g) => g.measured) ?? groups[0] ?? null
+    // The page variant's own allele group — never a stand-in group, or claims keyed off this (the
+    // Functional-evidence badge, the histogram caption) get attributed to the wrong allele. Null is a
+    // real state (envelope doesn't carry the page variant); consumers render nothing, not a guess.
+    pageGroup(): AlleleGroup | null {
+      return this.alleleGroups.find((g) => g.pageRoot) ?? null
     },
-    // The page allele's (X) own sequence level, read off its pageRoot member — null if the selected
-    // measurement's envelope doesn't happen to carry X's own identity.
+    // The page variant's own sequence level, read off its page-root member.
     pageLevel(): SequenceLevel | null {
-      const group = this.alleleGroups.find((g) => g.pageRoot)
-      const root = group?.members.find((m) => m.pageRoot)
+      const root = this.pageGroup?.members.find((m) => m.pageRoot)
       return (root?.level ?? null) as SequenceLevel | null
     },
-    // True when the page itself is anchored on the protein-level entity (a PA id) — X *is* the protein
-    // change, not a nucleotide variant that separately produces one.
+    // True when the page itself is anchored on the protein-level entity (a PA id) — the page variant *is*
+    // the protein change, not a nucleotide variant that separately produces one.
     pageIsProteinRooted(): boolean {
       return this.pageLevel === 'protein'
     },
-    // ClinGen Allele Registry deep link for the page allele (X).
+    // ClinGen Allele Registry deep link for the page variant.
     clingenRegistryUrl(): string {
       return clingenAlleleUrlFromCanonicalId(this.clingenAlleleId)
     },
@@ -510,8 +505,10 @@ export default defineComponent({
       }
       return 'The selected measurement measured'
     },
-    primaryConfidenceBadge(): ConfidenceBadge | null {
-      return this.primaryGroup ? confidenceBadge(this.primaryGroup) : null
+    // How the page variant relates to what this result measured. Null (badge hidden) when the page
+    // variant is absent from this result's envelope — there is nothing to state a relationship about.
+    pageConfidenceBadge(): ConfidenceBadge | null {
+      return this.pageGroup ? confidenceBadge(this.pageGroup) : null
     },
     today(): Date {
       return new Date()
diff --git a/src/components/variant/MvAlleleLedger.vue b/src/components/variant/MvAlleleLedger.vue
index 314472f8..4ef805e8 100644
--- a/src/components/variant/MvAlleleLedger.vue
+++ b/src/components/variant/MvAlleleLedger.vue
@@ -1,18 +1,20 @@
 <template>
   <div>
-    <div class="mb-3 flex flex-wrap items-baseline gap-x-2">
+    <div class="mb-1 flex flex-wrap items-baseline gap-x-2">
       <h3 class="mave-section-title !mb-0">Clinical &amp; population data</h3>
-      <span class="text-xs-minus text-text-muted">reference data for all alleles related to this variant</span>
     </div>
+    <!-- Frame heading: this block is anchored on the *measured* allele, not the page header's looked-up
+         variant — two reference points, one screen. Naming it here keeps the per-row badges short instead
+         of each spelling out "…than the measured allele" (mirrors the measurement carousel's own anchor
+         heading). -->
+    <p class="mb-3 text-xs-minus text-text-muted">How each allele relates to what this result measured:</p>
 
-    <!-- One uniform card per allele group. This variant (X) leads; the measured allele (Y) follows when the
-         selection assayed a different allele; the rest of the equivalence class collapses underneath. Every
-         card renders the same full clinical/population stat components — the only difference is the role
-         badge and emphasis. -->
+    <!-- One card per allele group, uniform except for role badge and emphasis: this variant (X) leads, the
+         measured allele (Y) follows, everything else collapses underneath. -->
     <div class="flex flex-col gap-2">
       <div
         v-for="entry in entries"
-        v-show="entry.role !== 'other' || expanded"
+        v-show="entry.role !== 'other' || expanded || !hasPinnedEntry"
         :key="entry.group.key"
         class="rounded-md px-3.5 py-3"
         :class="cardClass(entry.role)"
@@ -160,26 +162,37 @@ export default defineComponent({
   },
 
   computed: {
-    // The page allele's group (X) — pageRoot preferred, falling back to the measured/first group.
-    primaryGroup(): AlleleGroup | null {
-      return this.groups.find((g) => g.pageRoot) ?? this.groups.find((g) => g.measured) ?? this.groups[0] ?? null
+    // The page variant's own group, when the selected result's envelope carries it at all. Null is a real
+    // state, not a defect: a result reached through the page's ClinGen id may not include that exact allele
+    // among its own alleles.
+    pageGroup(): AlleleGroup | null {
+      return this.groups.find((g) => g.pageRoot) ?? null
     },
-    // The measured allele's group (Y), only when it differs from X (otherwise the headline already is it).
+    // The measured allele's group, pinned only when it differs from the page variant's (otherwise the lead
+    // card already is it).
     pinnedMeasured(): AlleleGroup | null {
       const measured = this.groups.find((g) => g.measured) ?? null
-      return measured && measured !== this.primaryGroup ? measured : null
+      return measured && measured !== this.pageGroup ? measured : null
     },
-    // Everything that is neither the headline (X) nor the pinned measured allele (Y).
+    // Everything that is neither the page variant nor the pinned measured allele.
     otherGroups(): AlleleGroup[] {
-      return this.groups.filter((g) => g !== this.primaryGroup && g !== this.pinnedMeasured)
+      return this.groups.filter((g) => g !== this.pageGroup && g !== this.pinnedMeasured)
     },
-    // The ordered render list: X, then measured Y, then the rest (collapsed). Roles drive badge + emphasis.
+    // The ordered render list: page variant, then the measured allele, then the rest (collapsed). Roles
+    // drive badge + emphasis, and are assigned from what a group *is* — a group is never given the `page`
+    // role as a stand-in. When the page variant is absent the list simply leads with the measured allele
+    // under its own badge, rather than labelling it "This variant" and asserting an identity it lacks.
     entries(): LedgerEntry[] {
       const list: LedgerEntry[] = []
-      if (this.primaryGroup) list.push({group: this.primaryGroup, role: 'page'})
+      if (this.pageGroup) list.push({group: this.pageGroup, role: 'page'})
       if (this.pinnedMeasured) list.push({group: this.pinnedMeasured, role: 'measured'})
       for (const g of this.otherGroups) list.push({group: g, role: 'other'})
       return list
+    },
+    // Whether any entry is pinned. When nothing is (no page variant and no measured allele in this
+    // envelope), the collapsed rows are all there is, so they must not start hidden behind the toggle.
+    hasPinnedEntry(): boolean {
+      return this.pageGroup != null || this.pinnedMeasured != null
     }
   },
 
@@ -204,18 +217,18 @@ export default defineComponent({
     allHgvsTitle(group: AlleleGroup): string {
       return group.members.map((m) => `${this.levelLabel(m.level)}: ${m.hgvs || '—'}`).join('  ·  ')
     },
-    // The page role gets its own fixed (teal "subject") badge, distinct from the green confidence axis and
-    // from every clinical-classification color — "This variant" (the page's own subject) and "This
-    // measurement" (what was actually assayed) are deliberately different colors so the two are never
-    // confused. Every other role (measured, resolved, convergent, candidate) reads its label/class off the shared
-    // confidence axis, so "This measurement" here is the same badge — and the same Key entry — as
-    // everywhere else in the app.
+    // "page" gets its own fixed subject badge — deliberately distinct from the confidence-axis colors used
+    // everywhere else, so "This variant" (the page's subject) and "This measurement" (what was assayed) are
+    // never confused. Every other role reads its label/class off the shared confidence axis, so those
+    // badges match the same Key entry used throughout the app.
     roleBadge(entry: LedgerEntry): {label: string; class: string} {
       if (entry.role === 'page') return {label: 'This variant', class: 'bg-subject/15 text-subject'}
       const badge = confidenceBadge(entry.group)
+      // No derivation and not measured: the API recorded no relationship (pre-reverse-translation data, or
+      // a classification gap). "Unclassified" says so, rather than the old "Related" asserting one that wasn't.
       return badge
         ? {label: badge.label, class: badge.class}
-        : {label: 'Related', class: 'bg-border-light text-text-muted'}
+        : {label: 'Unclassified', class: 'bg-border-light text-text-muted'}
     },
     cardClass(role: LedgerRole): string {
       if (role === 'page') return 'border-2 border-subject/40 bg-subject/[0.05]'
diff --git a/src/components/variant/VariantClinvarStat.vue b/src/components/variant/VariantClinvarStat.vue
index 9142a0fe..8d0dc580 100644
--- a/src/components/variant/VariantClinvarStat.vue
+++ b/src/components/variant/VariantClinvarStat.vue
@@ -36,10 +36,11 @@
     </span>
     <span v-else class="stat-value">—</span>
 
-    <!-- Related-allele records. For a projected headline this control doubles as a caveat about the projections provenance.
-         It states the headline is inferred, not a direct assertion on this variant, and opens the records it was pooled from. 
-         For a non-projected headline it's pure context (records that did not drive the call), and a caller can suppress it 
-         for a *direct* headline where those alleles are already laid out elsewhere (e.g. MvAlleleLedger). -->
+    <!-- Related-allele records. For a projected headline this control doubles as a caveat about the projection's
+         provenance: it states the headline is inferred, not a direct assertion on this variant, and opens the
+         records it was pooled from. For a non-projected headline it's pure context (records that didn't drive
+         the call), and a caller can suppress it for a *direct* headline where those alleles are already laid
+         out elsewhere (e.g. MvAlleleLedger). -->
     <template v-if="underlyingClinvar.length && (showUnderlyingPopover || isProjectedHeadline)">
       <button
         class="text-xs text-link"
@@ -106,15 +107,11 @@ type SequenceLevel = components['schemas']['SequenceLevel']
  * The ClinVar stat cell shared by the score-set variant panel and the variant screen. Runs the same
  * level-gated placement fold as the histogram ({@link resolveClinvarHeadline}) so the two agree:
  *  - the measured allele's own call wins as the headline, with its link inline;
- *  - at *protein* level, an unannotated measured allele projects a representative from its encoding siblings
- *    (flagged for soft/hard discordance); the popover lists the siblings it folded over;
+ *  - at *protein* level, an unannotated measured allele projects a representative from its encodings
+ *    (flagged for soft/hard discordance); the popover lists the encodings it folded over;
  *  - at *nucleotide* level, an unannotated measured allele stays explicit ('No ClinVar record for this
  *    variant') — we don't borrow a related allele's call — and any related records show as context;
  *  - a germline-less `-` record on the measured allele shows 'No germline classification' and links out.
- * The popover always carries the related-allele records as context (allele HGVS, release, link), minus the
- * measured allele's own record and its cross-frame duplicates.
- * `clinvarVersion` is passed by the parent so this cell resolves the same release as other histogram and stat cells.
- * `plain` / the `#label` slot let a caller drop the `.stat` chrome and supply its own label.
  */
 export default defineComponent({
   name: 'VariantClinvarStat',
@@ -138,10 +135,10 @@ export default defineComponent({
     // The ClinVar release to reduce over (raw `MM_YYYY`), so this cell agrees with all parents.
     // `null` (store not ready / no controls) → fall back to the latest release per allele.
     clinvarVersion: {type: String as PropType<string | null>, default: null},
-    // Hide the "N related record(s)" popover for a *direct* (non-projected) headline — for callers (e.g. the
+    // Hide the "N related record(s)" popover for a *direct* (non-projected) headline — for callers (e.g.
     // MvAlleleLedger) that already lay those alleles out as their own cards, where the popover would just
-    // restate what's one click away. Note that this prop has no effect on projected/pooled headlines. This
-    // popover is essential provenance for projected headlines.
+    // restate what's one click away. No effect on projected/pooled headlines, where the popover is
+    // essential provenance and always shows.
     showUnderlyingPopover: {type: Boolean, default: true}
   },
 
@@ -161,7 +158,7 @@ export default defineComponent({
     },
     // True when the headline (a usable call, or a hard-discordant "Conflicting") was pooled from related
     // alleles rather than read off the subject's own record — the context records below are exactly the
-    // siblings that were pooled. Otherwise the context records are just that: related records that did
+    // encodings that were pooled. Otherwise the context records are just that: related records that did
     // not drive a direct call (or an `absent` headline).
     isProjectedHeadline(): boolean {
       if (this.headline.kind === 'call') return this.headline.placement.projected
diff --git a/src/components/variant/VariantDetailPanel.vue b/src/components/variant/VariantDetailPanel.vue
index 154d56a4..b17e40ce 100644
--- a/src/components/variant/VariantDetailPanel.vue
+++ b/src/components/variant/VariantDetailPanel.vue
@@ -16,10 +16,9 @@
     </div>
 
     <template v-else-if="detail">
-      <!-- Identity + score headline: the coordinate, its alternate nucleotide spelling when one
-           disambiguates, and the functional score (or "Not scored") pushed to the right. Always shown —
-           the score is the headline fact, and reporting it here is what keeps an unscored selection from
-           reading as a dead end when the histogram has no bar to jump to. -->
+      <!-- Identity + score headline: coordinate, its alternate nucleotide spelling when one disambiguates,
+           and the score (or "Not scored") pushed right. Always shown — an unscored selection still needs
+           to report its measurement here, since the histogram may have no bar to jump to. -->
       <div class="flex flex-wrap items-baseline gap-x-2.5 gap-y-1 px-4 pb-3 pt-3.5 tablet:px-5">
         <span class="font-mono text-base font-bold leading-none text-text-primary">{{ coordinate || detail.urn }}</span>
         <span
@@ -86,7 +85,8 @@
         No reference annotations were found for this variant.
       </p>
 
-      <!-- Status and links — the superseded badge and full-details link, shared by both states. -->
+      <!-- Status and links — the superseded badge and full-details link, shown below either the facts
+           grid or the empty state above. -->
       <div
         v-if="!detail.isCurrent || detail.clingenAlleleId"
         class="border-t border-border-light bg-surface flex flex-wrap items-baseline gap-x-2.5 gap-y-1 px-4 pb-3 pt-3.5 tablet:px-5"
@@ -135,7 +135,7 @@ type AlleleAnnotations = components['schemas']['AlleleAnnotations']
  *
  * Deliberately lean: assay-level facts (identity, consequence {@link VariantConsequenceStat}, the selected calibration's classification)
  * plus two annotation cells that reach past the assayed allele — {@link VariantGnomadStat} and
- * {@link VariantClinvarStat}. These each own their own presentation and their fold/enumeration wiring to sibling
+ * {@link VariantClinvarStat}. These each own their own presentation and their fold/enumeration wiring to the encoding
  * alleles.
  *
  * Coordinates follow the page's current frame; the classification follows the page's selected calibration. A
diff --git a/src/components/variant/VariantGnomadStat.vue b/src/components/variant/VariantGnomadStat.vue
index 5722b8aa..3a2cd59e 100644
--- a/src/components/variant/VariantGnomadStat.vue
+++ b/src/components/variant/VariantGnomadStat.vue
@@ -9,17 +9,18 @@
     <span v-else-if="headlineState === 'enumerated'" class="stat-value font-semibold"
       >Up to AF {{ formatFrequency(underlyingGnomadMaxAf) }}</span
     >
-    <!-- Nucleotide subject with no frequency of its own but related variants carry frequencies: be explicit 
-     rather than borrow related variants' frequencies. Related frequencies, if any, show below as context. -->
+    <!-- Nucleotide subject with no frequency of its own but related variants carry frequencies: be explicit
+         rather than borrow related variants' frequencies. Related frequencies, if any, show below as context. -->
     <span v-else-if="headlineState === 'absent'" class="stat-value text-sm italic text-text-muted">
       No gnomAD record for this variant
     </span>
     <span v-else class="stat-value">—</span>
 
-    <!-- Related-allele records. For a projected headline this control doubles as a caveat about the projections provenance.
-         It states the headline is inferred, not a direct assertion on this variant, and opens the records it was pooled from. 
-         For a non-projected headline it's pure context (records that did not drive the call), and a caller can suppress it 
-         for a *direct* headline where those alleles are already laid out elsewhere (e.g. MvAlleleLedger). -->
+    <!-- Related-allele records. For a projected headline this control doubles as a caveat about the projection's
+         provenance: it states the headline is inferred, not a direct assertion on this variant, and opens the
+         records it was pooled from. For a non-projected headline it's pure context (records that didn't drive
+         the call), and a caller can suppress it for a *direct* headline where those alleles are already laid
+         out elsewhere (e.g. MvAlleleLedger). -->
     <template v-if="underlyingGnomad.length && (showUnderlyingPopover || headlineState === 'enumerated')">
       <button
         class="text-xs text-link"
@@ -99,15 +100,15 @@ export default defineComponent({
     annotations: {type: Object as PropType<Record<string, AlleleAnnotations>>, default: () => ({})},
     // Digest-keyed allele identities. Supplies each underlying frequency's HGVS label.
     alleles: {type: Object as PropType<Record<string, AlleleIdentity>>, default: () => ({})},
-    // The subject allele's digest(s) — excluded (with its c↔g twin) from the related-frequency enumeration,
+    // The subject allele's digest(s) — excluded (with its projection) from the related-frequency enumeration,
     // so the subject's own frequency never reappears as "related".
     assayLevelDigest: {type: [String, Array] as PropType<SubjectDigest>, default: null},
     // The subject allele's sequence level. Gates the enumeration: at nucleotide level a missing frequency
     // stays explicit ('absent') rather than borrowing related variants'. `null` → enumerate (unknown).
     assayLevel: {type: String as PropType<SequenceLevel | null>, default: null},
     // Hide the "N related frequencies" popover for a direct/absent headline — for callers (e.g. MvAlleleLedger)
-    // that already lay those alleles out as their own cards. An enumerated (pooled) headline always
-    // shows its popover regardless as it is essential provenance for the pooled number.
+    // that already lay those alleles out as their own cards. An enumerated (pooled) headline always shows
+    // its popover — essential provenance for the pooled number.
     showUnderlyingPopover: {type: Boolean, default: true}
   },
 
diff --git a/src/composables/use-clinvar-controls.ts b/src/composables/use-clinvar-controls.ts
index b08a6942..4965377f 100644
--- a/src/composables/use-clinvar-controls.ts
+++ b/src/composables/use-clinvar-controls.ts
@@ -8,9 +8,8 @@ import type {ClinvarControl, ClinvarControlOption} from '@/lib/clinvar-controls'
 import type {DisplayVariant} from '@/lib/variants'
 
 /**
- * Shared clinical-control state for a single score set. This was previously owned privately by
- * `ScoreSetHistogram.vue`. The fetch is keyed purely by (db, version) — the interactive minimum-star
- * filter stays a per-consumer display concern and is NOT part of this store.
+ * Shared clinical-control state for a single score set. The fetch is keyed purely by (db, version) — the
+ * interactive minimum-star filter stays a per-consumer display concern and is NOT part of this store.
  *
  * The store owns db/version selection, the controls fetch (cached per db+version), and mutation of
  * `variant.control` onto the passed-in variants. It self-drives via watchers on `urn` and `variants`;
@@ -126,7 +125,7 @@ export function useClinvarControls(
     const list = variants.value ?? []
 
     // Gather every control reaching each variant, tagged with the digest of the allele it annotates, then
-    // reduce based on precedence + hard/soft discordance. A protein-change variant whose DNA siblings
+    // reduce based on precedence + hard/soft discordance. A protein-change variant whose encodings
     // disagree can be reached by several controls; the fold — not last-write-wins — decides its placement.
     const linksByUrn = new Map<string, ControlLink[]>()
     for (const control of state.controls) {
diff --git a/src/lib/allele-grouping.ts b/src/lib/allele-grouping.ts
index a26f6bc1..1735d3c7 100644
--- a/src/lib/allele-grouping.ts
+++ b/src/lib/allele-grouping.ts
@@ -13,6 +13,8 @@ import type {KeySection} from '@/composables/use-key-drawer'
 type AlleleIdentity = components['schemas']['AlleleIdentity']
 type AlleleAnnotations = components['schemas']['AlleleAnnotations']
 
+// ── CONFIDENCE BADGES: how a group's coordinate was established ──
+
 /**
  * Confidence/provenance axis (orthogonal to Cat-VRS's `relation`); strongest confidence first. The
  * measured allele carries no derivation — it is flagged `isFocus` on the identity instead (the API
@@ -62,12 +64,15 @@ export interface ConfidenceBadge {
 }
 
 // Single source for the confidence axis (badges + the Key drawer's "confidence" section), keyed by outcome
-// rather than raw `Derivation`. `convergent` and `candidate` share a color (identity ambiguity);
-// `projection` gets its own (certain but derived). Insertion order is the drawer's display order.
+// rather than raw `Derivation`. Each value paints from its own same-named CSS token (see the "Allele
+// relationship axis" block in assets/app.css) so a token can never drift from the label it styles.
+// `convergent` and `candidate` share a hex — both say "not the change that was measured" — but hold
+// separate tokens so they can diverge without touching this file. Insertion order is the drawer's
+// display order.
 export const ALLELE_CONFIDENCE: Record<string, ConfidenceBadge> = {
   measured: {
     label: 'This measurement',
-    class: 'bg-sage/15 text-sage',
+    class: 'bg-measured-light text-measured',
     definition: 'Directly measured in this assay.'
   },
   projection: {
@@ -77,13 +82,13 @@ export const ALLELE_CONFIDENCE: Record<string, ConfidenceBadge> = {
   },
   convergent: {
     label: 'Convergent',
-    class: 'bg-synonymous-nucleotide-light text-synonymous-nucleotide',
+    class: 'bg-convergent-light text-convergent',
     definition:
       'A different nucleotide change than what was measured, which happens to produce the same protein change as the measured variant.'
   },
   candidate: {
     label: 'Candidate',
-    class: 'bg-synonymous-nucleotide-light text-synonymous-nucleotide',
+    class: 'bg-candidate-light text-candidate',
     definition:
       'A possible nucleotide change encoding a protein-level measurement. This variant is one of several synonymous codons. The assay did not report which one was measured.'
   }
@@ -101,6 +106,8 @@ export function confidenceBadge(group: Pick<AlleleGroup, 'measured' | 'derivatio
   return group.derivation ? (ALLELE_CONFIDENCE[group.derivation] ?? null) : null
 }
 
+// ── GROUPING: collapse a variant's alleles into rendered groups ──
+
 export interface GroupAllelesInput {
   alleles: Record<string, AlleleIdentity>
   annotations: Record<string, AlleleAnnotations>
@@ -142,17 +149,19 @@ function pickDerivation(members: AlleleMember[]): Derivation | null {
   return best
 }
 
-// Mutual by construction, but honor a one-sided link too so a group is never split by iteration order.
-function buildPartnerMap(alleles: Record<string, AlleleIdentity>): Map<string, string> {
-  const partnerOf = new Map<string, string>()
+// A digest -> its projection map: the two members of a projection pair (the same change expressed at
+// coding and genomic level). Mutual by construction, but honor a one-sided link too so a pair is never
+// split by iteration order.
+function buildProjectionMap(alleles: Record<string, AlleleIdentity>): Map<string, string> {
+  const projectionOf = new Map<string, string>()
   for (const [digest, identity] of Object.entries(alleles)) {
-    const sibling = identity.projectionOf
-    if (sibling && sibling !== digest && alleles[sibling]) {
-      partnerOf.set(digest, sibling)
-      partnerOf.set(sibling, digest)
+    const projection = identity.projectionOf
+    if (projection && projection !== digest && alleles[projection]) {
+      projectionOf.set(digest, projection)
+      projectionOf.set(projection, digest)
     }
   }
-  return partnerOf
+  return projectionOf
 }
 
 function makeMember(
@@ -182,25 +191,24 @@ function makeMember(
  */
 export function groupAlleles(input: GroupAllelesInput): AlleleGroup[] {
   const {alleles, annotations, pageClingenAlleleId} = input
-  const partnerOf = buildPartnerMap(alleles)
+  const projectionOf = buildProjectionMap(alleles)
 
-  // Pair-and-consume: each allele is visited once; its projection partner (if any) is pulled in immediately.
+  // Pair-and-consume: each allele is visited once; its projection (if any) is pulled in immediately.
   const done = new Set<string>()
   const groups: AlleleGroup[] = []
   for (const [digest, identity] of Object.entries(alleles)) {
     if (done.has(digest)) continue
     done.add(digest)
     const members = [makeMember(digest, identity, annotations, pageClingenAlleleId)]
-    const sibling = partnerOf.get(digest)
-    if (sibling && !done.has(sibling)) {
-      done.add(sibling)
-      members.push(makeMember(sibling, alleles[sibling], annotations, pageClingenAlleleId))
+    const projection = projectionOf.get(digest)
+    if (projection && !done.has(projection)) {
+      done.add(projection)
+      members.push(makeMember(projection, alleles[projection], annotations, pageClingenAlleleId))
     }
     // Sort members genomic → cDNA → protein so the group reads consistently regardless of input order.
     members.sort((a, b) => (LEVEL_ORDER[a.level ?? ''] ?? 99) - (LEVEL_ORDER[b.level ?? ''] ?? 99))
 
-    // Coalesce annotations across levels (present-wins); only a real present-vs-present disagreement
-    // counts as divergence. Missing-on-one-level is not treated as different.
+    // See coalesceAnnotations for the present-wins/conflict rule.
     const {merged, conflict} = coalesceAnnotations(members)
 
     groups.push({
diff --git a/src/lib/clinvar-control-placement.ts b/src/lib/clinvar-control-placement.ts
index 6e523358..d72bd528 100644
--- a/src/lib/clinvar-control-placement.ts
+++ b/src/lib/clinvar-control-placement.ts
@@ -5,7 +5,7 @@
  * For an AA-resolution score set one measured protein change is encoded by several DNA variants, whose
  * ClinVar classifications can disagree. This module reduces the set of controls that reach a single
  * variant to one placement the histogram can bin off — applying source precedence (the assayed-level
- * allele's own call wins; projection siblings are only a fallback) and grading how the winning calls
+ * allele's own call wins; the encodings are only a fallback) and grading how the winning calls
  * disagree ({@link Discordance}). Directional-over-uncertain is precedence, not discordance.
  */
 
@@ -25,6 +25,8 @@ import type {components} from '@/schema/openapi'
 type ClinvarAnnotation = components['schemas']['ClinvarAnnotation']
 type SequenceLevel = components['schemas']['SequenceLevel']
 
+// ── PLACEMENT: reduce one variant's ClinVar controls to a single call ──
+
 /**
  * How the ClinVar calls reaching a measurement disagree, ordered by placement difficulty.
  * - `none` — a single call, or uncertain-only records (a lone VUS, VUS + Conflicting). Nothing to reconcile.
@@ -52,10 +54,10 @@ export interface ControlLink extends ControlClassification {
 
 /** Fields present on every placement, usable or not — enough to reconstruct the winning set behind the fold. */
 interface BaseControlPlacement {
-  /** The winning set's distinct calls (assayed-level controls if any, else the projection siblings). */
+  /** The winning set's distinct calls (assayed-level controls if any, else the encodings). */
   classifications: ControlClassification[]
   /**
-   * True when the winning set came from **projection siblings**. The measured allele itself had no
+   * True when the winning set came from the **encodings**. The measured allele itself had no
    * ClinVar record, so this classification is about a *related* variant at a different level, not the
    * entity we assayed.
    */
@@ -102,22 +104,19 @@ const starsOf = (reviewStatus: string) => CLINVAR_REVIEW_STATUS_STARS[reviewStat
  * Reduce the ClinVar controls reaching one variant to a single {@link ClinvarControlPlacement}.
  *
  * **Precedence:** if any control annotates the variant's own subject allele (`alleleDigest` ∈ the subject
- * digest set — the measured/page allele, including its c↔g twin), those controls are the winning set and the
- * projection siblings are ignored — a direct call on the assayed entity is not diluted by the fan-out.
+ * digest set — the measured/page allele, including its projection), those controls are the winning set and
+ * the encodings are ignored — a direct call on the assayed entity is not diluted by the fan-out.
+ *
+ * **Falling back to the encodings is level-gated.** It's only legitimate at *protein* assay level, where
+ * ClinVar (a nucleotide resource) cannot annotate the measured allele itself, so the encodings are the only
+ * available signal. At nucleotide level (`cdna`/`genomic`) the measured variant *can* carry its own record,
+ * so its absence is real information: we do **not** borrow an encoding's call (that would both overreach and
+ * double-count — the encoding is its own scored row). With no direct record at nucleotide level, this
+ * returns `null`.
  *
- * **Projection is level-gated.** Falling through to sibling controls is only legitimate at the *protein*
- * assay level, where ClinVar (a nucleotide resource) cannot annotate the measured allele itself, so the
- * encoding siblings are the only available signal. At nucleotide level (`cdna`/`genomic`) the measured
- * variant *can* carry its own record, so its absence is real information: we do **not** borrow a sibling's
- * call (which would both overreach and double-count — that sibling is its own scored row). With no direct
- * record at nucleotide level, this returns `null`. Otherwise the siblings are the winning set. Over it:
- *   - **hard** (both a P/LP and a B/LB call) → `discordance: 'hard'`, not a usable control;
- *   - **soft** (a directional lean + an uncertain record — a VUS or a ClinVar-*Conflicting* call) →
- *     `discordance: 'soft'`, usable — the lean is the representative, but the surface can flag the soft conflict;
- *   - **concordant** (≥2 distinct calls in a single direction, e.g. LB + B, no uncertain record) →
- *     `discordance: 'concordant'`, usable, representative by star tiebreak;
- *   - the distinct calls flow through as `classifications`, and `directional` records whether any confident
- *     P/LP or B/LB call is present, so the histogram can drop VUS when a directional call dominates.
+ * The winning set is then graded for {@link Discordance} and reduced to a representative call
+ * (directional-preferred, then highest star). `directional` records whether any confident P/LP or B/LB call
+ * is present, so callers can drop VUS when a directional call dominates.
  *
  * Returns `null` when no *classified* control reaches the variant.
  */
@@ -127,7 +126,7 @@ export function reduceControlPlacement(
   assayLevel?: SequenceLevel | null
 ): ClinvarControlPlacement | null {
   // Drop ClinVar "no classification" placeholders (a literal `-`/empty) up front, so they neither become a
-  // call nor — as a `-` on the assayed allele — block fall-through to a real projection sibling.
+  // call nor — as a `-` on the assayed allele — block fall-through to a real encoding.
   const classified = links.filter((link) => isClassifiedSignificance(link.significance))
   if (classified.length === 0) {
     return null
@@ -143,7 +142,7 @@ export function reduceControlPlacement(
   if (winning.length === 0) {
     return null
   }
-  // Fell through to siblings — but only *claim* projection when the subject digest is known; an absent
+  // Fell through to the encodings — but only *claim* projection when the subject digest is known; an absent
   // digest means unknown provenance, which we don't surface as "related variant" (avoids mislabeling).
   const projected = subjectSet.size > 0 && assayedLevel.length === 0
 
@@ -163,9 +162,8 @@ export function reduceControlPlacement(
   // Any non-directional call is "uncertain" — a VUS *or* ClinVar's own aggregate Conflicting value.
   const uncertainPresent = classifications.some((c) => !isDirectional(c.significance))
 
-  // Grade the disagreement. Opposite directions is hard (unusable). Otherwise, with a single direction:
-  // a co-occurring uncertain record (VUS/Conflicting) is a *soft conflict* — the lean stands but the direction
-  // may not be settled; ≥2 distinct calls in that one direction (no uncertain record) is merely concordant.
+  // Grade per Discordance: opposing directions is hard; a single direction plus an uncertain record is soft;
+  // ≥2 same-direction calls alone is concordant.
   if (pathogenicCalls.length > 0 && benignCalls.length > 0) {
     // Hard: opposing directional assertions break the projection premise, so there is no single winning call.
     // No representative is computed, and the type withholds those fields so no surface can read a fake one.
@@ -198,6 +196,8 @@ export function reduceControlPlacement(
   }
 }
 
+// ── HEADLINE: what a one-line ClinVar surface displays ──
+
 /**
  * A note qualifying a representative `call` — what, beyond the call itself, the headline should say.
  * - `none` — a lone, unambiguous call; show it plainly.
@@ -215,7 +215,7 @@ export type ClinvarCallNote = 'none' | 'concordant' | 'soft-vus' | 'soft-conflic
  * What a one-headline ClinVar surface should display for a measurement — a discriminated union so the
  * component switches on `kind` instead of re-deriving a precedence ladder in its template.
  * - `conflicting` — hard-discordant winning set; no single call to show.
- * - `call` — the representative usable call (assayed-level or a projection sibling), with a {@link ClinvarCallNote}
+ * - `call` — the representative usable call (assayed-level or an encoding), with a {@link ClinvarCallNote}
  *   qualifying it (concordant aside, or a soft-conflict flag). The lib owns that decision so the template renders it.
  * - `presence` — no usable call, but a ClinVar record exists on the measurement (a `-` germline-less
  *   submission); name the state and link out.
@@ -242,14 +242,13 @@ function resolveCallNote(placement: UsableControlPlacement): ClinvarCallNote {
 
 /**
  * Resolve what a one-headline ClinVar surface shows, over a resolved walk. Runs the level-gated fold, then
- * falls back through a fixed precedence so every such surface (stat cell, variant screen) agrees:
+ * falls back through a fixed precedence — see {@link ClinvarHeadline} for what each kind means — so every
+ * such surface (stat cell, variant screen) agrees:
  *   1. a usable/hard placement → `call`/`conflicting`;
- *   2. the measured allele's *own* record (a `-`, since a classification would have folded above) → `presence`,
- *      naming the germline-less state and linking out;
- *   3. no record on the measured allele, but records reach related alleles (a nucleotide measurement we
- *      declined to project) → `absent` — the measured variant has no ClinVar record; the related records are
- *      offered as context, never promoted to a call or a germline-less state on this variant;
- *   4. nothing reaches the measurement → `none`.
+ *   2. else the measured allele's own record, if any (a `-`, since a classification would have folded
+ *      above) → `presence`;
+ *   3. else, if related alleles carry records → `absent` (never promoted to a call);
+ *   4. else → `none`.
  */
 export function resolveClinvarHeadline(
   records: MeasurementClinvarRecord[],
@@ -273,7 +272,7 @@ export function resolveClinvarHeadline(
     }
   }
   // The subject allele's own record (if any) is germline-less — a classification would have folded above.
-  // `onAssayed` was tagged against this same subject, so it covers the c↔g twin too.
+  // `onAssayed` was tagged against this same subject, so it covers its projection too.
   const assayedRecord = records.find((r) => r.onAssayed)
   if (assayedRecord) return {kind: 'presence', record: assayedRecord}
   // No record on the measured allele. Any records that reach it are on *related* alleles — we won't promote
diff --git a/src/lib/clinvar-controls.ts b/src/lib/clinvar-controls.ts
index 12b45a5d..b62e2e09 100644
--- a/src/lib/clinvar-controls.ts
+++ b/src/lib/clinvar-controls.ts
@@ -37,20 +37,9 @@ type AlleleAnnotations = components['schemas']['AlleleAnnotations']
 type ClinvarAnnotation = components['schemas']['ClinvarAnnotation']
 
 /**
- * List of ClinVar clinical significance classifications.
- *
- * Each classification contains:
- * - `name`: The full name of the clinical significance (e.g., "Pathogenic").
- * - `description`: A detailed description of the classification.
- * - `shortDescription`: An abbreviated or short label for the classification.
- *
- * These classifications are used to describe the clinical significance of variants
- * according to ClinVar standards, including categories such as "Pathogenic", "Likely pathogenic",
- * "Benign", "Likely benign", "Uncertain significance", and combinations thereof.
- *
- * NOTE: The "Conflicting" classification is dynamically generated based on the version of ClinVar,
- * as the terminology changed in 2025. The function `clinvarConflictingSignificanceClassification`
- * adjusts the label accordingly provided a ClinVar version.
+ * ClinVar clinical significance classifications, excluding "Conflicting" — that one is version-dependent
+ * (ClinVar's terminology changed in 2025) and generated separately by
+ * {@link clinvarConflictingSignificanceClassificationForVersion}.
  */
 export const CLINVAR_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS = [
   {
@@ -221,7 +210,7 @@ export function latestClinvar(annotations: AlleleAnnotations | null): ClinvarAnn
 export interface MeasurementClinvarRecord {
   /** VRS digest of the allele this record annotates. */
   digest: string
-  /** True when the record is on the measured allele itself (digest === assayLevelDigest), not a sibling. */
+  /** True when the record is on the measured allele itself (digest === assayLevelDigest), not an encoding. */
   onAssayed: boolean
   /** Reference-frame HGVS of the annotated allele, for labeling; null when the sidecar has none. */
   hgvs: string | null
@@ -231,7 +220,7 @@ export interface MeasurementClinvarRecord {
 }
 
 /** Canonical identity of a ClinVar record: the variation id when present, else the allele id. Dedupes records
- *  shared across reference frames, keys them in a list, and excludes the one already shown in a headline. */
+ * shared across reference frames, keys them in a list, and excludes the one already shown in a headline. */
 export function clinvarRecordId(clinvar: {clinvarVariationId?: string | null; clinvarAlleleId: string}): string {
   return clinvar.clinvarVariationId ?? clinvar.clinvarAlleleId
 }
@@ -267,16 +256,16 @@ export function resolveClinvarRecords(
 }
 
 /**
- * The distinct *underlying* records for the popover, projected from a resolved walk — the records on sibling
- * alleles the headline folded over. Excludes the measured allele's own record (`onAssayed`): that is the
+ * The distinct *underlying* records for the popover, projected from a resolved walk — the records on the
+ * encodings the headline folded over. Excludes the measured allele's own record (`onAssayed`): that is the
  * primary, already shown as the headline, not "underlying" — so a lone assayed record yields no popover, and
- * a protein-level allele's projected headline still lists the nucleotide sibling it was drawn from.
+ * a protein-level allele's projected headline still lists the encoding it was drawn from.
  *
  * These are the *related-allele* records offered as context — beside a direct call (transparency: records
- * that did not drive it), beneath a projected call (the siblings it folded over), or under an `absent`
+ * that did not drive it), beneath a projected call (the encodings it folded over), or under an `absent`
  * nucleotide headline. Excludes the measured allele's own record (`onAssayed`) **and its cross-frame
  * duplicates**: the same ClinVar record seen under another reference-frame digest is the very record already
- * shown, not a distinct sibling, so it must not reappear here.
+ * shown, not a distinct encoding, so it must not reappear here.
  *
  * Germline-less `-` submissions are kept (a record that exists is worth linking to; only the control fold
  * drops `-`). Dedupes by ClinVar record id across the DNA/protein frames that share one record (preferring a
@@ -322,7 +311,7 @@ export function formatClinicalSignificance(significance: string | null | undefin
  * model emits a literal `-` (occasionally empty) on an axis with no submission — e.g. a record carrying
  * somatic/oncogenicity data but no germline classification. Such a value is not a usable classification:
  * it must not become a clinvar control, render as a call, or (as a `-` on the *assayed* allele) block
- * fall-through to a sibling allele. Filter significances through this before treating them as calls.
+ * fall-through to an encoding. Filter significances through this before treating them as calls.
  */
 export function isClassifiedSignificance(significance: string | null | undefined): boolean {
   const s = significance?.trim()
@@ -337,20 +326,7 @@ export function isUncertainSignificance(significance: string): boolean {
   )
 }
 
-/**
- * Returns an array of ClinVar clinical significance classifications,
- * appending a "Conflicting" classification with a description that
- * depends on the provided version string. ClinVar changed the verbiage
- * for conflicting classifications in 2025, so this function adjusts
- * the label based on the version.
- *
- * If the version (expected in the format "prefix_YYYY") is greater than 2024,
- * the "Conflicting classifications of pathogenicity" label is used.
- * Otherwise, "Conflicting interpretations of pathogenicity" is used.
- *
- * @param version - The ClinVar version string, expected to contain a year after an underscore (e.g., "v_2023").
- * @returns An array of clinical significance classification objects, including the appropriate "Conflicting" classification.
- */
+/** {@link CLINVAR_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS} plus the version-appropriate "Conflicting" entry. */
 export function clinvarClinicalSignificanceClassifications(
   version: string | null
 ): typeof CLINVAR_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS {
@@ -361,14 +337,9 @@ export function clinvarClinicalSignificanceClassifications(
 }
 
 /**
- * Returns the appropriate ClinVar conflicting significance classification object for a given version.
- *
- * Depending on the version string (expected in the format "prefix_YYYY"), this function returns
- * an object containing the name, description, and shortDescription for the conflicting significance
- * classification. For versions after 2024, the naming reflects updated ClinVar terminology.
- *
- * @param version - The version string, expected to contain a year after an underscore (e.g., "clinvar_2025").
- * @returns An object with `name`, `description`, and `shortDescription` fields describing the conflicting classification.
+ * The "Conflicting" classification, worded for the given ClinVar version — ClinVar renamed this from
+ * "interpretations" to "classifications" starting with the 2025 releases (`version`'s year after 2024).
+ * `null` (unknown version) is treated as post-rename.
  */
 export function clinvarConflictingSignificanceClassificationForVersion(version: string | null): {
   name: string
@@ -391,14 +362,8 @@ export function clinvarConflictingSignificanceClassificationForVersion(version:
 }
 
 /**
- * Returns the appropriate label for conflicting clinical significance series based on the provided version string.
- *
- * The label changes depending on the numeric value after the underscore in the version string:
- * - If the numeric part is greater than 2024, returns "Conflicting classifications".
- * - Otherwise, returns "Conflicting interpretations".
- *
- * @param version - The version string in the format "prefix_number" (e.g., "v_2025").
- * @returns The label for conflicting clinical significance series.
+ * The "Conflicting classifications"/"Conflicting interpretations" series label — same version rule as
+ * {@link clinvarConflictingSignificanceClassificationForVersion}.
  */
 export function conflictingClinicalSignificanceSeriesLabelForVersion(version: string | null): string {
   if (version === null || Number(version.split('_')[1]) > 2024) {
diff --git a/src/lib/notables.ts b/src/lib/notables.ts
index e314cf1c..1c521914 100644
--- a/src/lib/notables.ts
+++ b/src/lib/notables.ts
@@ -66,9 +66,9 @@ export function clinicalExtremesPerClass(
   const benign = definitive(BENIGN_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS)
   if (!pathogenic.length && !benign.length) return []
 
-  // A direct call on the assayed allele is a stronger headliner than one projected from a sibling allele,
+  // A direct call on the assayed allele is a stronger headliner than one projected from an encoding,
   // so pick the exemplar from the direct members when a class has any; fall back to the whole (projected)
-  // group only when the class is present solely via siblings.
+  // group only when the class is present solely via the encodings.
   const preferDirect = (group: DisplayVariant[]) => {
     const direct = group.filter((v) => !v.control?.projected)
     return direct.length ? direct : group
@@ -78,8 +78,7 @@ export function clinicalExtremesPerClass(
   const furthestFrom = (group: DisplayVariant[], anchor: number) =>
     group.reduce((best, v) => (Math.abs(scoreOf(v) - anchor) > Math.abs(scoreOf(best) - anchor) ? v : best))
 
-  // Both classes present: separate along the learned damaging direction. Only one: fall back to the
-  // variant furthest from the set's median (still a headline extreme, just without a contrast class).
+  // Single-class fallback (median-furthest) is still a headline extreme, just without a contrast class.
   if (pathogenic.length && benign.length) {
     const pathMedian = median(pathogenic.map(scoreOf))
     const benignMedian = median(benign.map(scoreOf))

From b1e5c3037c489b6a43b7cc377f230e97b7b89784 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Wed, 16 Sep 2026 09:13:55 -0700
Subject: [PATCH 81/84] fix(variant): distinguish reverse-translation fan-out
 from an empty annotation state
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

The compact variant picker showed "No reference annotations were found for this
variant" whenever the protein allele had no direct consequence and no pooled
gnomAD/ClinVar. For a reverse-translated protein change that assertion is false:
the change fans out to candidate nucleotide alleles that carry their own VEP
consequence.

Split the empty state — when candidate-derivation alleles are present, name the
fan-out and scope the absence to population/clinical evidence; keep the original
message only when there is genuinely nothing. The candidate count reuses
groupAlleles so a candidate's c↔g spellings count once.
---
 src/components/variant/VariantDetailPanel.vue | 21 ++++++++++++++++++-
 1 file changed, 20 insertions(+), 1 deletion(-)

diff --git a/src/components/variant/VariantDetailPanel.vue b/src/components/variant/VariantDetailPanel.vue
index b17e40ce..4ce09ca0 100644
--- a/src/components/variant/VariantDetailPanel.vue
+++ b/src/components/variant/VariantDetailPanel.vue
@@ -80,7 +80,13 @@
         />
       </div>
 
-      <!-- No facts to display: a quiet empty state. -->
+      <!-- No direct facts. A reverse-translation fan-out isn't "nothing": name candidate nucleotides
+           even if the protein change itself has no direct annotations. -->
+      <p v-else-if="candidateFanoutCount > 0" class="px-4 py-3 text-xs text-text-muted tablet:px-5">
+        This amino-acid change reverse-translates to {{ candidateFanoutCount }} candidate nucleotide allele{{
+          candidateFanoutCount === 1 ? '' : 's'
+        }}; no population or clinical evidence was found for this variant or the candidate nucleotide alleles.
+      </p>
       <p v-else class="px-4 py-3 text-xs text-text-muted tablet:px-5">
         No reference annotations were found for this variant.
       </p>
@@ -120,6 +126,7 @@ import VariantConsequenceStat from '@/components/variant/VariantConsequenceStat.
 import VariantGnomadStat from '@/components/variant/VariantGnomadStat.vue'
 import VariantClinvarStat from '@/components/variant/VariantClinvarStat.vue'
 import {getVariantDetail} from '@/api/mavedb/variants'
+import {groupAlleles} from '@/lib/allele-grouping'
 import {collectGnomadFrequencies} from '@/lib/gnomad'
 import {formatScore} from '@/lib/scores'
 import {enumerateUnderlyingClinvar, resolveClinvarRecords} from '@/lib/clinvar-controls'
@@ -230,6 +237,18 @@ export default defineComponent({
     anyAnnotationsAvailable(): boolean {
       return !!this.consequence?.consequence || this.selectedClassification != null || this.hasGnomad || this.hasClinvar
     },
+    // Count of `candidate`-derivation groups: a protein change reverse-translates to N candidate nucleotide
+    // alleles (ambiguous codon choice). Grouped so a candidate's c↔g spellings count once. Lets the empty
+    // state say "no direct evidence, but a fan-out exists" instead of asserting a blanket absence — the
+    // candidates carry their own (VEP) consequence, reachable via full details, so "nothing found" is false.
+    candidateFanoutCount(): number {
+      if (!this.detail?.alleles) return 0
+      return groupAlleles({
+        alleles: this.detail.alleles,
+        annotations: this.detail.annotations ?? {},
+        pageClingenAlleleId: this.detail.clingenAlleleId ?? null
+      }).filter((group) => group.derivation === 'candidate').length
+    },
     // A distinct underlying nucleotide coordinate — an alternate spelling worth keeping the identity line for,
     // so it disambiguates coding variants that collapse to the same protein change.
     hasAlternateSpelling(): boolean {

From fc7b43a54b92f7eafc097577e7b55042d39bd1e9 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Tue, 29 Sep 2026 22:37:29 -0700
Subject: [PATCH 82/84] fix(downloads): send credentials with the NDJSON
 download streams

The variant-details and annotated-variants downloads use fetch, which the
axios auth interceptor doesn't cover, so they went out unauthenticated and
an owner downloading an unpublished score set got a 404.
---
 .../use-score-set-downloads.test.ts           | 25 +++++++++++++++++++
 src/composables/use-score-set-downloads.ts    |  9 ++++++-
 2 files changed, 33 insertions(+), 1 deletion(-)

diff --git a/src/composables/use-score-set-downloads.test.ts b/src/composables/use-score-set-downloads.test.ts
index a4e328b5..991790d2 100644
--- a/src/composables/use-score-set-downloads.test.ts
+++ b/src/composables/use-score-set-downloads.test.ts
@@ -14,6 +14,9 @@ vi.mock('@/api/mavedb', () => ({
 // The real one reaches for `document`; these tests run in the node environment.
 vi.mock('@/lib/downloads', () => ({triggerDownload: vi.fn()}))
 
+const authHeader = vi.fn((): Record<string, unknown> => ({}))
+vi.mock('@/lib/auth', () => ({authHeader: () => authHeader()}))
+
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
 const SCORE_SET = ref({urn: 'urn:mavedb:00000001-a-1'} as any)
 
@@ -308,6 +311,28 @@ describe('useScoreSetDownloads variant-details streaming', () => {
     expect(url).not.toContain('mapped-variants')
   })
 
+  it('sends the signed-in user\'s credentials, which fetch does not get from the axios interceptor', async () => {
+    authHeader.mockReturnValueOnce({Authorization: 'Bearer token', 'X-Active-Roles': ['admin', 'mapper']})
+    const fetchMock = mockStream()
+    const downloads = useScoreSetDownloads({scoreSet: SCORE_SET})
+
+    await downloads.streamVariantDetails()
+
+    expect(fetchMock.mock.calls[0][1].headers).toMatchObject({
+      Authorization: 'Bearer token',
+      'X-Active-Roles': 'admin,mapper'
+    })
+  })
+
+  it('sends no credentials when signed out', async () => {
+    const fetchMock = mockStream()
+    const downloads = useScoreSetDownloads({scoreSet: SCORE_SET})
+
+    await downloads.streamVariantDetails()
+
+    expect(fetchMock.mock.calls[0][1].headers).not.toHaveProperty('Authorization')
+  })
+
   it('shares the one download indicator', async () => {
     mockStream()
     const downloads = useScoreSetDownloads({scoreSet: SCORE_SET})
diff --git a/src/composables/use-score-set-downloads.ts b/src/composables/use-score-set-downloads.ts
index 2dc0a969..4a2673ee 100644
--- a/src/composables/use-score-set-downloads.ts
+++ b/src/composables/use-score-set-downloads.ts
@@ -3,6 +3,7 @@ import {computed, ref, type Ref} from 'vue'
 import {downloadScoreSetFile, downloadScoreSetVariantData} from '@/api/mavedb'
 import type {CsvExtraOption} from '@/composables/use-csv-namespaces'
 import config from '@/config'
+import {authHeader} from '@/lib/auth'
 import {triggerDownload} from '@/lib/downloads'
 import type {components} from '@/schema/openapi'
 
@@ -150,9 +151,15 @@ export function useScoreSetDownloads({scoreSet}: UseScoreSetDownloadsOptions) {
     streamController.value = new AbortController()
 
     try {
+      // fetch bypasses the axios interceptor that authenticates API calls, so send the credentials here.
+      // The API splits X-Active-Roles on bare commas.
+      const {Authorization, 'X-Active-Roles': activeRoles} = authHeader()
       const response = await fetch(`${config.apiBaseUrl}/score-sets/${urn}/${subPath}`, {
         signal: streamController.value.signal,
-        headers: {Accept: 'application/x-ndjson'}
+        headers: {
+          Accept: 'application/x-ndjson',
+          ...(Authorization ? {Authorization, 'X-Active-Roles': (activeRoles ?? []).join(',')} : {})
+        }
       })
 
       if (!response.ok) {

From f8b9093eba3317319fa110da045295d6db601e17 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Wed, 30 Sep 2026 13:42:57 -0700
Subject: [PATCH 83/84] feat(variant): name the page subject "Your variant" and
 merge the download buttons into one menu
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

The page's subject allele is now "Your variant" wherever it's badged, the
measured allele's badge reads "Measured", and the ClinVar and gnomAD empty
states say "this allele", since they describe one allele rather than the
page's variant. The variant header's two download split buttons become a
single "…" menu on every screen size, with VA-Spec downloads labelled and
the menu disabled while a download runs.
---
 src/components/layout/MvPageHeader.vue        |  4 +-
 src/components/screens/VariantScreen.vue      | 75 +++++--------------
 src/components/variant/MvAlleleLedger.vue     |  8 +-
 src/components/variant/MvMeasurementCard.vue  |  2 +-
 src/components/variant/VariantClinvarStat.vue |  4 +-
 src/components/variant/VariantDetailPanel.vue |  4 +-
 src/components/variant/VariantGnomadStat.vue  |  4 +-
 src/lib/allele-grouping.test.ts               |  2 +-
 src/lib/allele-grouping.ts                    |  2 +-
 src/lib/glossary-prose.ts                     | 14 ++--
 src/lib/measurement-types.ts                  | 12 +--
 11 files changed, 48 insertions(+), 83 deletions(-)

diff --git a/src/components/layout/MvPageHeader.vue b/src/components/layout/MvPageHeader.vue
index 0acf3f94..df84c7de 100644
--- a/src/components/layout/MvPageHeader.vue
+++ b/src/components/layout/MvPageHeader.vue
@@ -10,10 +10,10 @@
 
       <div
         v-if="$slots.actions"
-        class="flex flex-row justify-between gap-4 tablet:gap-5"
+        class="flex flex-row flex-wrap justify-between gap-x-4 gap-y-3 tablet:gap-x-5"
         :class="variant === 'toolbar' ? 'items-center' : 'items-start'"
       >
-        <div class="min-w-0 flex-1">
+        <div class="min-w-min flex-1">
           <h1 :class="titleClasses">{{ title }}</h1>
           <slot name="subtitle" />
           <slot />
diff --git a/src/components/screens/VariantScreen.vue b/src/components/screens/VariantScreen.vue
index 04497942..eced3470 100644
--- a/src/components/screens/VariantScreen.vue
+++ b/src/components/screens/VariantScreen.vue
@@ -3,32 +3,7 @@
     <template #header>
       <MvPageHeader eyebrow="Variant" max-width="1000px" :title="pageTitle">
         <template v-if="lookup.variants.value.length > 0" #actions>
-          <div class="hidden tablet:flex tablet:items-center tablet:gap-2">
-            <SplitButton
-              :disabled="downloadInProgress"
-              :model="tableDownloadMenu"
-              severity="secondary"
-              size="small"
-              @click="primaryTableDownload.command()"
-            >
-              <template #default>
-                <i class="pi pi-table mr-1.5 text-xs" />
-                Download variant CSV
-              </template>
-            </SplitButton>
-            <SplitButton
-              v-if="annotationDownloadOptions.length > 0"
-              :disabled="downloadInProgress"
-              :model="annotationDownloadOptions"
-              severity="secondary"
-              size="small"
-              @click="primaryAnnotationDownload?.command()"
-            >
-              <template #default>
-                <i class="pi pi-download mr-1.5 text-xs" />
-                Download VA-Spec annotations
-              </template>
-            </SplitButton>
+          <div class="flex items-center gap-2">
             <!-- Indeterminate: a gzipped download exposes no measurable total. -->
             <span
               v-if="downloadInProgress"
@@ -38,8 +13,8 @@
               <i class="pi pi-spin pi-spinner text-xs" />
               Preparing {{ lookup.downloadInProgressLabel.value }}…
             </span>
+            <MvRowActionMenu :actions="downloadActions" />
           </div>
-          <MvRowActionMenu :actions="downloadActions" class="tablet:hidden" />
         </template>
 
         <template v-if="lookup.variants.value.length > 0" #subtitle>
@@ -165,7 +140,7 @@
           <!-- Anchor heading: names the frame of reference so the per-card relationship badges read as
                self-explaining without needing a per-badge tooltip. -->
           <div class="px-4 tablet:px-5 pt-3.5 text-xs-minus text-text-muted">
-            What each result assayed, relative to this variant:
+            What each result assayed, relative to your variant:
           </div>
           <div class="measurement-switcher hidden tablet:flex gap-3 overflow-x-auto px-5 py-4">
             <MvMeasurementCard
@@ -208,7 +183,7 @@
             v-if="lookup.selectedVariantDetail.value"
             class="border-t border-border-light bg-sage/[0.06] px-4 tablet:px-5 py-3 text-sm text-text-secondary"
           >
-            {{ relationshipPrefix }} <span class="font-semibold text-text-primary">this variant</span
+            {{ relationshipPrefix }} <span class="font-semibold text-text-primary">your variant</span
             >{{ isDirectMeasurement ? ' directly' : '' }}.
           </div>
         </div>
@@ -384,7 +359,6 @@
 <script lang="ts">
 import DatePicker from 'primevue/datepicker'
 import Select from 'primevue/select'
-import SplitButton from 'primevue/splitbutton'
 import {defineComponent, toRef, type PropType} from 'vue'
 import {useRoute} from 'vue-router'
 import {useHead} from '@unhead/vue'
@@ -451,8 +425,7 @@ export default defineComponent({
     MvPageLoading,
     MvCsvColumnDialog,
     PSelect: Select,
-    ScoreSetHistogram,
-    SplitButton
+    ScoreSetHistogram
   },
 
   props: {
@@ -543,7 +516,7 @@ export default defineComponent({
     isDirectMeasurement(): boolean {
       return this.lookup.selectedVariant.value?.relationship === 'direct'
     },
-    // Leading half of the relationship line — everything up to the bold "this variant".
+    // Leading half of the relationship line — everything up to the bold "your variant".
     relationshipPrefix(): string {
       const rel = this.lookup.selectedVariant.value?.relationship
       if (rel === 'protein_consequence') return 'The selected measurement measured the protein consequence of'
@@ -605,23 +578,12 @@ export default defineComponent({
       ]
     },
 
-    /** What clicking the table button itself does: download with the default column set. */
-    primaryTableDownload(): DownloadOption {
-      return this.tableDownloadOptions[0]
-    },
-
-    /** What its caret offers: everything beyond the one-click default. */
-    tableDownloadMenu(): DownloadOption[] {
-      return this.tableDownloadOptions.slice(1)
-    },
-
     /**
      * The VA-Spec downloads: nested, standards-compliant annotation objects.
      *
      * A different product from the table — machine-readable GA4GH structures rather than something to
-     * open in a spreadsheet — so they get their own control rather than sharing a menu. Each requires
-     * progressively more of the variant to exist, so the list is empty for an unmapped variant and the
-     * button is hidden entirely.
+     * open in a spreadsheet — so the menu sets them apart under a separator. Each requires progressively
+     * more of the variant to exist, so the list is empty for an unmapped variant and the group is omitted.
      */
     annotationDownloadOptions(): DownloadOption[] {
       const options: DownloadOption[] = []
@@ -654,18 +616,21 @@ export default defineComponent({
       return options
     },
 
-    /** What clicking the annotations button itself does: the highest-level statement available. */
-    primaryAnnotationDownload(): DownloadOption | undefined {
-      return this.annotationDownloadOptions[0]
-    },
-
-    /** The narrow-screen equivalent: both groups in one menu, separated so they stay distinguishable. */
+    /** The header's single "…" menu: table downloads, then VA-Spec annotations, disabled while one is in flight. */
     downloadActions(): RowAction[] {
-      const asAction = (option: DownloadOption): RowAction => ({label: option.label, handler: option.command})
+      const disabled = this.downloadInProgress
+      const asAction = (option: DownloadOption, description?: string): RowAction => ({
+        label: option.label,
+        description,
+        disabled,
+        handler: option.command
+      })
       const annotations = this.annotationDownloadOptions
       return [
-        ...this.tableDownloadOptions.map(asAction),
-        ...(annotations.length > 0 ? [{separator: true} as RowAction, ...annotations.map(asAction)] : [])
+        ...this.tableDownloadOptions.map((o) => asAction(o)),
+        ...(annotations.length > 0
+          ? [{separator: true} as RowAction, ...annotations.map((o) => asAction(o, 'VA-Spec annotation'))]
+          : [])
       ]
     }
   },
diff --git a/src/components/variant/MvAlleleLedger.vue b/src/components/variant/MvAlleleLedger.vue
index 4ef805e8..b300ada9 100644
--- a/src/components/variant/MvAlleleLedger.vue
+++ b/src/components/variant/MvAlleleLedger.vue
@@ -21,7 +21,7 @@
       >
         <div class="mb-2 flex flex-wrap items-center gap-x-2 gap-y-1">
           <span
-            v-key-term="entry.role === 'page' ? 'this-variant' : 'confidence'"
+            v-key-term="entry.role === 'page' ? 'your-variant' : 'confidence'"
             class="rounded-sm px-1.5 py-0.5 text-[10px] font-bold uppercase tracking-[0.3px]"
             :class="roleBadge(entry).class"
             >{{ roleBadge(entry).label }}</span
@@ -181,7 +181,7 @@ export default defineComponent({
     // The ordered render list: page variant, then the measured allele, then the rest (collapsed). Roles
     // drive badge + emphasis, and are assigned from what a group *is* — a group is never given the `page`
     // role as a stand-in. When the page variant is absent the list simply leads with the measured allele
-    // under its own badge, rather than labelling it "This variant" and asserting an identity it lacks.
+    // under its own badge, rather than labelling it "Your variant" and asserting an identity it lacks.
     entries(): LedgerEntry[] {
       const list: LedgerEntry[] = []
       if (this.pageGroup) list.push({group: this.pageGroup, role: 'page'})
@@ -218,11 +218,11 @@ export default defineComponent({
       return group.members.map((m) => `${this.levelLabel(m.level)}: ${m.hgvs || '—'}`).join('  ·  ')
     },
     // "page" gets its own fixed subject badge — deliberately distinct from the confidence-axis colors used
-    // everywhere else, so "This variant" (the page's subject) and "This measurement" (what was assayed) are
+    // everywhere else, so "Your variant" (the page's subject) and "Measured" (what was assayed) are
     // never confused. Every other role reads its label/class off the shared confidence axis, so those
     // badges match the same Key entry used throughout the app.
     roleBadge(entry: LedgerEntry): {label: string; class: string} {
-      if (entry.role === 'page') return {label: 'This variant', class: 'bg-subject/15 text-subject'}
+      if (entry.role === 'page') return {label: 'Your variant', class: 'bg-subject/15 text-subject'}
       const badge = confidenceBadge(entry.group)
       // No derivation and not measured: the API recorded no relationship (pre-reverse-translation data, or
       // a classification gap). "Unclassified" says so, rather than the old "Related" asserting one that wasn't.
diff --git a/src/components/variant/MvMeasurementCard.vue b/src/components/variant/MvMeasurementCard.vue
index fa2c6b1f..f796258f 100644
--- a/src/components/variant/MvMeasurementCard.vue
+++ b/src/components/variant/MvMeasurementCard.vue
@@ -20,7 +20,7 @@
         {{ levelLabel }}
       </span>
       <span
-        v-key-term="relationship === 'direct' ? 'this-variant' : 'relationship'"
+        v-key-term="relationship === 'direct' ? 'your-variant' : 'relationship'"
         class="inline-block rounded-sm px-2 py-0.5 text-[10px] font-semibold uppercase tracking-[0.3px]"
         :class="relationshipClass"
       >
diff --git a/src/components/variant/VariantClinvarStat.vue b/src/components/variant/VariantClinvarStat.vue
index 8d0dc580..5f005ddd 100644
--- a/src/components/variant/VariantClinvarStat.vue
+++ b/src/components/variant/VariantClinvarStat.vue
@@ -32,7 +32,7 @@
     <!-- Nucleotide measurement with no ClinVar record of its own: be explicit rather than borrow a related
          allele's call. Related records (if any) are offered below as context, not promoted to a call. -->
     <span v-else-if="headline.kind === 'absent'" class="stat-value text-sm italic text-text-muted">
-      No ClinVar record for this variant
+      No ClinVar record for this allele
     </span>
     <span v-else class="stat-value">—</span>
 
@@ -179,7 +179,7 @@ export default defineComponent({
     },
     underlyingClinvarNote(): string {
       return this.isProjectedHeadline
-        ? 'This variant has no ClinVar record. The classification above is inferred from these nucleotide variants that encode the same protein change and does not represent a ClinVar assertion for this variant.'
+        ? 'This allele has no ClinVar record. The classification above is inferred from these nucleotide variants that encode the same protein change and does not represent a ClinVar assertion for this allele.'
         : 'Other variants with the same protein consequence that also carry ClinVar records.'
     }
   },
diff --git a/src/components/variant/VariantDetailPanel.vue b/src/components/variant/VariantDetailPanel.vue
index 4ce09ca0..a8345bb9 100644
--- a/src/components/variant/VariantDetailPanel.vue
+++ b/src/components/variant/VariantDetailPanel.vue
@@ -85,10 +85,10 @@
       <p v-else-if="candidateFanoutCount > 0" class="px-4 py-3 text-xs text-text-muted tablet:px-5">
         This amino-acid change reverse-translates to {{ candidateFanoutCount }} candidate nucleotide allele{{
           candidateFanoutCount === 1 ? '' : 's'
-        }}; no population or clinical evidence was found for this variant or the candidate nucleotide alleles.
+        }}; no population or clinical evidence was found for this allele or the candidate nucleotide alleles.
       </p>
       <p v-else class="px-4 py-3 text-xs text-text-muted tablet:px-5">
-        No reference annotations were found for this variant.
+        No reference annotations were found for this allele.
       </p>
 
       <!-- Status and links — the superseded badge and full-details link, shown below either the facts
diff --git a/src/components/variant/VariantGnomadStat.vue b/src/components/variant/VariantGnomadStat.vue
index 3a2cd59e..eecc8eea 100644
--- a/src/components/variant/VariantGnomadStat.vue
+++ b/src/components/variant/VariantGnomadStat.vue
@@ -12,7 +12,7 @@
     <!-- Nucleotide subject with no frequency of its own but related variants carry frequencies: be explicit
          rather than borrow related variants' frequencies. Related frequencies, if any, show below as context. -->
     <span v-else-if="headlineState === 'absent'" class="stat-value text-sm italic text-text-muted">
-      No gnomAD record for this variant
+      No gnomAD record for this allele
     </span>
     <span v-else class="stat-value">—</span>
 
@@ -81,7 +81,7 @@ type SequenceLevel = components['schemas']['SequenceLevel']
  *  - the subject allele's own frequency wins as the headline, with its link;
  *  - at *protein* level, a subject with no frequency of its own enumerates its encoding variants' distinct
  *    frequencies (max-AF headline + popover), noting it isn't established which underlies the measurement;
- *  - at *nucleotide* level, a subject with no frequency stays explicit ('No gnomAD record for this variant') —
+ *  - at *nucleotide* level, a subject with no frequency stays explicit ('No gnomAD record for this allele') —
  *    we don't borrow a related variant's frequency — and any related frequencies show below as context.
  * The subject is the measured allele on the score-set panel, or the page's own allele on the variant page.
  */
diff --git a/src/lib/allele-grouping.test.ts b/src/lib/allele-grouping.test.ts
index ce765930..c998d379 100644
--- a/src/lib/allele-grouping.test.ts
+++ b/src/lib/allele-grouping.test.ts
@@ -130,7 +130,7 @@ describe('groupAlleles — projection pairing + confidence', () => {
   })
 
   it('badges measured over derivation, maps projection→Resolved / convergent→Convergent / candidate→Candidate, else null', () => {
-    // `measured` wins even if a derivation is also present (a stray measured member still reads "This measurement").
+    // `measured` wins even if a derivation is also present (a stray measured member still reads "Measured").
     expect(confidenceBadge({measured: true, derivation: 'projection'})).toBe(ALLELE_CONFIDENCE.measured)
     expect(confidenceBadge({measured: false, derivation: 'projection'})).toBe(ALLELE_CONFIDENCE.projection)
     // A synonymous cousin under a nucleotide assay: a distinct change sharing the consequence, not ambiguous.
diff --git a/src/lib/allele-grouping.ts b/src/lib/allele-grouping.ts
index 1735d3c7..3ddaa393 100644
--- a/src/lib/allele-grouping.ts
+++ b/src/lib/allele-grouping.ts
@@ -71,7 +71,7 @@ export interface ConfidenceBadge {
 // display order.
 export const ALLELE_CONFIDENCE: Record<string, ConfidenceBadge> = {
   measured: {
-    label: 'This measurement',
+    label: 'Measured',
     class: 'bg-measured-light text-measured',
     definition: 'Directly measured in this assay.'
   },
diff --git a/src/lib/glossary-prose.ts b/src/lib/glossary-prose.ts
index 2bfb6618..4e3904ff 100644
--- a/src/lib/glossary-prose.ts
+++ b/src/lib/glossary-prose.ts
@@ -1,18 +1,18 @@
 import type {KeySection} from '@/composables/use-key-drawer'
 
-// Single source for the "This variant" concept — the page's own subject allele — wherever it's badged:
+// Single source for the "Your variant" concept — the page's own subject allele — wherever it's badged:
 // the allele ledger's page-role entry (MvAlleleLedger) and a measurement's direct-relationship badge
 // (MvMeasurementCard) are the same fact from two objects, so they share this one definition rather than
 // each carrying their own. Leads GLOSSARY_SECTIONS (glossary.ts): establishing the subject first lets
-// "Relationship to this variant" read naturally right after it — how other results relate to the thing
+// "Relationship to your variant" read naturally right after it — how other results relate to the thing
 // this section just defined.
 export const THIS_VARIANT_KEY_SECTION: KeySection = {
-  id: 'this-variant',
-  title: 'This variant',
+  id: 'your-variant',
+  title: 'Your variant',
   terms: [
     {
-      label: 'This variant',
-      definition: 'The ClinGen allele this page is anchored on.',
+      label: 'Your variant',
+      definition: 'The allele this page is about.',
       class: 'bg-subject/15 text-subject'
     }
   ]
@@ -48,7 +48,7 @@ export const SUPERSEDED_KEY_SECTION: KeySection = {
     {
       label: 'Superseded',
       definition:
-        'This measurement is from an older version of its score set and might have outdated scores or classifications. Note that the score set which supersedes the older version may not include this variant.',
+        'This measurement is from an older version of its score set and might have outdated scores or classifications. Note that the score set which supersedes the older version may not include your variant.',
       class: 'bg-superseded-light text-superseded'
     }
   ]
diff --git a/src/lib/measurement-types.ts b/src/lib/measurement-types.ts
index 04e2ef22..f228d165 100644
--- a/src/lib/measurement-types.ts
+++ b/src/lib/measurement-types.ts
@@ -16,28 +16,28 @@ export function assayLevelBucket(level: string | null | undefined): LevelBucket
 /**
  * Single source of truth for the measurement-to-query relationship vocabulary (the RT asymmetry): the
  * card label, an optional chip class, and the Key-drawer gloss. Phrased relative to the page's own variant
- * so the labels self-explain under the "relative to this variant" anchor. Insertion order is display order.
+ * so the labels self-explain under the "relative to your variant" anchor. Insertion order is display order.
  */
 export const RELATIONSHIPS: Record<MeasurementRelationship, {label: string; class?: string; definition?: string}> = {
   // No `definition`: a direct result is the page's own subject allele — the same concept as the Key
-  // drawer's "This variant" section (glossary-prose.ts), defined once there rather than twice.
+  // drawer's "Your variant" section (glossary-prose.ts), defined once there rather than twice.
   direct: {
-    label: 'This variant',
+    label: 'Your variant',
     class: 'bg-subject/15 text-subject'
   },
   protein_consequence: {
     label: 'Its protein consequence',
-    definition: 'The result assayed the protein change this variant produces.'
+    definition: 'The result assayed the protein change your variant produces.'
   },
   nucleotide_encoding: {
     label: 'Encodes the protein consequence',
-    definition: 'The result assayed a nucleotide allele that encodes the same protein change as this variant.'
+    definition: 'The result assayed a nucleotide allele that encodes the same protein change as your variant.'
   }
 }
 
 export const RELATIONSHIP_KEY_SECTION: KeySection = {
   id: 'relationship',
-  title: 'Relationship to this variant',
+  title: 'Relationship to your variant',
   gloss: 'How each result relates to the allele you searched.',
   terms: Object.values(RELATIONSHIPS)
     .filter((r) => r.definition)

From bee68e66d1bd1d4444945937c9632e958d18f7d4 Mon Sep 17 00:00:00 2001
From: Benjamin Capodanno <bencap@outlook.com>
Date: Wed, 30 Sep 2026 15:03:02 -0700
Subject: [PATCH 84/84] feat(variant): simplify variant-page vocabulary and
 relationship display

Measurement relationship
- Badge is now Direct / Indirect; both related-variant relationships share
  Indirect. The detail is stated once, as the first element of the
  Functional evidence box: "This score was measured on a different variant
  which has the same protein change as yours: <HGVS>".
- Remove the relationship sentence under the carousel and the unlabeled
  confidence pill on Functional evidence.

Clinical & population ledger
- "Measured" is a page-wide fact (lookup.measuredDigests, from the loaded
  measurement envelopes), so the page variant reads "Your variant" +
  "Measured" instead of flipping to Convergent when another card is selected.
- The selected measurement's variant gets a solid "Selected measurement"
  badge and a sage border echoing the selected card. Resolved / Convergent /
  Candidate stay relative to the selection and only appear on variants
  without a measurement of their own.
- Extract titleMember into allele-grouping and reuse it for the notice.

Page controls
- Move "MaveDB as of" and the superseded toggle into a View options panel
  opened from the header (count badge when non-default, as-of shown in the
  subtitle); Key becomes a header button.

Wording
- One noun per referent (variant / score set), "protein change" instead of
  "protein consequence", "Functional impact" for the classification,
  "Molecular mechanism", sentence-case "Assay facts", and "Detects ...
  variants" labels matching the docs.
- Add Calibration and NMD Key-drawer entries, retitle the confidence
  section, and point the drawer's "more" link at the
  interpreting-annotated-variants doc.
- Update variant-page and assay-facts docs to match.
---
 docs/content/mavemd/variant-page.md           |  10 +-
 docs/content/reference/assay-facts.md         |   2 +-
 src/components/common/MvAssayFactsCard.vue    |   6 +-
 .../score-set/ScoreSetHistogram.vue           |   8 +-
 src/components/screens/ScoreSetView.vue       |   2 +-
 src/components/screens/VariantScreen.vue      | 160 +++++++++---------
 src/components/variant/MvAlleleLedger.vue     | 112 ++++++------
 src/components/variant/MvMeasurementCard.vue  |  12 +-
 src/components/variant/VariantClinvarStat.vue |  12 +-
 src/components/variant/VariantDetailPanel.vue |   2 +-
 src/components/variant/VariantGnomadStat.vue  |   2 +-
 src/composables/use-variant-lookup.ts         |  18 ++
 src/glossary.ts                               |  13 +-
 src/lib/allele-grouping.test.ts               |  67 +++++++-
 src/lib/allele-grouping.ts                    |  44 ++++-
 src/lib/clinvar-controls.ts                   |   2 +-
 src/lib/glossary-prose.ts                     |  39 ++++-
 src/lib/measurement-types.test.ts             |  18 +-
 src/lib/measurement-types.ts                  |  46 ++---
 19 files changed, 371 insertions(+), 204 deletions(-)

diff --git a/docs/content/mavemd/variant-page.md b/docs/content/mavemd/variant-page.md
index 5d52f1f1..a49dba74 100644
--- a/docs/content/mavemd/variant-page.md
+++ b/docs/content/mavemd/variant-page.md
@@ -20,6 +20,14 @@ This is important because different assays may measure different molecular prope
 
 You can also navigate to the full [score set page](../finding-data/visualizations.md) for the selected assay to view the complete dataset, including the heatmap, all variant scores, and detailed metadata.
 
+## Direct and indirect measurements
+
+Each measurement is flagged **Direct** or **Indirect**. A direct measurement assayed your variant itself. An indirect one assayed a related variant instead: the protein change your variant produces, or a different nucleotide variant that encodes the same protein change. When you select an indirect measurement, a notice at the top of the functional evidence section names the variant the score was measured on, because that score stands in for your variant rather than measuring it.
+
+## View options
+
+The **View options** button in the page header holds two settings that change which measurements are shown: **MaveDB as of**, which shows the molecular and annotation layer as MaveDB held it on a past date (scores never change), and **Show superseded score sets**. The button shows a count when either is set. The **Key** button beside it opens a glossary of the terms on this page.
+
 ## Assay facts
 
 Each dataset on the variant page includes an [assay fact](../reference/assay-facts.md) label that summarizes the key properties of the functional assay. These labels are designed to help you quickly assess whether an assay is relevant to your clinical context. Key properties include:
@@ -38,7 +46,7 @@ For the full list of assay fact properties and their definitions, see the [assay
 
 ## Annotations
 
-Beneath the assay details, an annotations card gathers evidence about the variant itself, independent of any one assay. **Classification** reports the selected measurement's functional score, ACMG code, and OddsPath ratio.
+Beneath the assay details, an annotations card gathers evidence about the variant itself, independent of any one assay. **Functional impact** reports the selected measurement's functional score, ACMG code, and OddsPath ratio.
 
 **Population frequency** reports the variant's frequency in [gnomAD](../finding-data/external-integrations.md#gnomad), where it is present:
 
diff --git a/docs/content/reference/assay-facts.md b/docs/content/reference/assay-facts.md
index 31a9e274..dc47a049 100644
--- a/docs/content/reference/assay-facts.md
+++ b/docs/content/reference/assay-facts.md
@@ -28,7 +28,7 @@ MaveDB captures key facts about the experimental assay used to generate variant
 :   Whether the assay is capable of detecting splicing variants. Based on assay design, and inferred based on a combination of the [variant library creation method](controlled-vocabulary.md#variant-library-creation-methods) and other terms.
 
 **Detects NMD variants**
-:   Whether the assay is capable of detecting NMD variants. Based on assay design, and inferred based on a combination of the [variant library creation method](controlled-vocabulary.md#variant-library-creation-methods) and other terms.
+:   Whether the assay is capable of detecting variants that trigger nonsense-mediated decay (NMD). Based on assay design, and inferred based on a combination of the [variant library creation method](controlled-vocabulary.md#variant-library-creation-methods) and other terms.
 
 **OddsPaths**
 :   The OddsPath score calculated for abnormal and normal functional readouts, if applicable. These OddsPaths are based on the framework described in [Brnich et al., 2019](https://doi.org/10.1186/s13073-019-0690-2).
diff --git a/src/components/common/MvAssayFactsCard.vue b/src/components/common/MvAssayFactsCard.vue
index 2cc378b3..746cbca8 100644
--- a/src/components/common/MvAssayFactsCard.vue
+++ b/src/components/common/MvAssayFactsCard.vue
@@ -1,6 +1,6 @@
 <template>
   <div>
-    <h3 class="mave-section-title">Assay Facts</h3>
+    <h3 class="mave-section-title">Assay facts</h3>
     <div v-if="scoreSet" class="mb-2.5 pb-2.5 border-b border-border">
       <div class="text-base font-semibold text-text-primary leading-[1.3] mb-0.5">
         <router-link
@@ -34,7 +34,7 @@
       />
       <MvDetailRow fallback="Not specified" label="Model system" :value="getKeyword('Phenotypic Assay Model System')" />
       <MvDetailRow fallback="Not mapped" label="Assay level" term="assay-level" :value="assayLevelLabel" />
-      <MvDetailRow fallback="Not specified" label="Detects splicing?">
+      <MvDetailRow fallback="Not specified" label="Detects splicing variants">
         <span
           v-if="detectsSplicing != null"
           :class="{'flex-1 bg-badge-alert px-1.5 py-px rounded': detectsSplicing === false}"
@@ -42,7 +42,7 @@
           {{ detectsSplicing ? 'Yes' : 'No' }}
         </span>
       </MvDetailRow>
-      <MvDetailRow fallback="Not specified" label="Detects NMD?">
+      <MvDetailRow fallback="Not specified" label="Detects NMD variants" term="nmd">
         <span v-if="detectsNmd != null" :class="{'flex-1 bg-badge-alert px-1.5 py-px rounded': detectsNmd === false}">
           {{ detectsNmd ? 'Yes' : 'No' }}
         </span>
diff --git a/src/components/score-set/ScoreSetHistogram.vue b/src/components/score-set/ScoreSetHistogram.vue
index ed1fc0a6..001a46de 100644
--- a/src/components/score-set/ScoreSetHistogram.vue
+++ b/src/components/score-set/ScoreSetHistogram.vue
@@ -1118,10 +1118,10 @@ export default defineComponent({
               CONFLICTING_CLINICAL_SIGNIFICANCE_CLASSIFICATIONS.includes(c.significance)
             )
             ? tooltipFootnote(
-                'A related variant with the same protein consequence is conflicting — the directional call is shown.'
+                'A related variant with the same protein change is conflicting — the directional call is shown.'
               )
             : tooltipFootnote(
-                'A related variant with the same protein consequence is of uncertain significance — the directional call is shown.'
+                'A related variant with the same protein change is of uncertain significance — the directional call is shown.'
               )
           : null
       const reviewStatus = control[DEFAULT_CLNREVSTAT_FIELD]
@@ -1144,7 +1144,7 @@ export default defineComponent({
       // variants"), rather than a bare asterisk that needs its own legend to decode.
       const projectedNote = control.projected
         ? tooltipFootnote(
-            'This classification is inferred from a related variant with the same protein consequence. The measured variant has no ClinVar record of its own.'
+            'This classification is inferred from a related variant with the same protein change. The measured variant has no ClinVar record of its own.'
           )
         : null
 
@@ -1283,7 +1283,7 @@ export default defineComponent({
       return resolveControlSeries(variant.control, opts)
     },
     // A series's calls can be a mix of direct ClinVar records and ones inferred from a related allele at
-    // the same protein consequence — flag it right on the series that actually has them, rather than a
+    // the same protein change — flag it right on the series that actually has them, rather than a
     // single blanket note for the whole chart. Returned as two lines (the legend wraps a `string[]` title)
     // rather than one long line, which would widen the legend enough to cover plotted data.
     seriesTitle(baseTitle: string, classifier: (d: HistogramDatum) => boolean): string | string[] {
diff --git a/src/components/screens/ScoreSetView.vue b/src/components/screens/ScoreSetView.vue
index 74ce287b..91d3790e 100644
--- a/src/components/screens/ScoreSetView.vue
+++ b/src/components/screens/ScoreSetView.vue
@@ -351,7 +351,7 @@
           <hr class="mb-4 border-border" />
         </div>
 
-        <!-- Assay Facts -->
+        <!-- Assay facts -->
         <div class="mb-4 mave-gradient-bar relative overflow-hidden rounded-lg border border-border bg-white p-5">
           <MvAssayFactsCard :assay-level="assayLevel" :link-title="false" :score-set="item" />
         </div>
diff --git a/src/components/screens/VariantScreen.vue b/src/components/screens/VariantScreen.vue
index e6458280..b5f1e65d 100644
--- a/src/components/screens/VariantScreen.vue
+++ b/src/components/screens/VariantScreen.vue
@@ -2,7 +2,7 @@
   <MvLayout>
     <template #header>
       <MvPageHeader eyebrow="Variant" max-width="1000px" :title="pageTitle">
-        <template v-if="lookup.variants.value.length > 0" #actions>
+        <template #actions>
           <div class="flex items-center gap-2">
             <!-- Indeterminate: a gzipped download exposes no measurable total. -->
             <span
@@ -13,7 +13,34 @@
               <i class="pi pi-spin pi-spinner text-xs" />
               Preparing {{ lookup.downloadInProgressLabel.value }}…
             </span>
-            <MvRowActionMenu :actions="downloadActions" />
+            <button
+              :aria-expanded="viewOptionsOpen"
+              class="flex cursor-pointer items-center gap-1.5 rounded-md border px-2.5 py-1 text-xs font-semibold transition-colors"
+              :class="
+                viewOptionsOpen || viewOptionCount > 0
+                  ? 'border-sage bg-sage text-white'
+                  : 'border-border bg-surface text-text-secondary hover:border-sage hover:text-sage'
+              "
+              type="button"
+              @click="viewOptionsOpen = !viewOptionsOpen"
+            >
+              <i class="pi pi-sliders-h text-[11px]" />
+              View options<template v-if="viewOptionCount > 0"> ({{ viewOptionCount }})</template>
+            </button>
+            <button
+              class="flex cursor-pointer items-center gap-1.5 rounded-md border px-2.5 py-1 text-xs font-semibold transition-colors"
+              :class="
+                keyDrawer.isOpen.value
+                  ? 'border-sage bg-sage text-white'
+                  : 'border-border bg-surface text-text-secondary hover:border-sage hover:text-sage'
+              "
+              type="button"
+              @click="keyDrawer.isOpen.value ? keyDrawer.close() : keyDrawer.open()"
+            >
+              <i class="pi pi-question-circle text-[11px]" />
+              Key
+            </button>
+            <MvRowActionMenu v-if="lookup.variants.value.length > 0" :actions="downloadActions" />
           </div>
         </template>
 
@@ -28,6 +55,7 @@
             <template v-if="lookup.uniqueAssayCount.value > 1">
               across {{ lookup.uniqueAssayCount.value }} score sets</template
             >
+            <template v-if="lookup.asOf.value"> &middot; MaveDB as of {{ lookup.asOf.value }}</template>
             <template v-if="clingenAlleleId">
               &middot;
               <a
@@ -43,11 +71,13 @@
     </template>
 
     <div class="mx-auto w-full px-4 tablet:px-6 py-6 tablet:py-8" style="max-width: 1000px">
-      <!-- ── CONTROL ROW (query axes) ── -->
+      <!-- ── VIEW OPTIONS (query axes) ── opened from the header; the button carries a count so a non-default
+           view (past date, superseded included) is never invisible while the panel is closed. -->
       <div
-        class="mave-gradient-bar relative overflow-hidden mb-4 flex flex-col gap-3 rounded-lg border border-border bg-surface px-4 py-3 tablet:flex-row tablet:flex-wrap tablet:items-center tablet:gap-x-5 tablet:gap-y-2 tablet:px-5 tablet:py-2.5"
+        v-if="viewOptionsOpen"
+        class="mave-gradient-bar relative overflow-hidden mb-4 flex flex-col gap-3 rounded-lg border border-border bg-surface px-4 py-3 tablet:flex-row tablet:flex-wrap tablet:items-center tablet:gap-x-6 tablet:gap-y-2 tablet:px-5 tablet:py-2.5"
       >
-        <div class="flex flex-1 items-center gap-2 text-xs text-text-secondary">
+        <div class="flex items-center gap-2 text-xs text-text-secondary">
           <span v-key-term="'as-of'" class="font-semibold uppercase tracking-[0.3px] text-[#aaa]">MaveDB as of</span>
           <DatePicker
             v-model="asOfDate"
@@ -81,20 +111,7 @@
           @click="lookup.includeSuperseded.value = !lookup.includeSuperseded.value"
         >
           <i class="pi text-[11px]" :class="lookup.includeSuperseded.value ? 'pi-check' : 'pi-plus'" />
-          {{ lookup.includeSuperseded.value ? 'Hide superseded variants' : 'Show superseded variants' }}
-        </button>
-        <button
-          class="flex cursor-pointer items-center gap-1.5 rounded-md border px-2.5 py-1 text-xs font-semibold transition-colors"
-          :class="
-            keyDrawer.isOpen.value
-              ? 'border-sage bg-sage text-white'
-              : 'border-border bg-surface text-text-secondary hover:border-sage hover:text-sage'
-          "
-          type="button"
-          @click="keyDrawer.isOpen.value ? keyDrawer.close() : keyDrawer.open()"
-        >
-          <i class="pi pi-key text-[11px]" />
-          Key
+          {{ lookup.includeSuperseded.value ? 'Hide superseded score sets' : 'Show superseded score sets' }}
         </button>
       </div>
 
@@ -116,7 +133,13 @@
               >{{ lookup.variants.value.length }}
               {{ lookup.variants.value.length === 1 ? 'Measurement' : 'Measurements' }}</span
             >
-            <div class="ml-auto flex gap-1.5">
+            <div class="ml-auto flex items-center gap-1.5">
+              <span
+                v-if="lookup.nucleotideCount.value > 0 || lookup.proteinCount.value > 0"
+                v-key-term="'assay-level'"
+                class="mr-0.5 text-[10px] font-semibold uppercase tracking-[0.3px] text-[#aaa]"
+                >Assay level</span
+              >
               <MvBadgeToggle
                 v-if="lookup.nucleotideCount.value > 0"
                 v-model="lookup.showNucleotide.value"
@@ -137,10 +160,10 @@
               />
             </div>
           </div>
-          <!-- Anchor heading: names the frame of reference so the per-card relationship badges read as
+          <!-- Anchor heading: names the frame of reference so the per-card Direct/Indirect badges read as
                self-explaining without needing a per-badge tooltip. -->
           <div class="px-4 tablet:px-5 pt-3.5 text-xs-minus text-text-muted">
-            What each result assayed, relative to your variant:
+            Each measurement, relative to your variant:
           </div>
           <div class="measurement-switcher hidden tablet:flex gap-3 overflow-x-auto px-5 py-4">
             <MvMeasurementCard
@@ -176,16 +199,6 @@
               class="pi pi-spin pi-spinner text-sage"
             />
           </div>
-
-          <!-- ── RELATIONSHIP LINE ── a plain sentence relating the selected measurement (Y) to the page
-               subject (X). -->
-          <div
-            v-if="lookup.selectedVariantDetail.value"
-            class="border-t border-border-light bg-sage/[0.06] px-4 tablet:px-5 py-3 text-sm text-text-secondary"
-          >
-            {{ relationshipPrefix }} <span class="font-semibold text-text-primary">your variant</span
-            >{{ isDirectMeasurement ? ' directly' : '' }}.
-          </div>
         </div>
 
         <!-- ── FUNCTIONAL EVIDENCE ── MaveDB's own contribution, centered as the lead of the body. -->
@@ -193,20 +206,26 @@
           v-if="lookup.selectedVariantDetail.value"
           class="relative mt-4 rounded-lg border bg-surface px-[18px] py-3.5"
         >
+          <!-- The one place the indirect relationship is spelled out; the badges elsewhere only flag it. -->
+          <div
+            v-if="indirectNotice"
+            class="mb-3 flex items-start gap-2 rounded-md border border-convergent/30 bg-convergent-light px-3 py-2 text-sm text-text-secondary"
+          >
+            <i class="pi pi-info-circle mt-0.5 text-xs text-convergent" />
+            <div>
+              This score was measured on a different variant which has the same protein change as yours<template
+                v-if="indirectNotice.hgvs"
+                >: <span class="font-mono font-semibold text-text-primary">{{ indirectNotice.hgvs }}</span></template
+              >.
+            </div>
+          </div>
           <div class="mb-2.5 flex flex-wrap items-center gap-2">
             <h3 class="mave-section-title !mb-0">Functional evidence</h3>
             <span class="text-xs-minus text-text-muted">measured in this score set</span>
-            <span
-              v-if="pageConfidenceBadge"
-              v-key-term="'confidence'"
-              class="ml-auto rounded-sm px-1.5 py-0.5 text-[10px] font-bold uppercase tracking-[0.3px]"
-              :class="pageConfidenceBadge.class"
-              >{{ pageConfidenceBadge.label }}</span
-            >
             <span
               v-if="lookup.selectedVariantDetail.value && !lookup.selectedVariantDetail.value.isCurrent"
               v-key-term="'superseded'"
-              class="rounded-sm px-1.5 py-0.5 text-[10px] font-bold uppercase tracking-[0.3px] bg-superseded-light text-superseded"
+              class="ml-auto rounded-sm px-1.5 py-0.5 text-[10px] font-bold uppercase tracking-[0.3px] bg-superseded-light text-superseded"
               >Superseded</span
             >
           </div>
@@ -240,7 +259,9 @@
               }}</span>
             </div>
             <div v-if="lookup.selectedVariantControlStatus.value" class="flex flex-col gap-0.5">
-              <span class="text-[10px] font-semibold uppercase tracking-[0.3px] text-[#aaa]">Calibration control</span>
+              <span v-key-term="'calibration'" class="text-[10px] font-semibold uppercase tracking-[0.3px] text-[#aaa]"
+                >Calibration control</span
+              >
               <span class="flex items-center">
                 <MvBadge :value="lookup.selectedVariantControlStatus.value" />
                 <span class="ml-1.5 text-xs text-text-muted">used to derive this calibration</span>
@@ -296,6 +317,7 @@
             :annotations="lookup.selectedVariantDetail.value.annotations"
             :clinvar-version="clinvarControls.controlVersion"
             :groups="alleleGroups"
+            :measured-digests="[...lookup.measuredDigests.value]"
             :variant-urn="lookup.selectedVariantDetail.value.urn"
           />
         </div>
@@ -336,8 +358,8 @@
               <!-- Shown only when the page variant is in this envelope but wasn't itself measured — otherwise
                    we can't say whether it was measured, so we say nothing rather than guess from a stand-in. -->
               <p v-if="pageGroup && !pageGroup.measured" class="mt-2 text-xs italic leading-tight text-text-muted">
-                This allele was not directly measured. The highlighted bin contains a measured allele that shares its
-                protein consequence.
+                Your variant was not directly measured. The highlighted bin contains a measured variant with the same
+                protein change.
               </p>
             </div>
             <div v-else class="flex min-h-[200px] items-center justify-center">
@@ -394,12 +416,9 @@ import {useVariantLookup} from '@/composables/use-variant-lookup'
 import {assayLevelDisplay} from '@/lib/measurement-types'
 import {formatScore} from '@/lib/scores'
 import {hasFunctionalCalibrations, hasPathogenicityCalibrations} from '@/lib/calibrations'
-import {confidenceBadge, groupAlleles, type AlleleGroup, type ConfidenceBadge} from '@/lib/allele-grouping'
-import type {components} from '@/schema/openapi'
+import {groupAlleles, titleMember, type AlleleGroup} from '@/lib/allele-grouping'
 import {clingenAlleleUrlFromCanonicalId} from '@/lib/clingen'
 
-type SequenceLevel = components['schemas']['SequenceLevel']
-
 /** One entry in a download control: a label and the download it triggers. */
 interface DownloadOption {
   label: string
@@ -471,7 +490,8 @@ export default defineComponent({
 
   data() {
     return {
-      csvDialogVisible: false
+      csvDialogVisible: false,
+      viewOptionsOpen: false
     }
   },
 
@@ -507,39 +527,21 @@ export default defineComponent({
     pageGroup(): AlleleGroup | null {
       return this.alleleGroups.find((g) => g.pageRoot) ?? null
     },
-    // The page variant's own sequence level, read off its page-root member.
-    pageLevel(): SequenceLevel | null {
-      const root = this.pageGroup?.members.find((m) => m.pageRoot)
-      return (root?.level ?? null) as SequenceLevel | null
-    },
-    // True when the page itself is anchored on the protein-level entity (a PA id) — the page variant *is*
-    // the protein change, not a nucleotide variant that separately produces one.
-    pageIsProteinRooted(): boolean {
-      return this.pageLevel === 'protein'
-    },
     // ClinGen Allele Registry deep link for the page variant.
     clingenRegistryUrl(): string {
       return clingenAlleleUrlFromCanonicalId(this.clingenAlleleId)
     },
-    // True when the selected measurement assayed the page allele itself (X == Y).
-    isDirectMeasurement(): boolean {
-      return this.lookup.selectedVariant.value?.relationship === 'direct'
-    },
-    // Leading half of the relationship line — everything up to the bold "your variant".
-    relationshipPrefix(): string {
+    // The one-time explanation of an indirect measurement, naming the measured variant by its HGVS when the
+    // envelope carries it. Null for a direct measurement — the badge alone says everything there is to say.
+    indirectNotice(): {hgvs: string | null} | null {
       const rel = this.lookup.selectedVariant.value?.relationship
-      if (rel === 'protein_consequence') return 'The selected measurement measured the protein consequence of'
-      if (rel === 'nucleotide_encoding') {
-        return this.pageIsProteinRooted
-          ? 'The selected measurement measured a variant that encodes'
-          : 'The selected measurement measured a variant that encodes the same protein consequence as'
-      }
-      return 'The selected measurement measured'
+      if (!rel || rel === 'direct') return null
+      const measuredGroup = this.alleleGroups.find((g) => g.measured)
+      return {hgvs: (measuredGroup && titleMember(measuredGroup)?.hgvs) || null}
     },
-    // How the page variant relates to what this result measured. Null (badge hidden) when the page
-    // variant is absent from this result's envelope — there is nothing to state a relationship about.
-    pageConfidenceBadge(): ConfidenceBadge | null {
-      return this.pageGroup ? confidenceBadge(this.pageGroup) : null
+    // Non-default view settings, surfaced on the closed View options button.
+    viewOptionCount(): number {
+      return (this.lookup.asOf.value ? 1 : 0) + (this.lookup.includeSuperseded.value ? 1 : 0)
     },
     today(): Date {
       return new Date()
@@ -548,12 +550,12 @@ export default defineComponent({
       if (this.lookup.asOf.value) {
         return this.lookup.includeSuperseded.value
           ? `No measurements found as of ${this.lookup.asOf.value}. Try a more recent date.`
-          : `No measurements found as of ${this.lookup.asOf.value}. Try a more recent date, or include superseded versions.`
+          : `No measurements found as of ${this.lookup.asOf.value}. Try a more recent date, or include superseded score sets.`
       }
       if (!this.lookup.includeSuperseded.value) {
-        return 'No current measurements were found for this allele. Try including superseded versions.'
+        return 'No current measurements were found for this variant. Try including superseded score sets.'
       }
-      return 'No measurements were found for this allele.'
+      return 'No measurements were found for this variant.'
     },
     asOfDate: {
       get(): Date | null {
@@ -565,7 +567,7 @@ export default defineComponent({
     },
     measurementOptions(): {label: string; urn: string}[] {
       return this.lookup.filteredVariants.value.map((m) => ({
-        label: `${m.scoreSetTitle || 'Untitled score set'} (${assayLevelDisplay(m.assayLevel).label})`,
+        label: `${m.scoreSetTitle || 'Untitled score set'} (${assayLevelDisplay(m.assayLevel).label}${m.relationship === 'direct' ? '' : ', indirect'})`,
         urn: m.variantUrn
       }))
     },
diff --git a/src/components/variant/MvAlleleLedger.vue b/src/components/variant/MvAlleleLedger.vue
index b300ada9..f9d87d64 100644
--- a/src/components/variant/MvAlleleLedger.vue
+++ b/src/components/variant/MvAlleleLedger.vue
@@ -3,14 +3,15 @@
     <div class="mb-1 flex flex-wrap items-baseline gap-x-2">
       <h3 class="mave-section-title !mb-0">Clinical &amp; population data</h3>
     </div>
-    <!-- Frame heading: this block is anchored on the *measured* allele, not the page header's looked-up
-         variant — two reference points, one screen. Naming it here keeps the per-row badges short instead
-         of each spelling out "…than the measured allele" (mirrors the measurement carousel's own anchor
-         heading). -->
-    <p class="mb-3 text-xs-minus text-text-muted">How each allele relates to what this result measured:</p>
+    <!-- Frame heading: "Measured" is a page-wide fact about a variant; only the derived labels (Resolved,
+         Convergent, Candidate) are relative, and they are relative to the *selected* measurement — not the
+         page variant. Saying so once keeps the per-row badges short. -->
+    <p class="mb-3 text-xs-minus text-text-muted">
+      Measured variants are marked. The rest are labeled relative to the selected measurement:
+    </p>
 
-    <!-- One card per allele group, uniform except for role badge and emphasis: this variant (X) leads, the
-         measured allele (Y) follows, everything else collapses underneath. -->
+    <!-- One card per allele group, uniform except for role badge and emphasis: your variant (X) leads, the
+         selected measurement's variant (Y) follows, everything else collapses underneath. -->
     <div class="flex flex-col gap-2">
       <div
         v-for="entry in entries"
@@ -21,10 +22,12 @@
       >
         <div class="mb-2 flex flex-wrap items-center gap-x-2 gap-y-1">
           <span
-            v-key-term="entry.role === 'page' ? 'your-variant' : 'confidence'"
+            v-for="badge in roleBadges(entry)"
+            :key="badge.label"
+            v-key-term="badge.term"
             class="rounded-sm px-1.5 py-0.5 text-[10px] font-bold uppercase tracking-[0.3px]"
-            :class="roleBadge(entry).class"
-            >{{ roleBadge(entry).label }}</span
+            :class="badge.class"
+            >{{ badge.label }}</span
           >
           <span
             v-key-term="'assay-level'"
@@ -35,7 +38,7 @@
           <span class="font-mono text-xs-plus font-semibold text-text-primary" :title="allHgvsTitle(entry.group)">{{
             titleMember(entry.group)?.hgvs || '—'
           }}</span>
-          <!-- This variant (X) is the page you're already on — no link out. Related alleles link to their
+          <!-- Your variant (X) is the page you're already on — no link out. Related variants link to their
                own variant page. -->
           <router-link
             v-for="caid in entry.role === 'page' ? [] : entry.group.clingenLinks"
@@ -103,8 +106,8 @@
     >
       {{
         expanded
-          ? 'Hide other related alleles'
-          : `Show ${otherGroups.length} other related ${otherGroups.length === 1 ? 'allele' : 'alleles'}`
+          ? 'Hide other related variants'
+          : `Show ${otherGroups.length} other related ${otherGroups.length === 1 ? 'variant' : 'variants'}`
       }}
     </button>
   </div>
@@ -116,7 +119,7 @@ import {defineComponent, type PropType} from 'vue'
 import VariantConsequenceStat from '@/components/variant/VariantConsequenceStat.vue'
 import VariantGnomadStat from '@/components/variant/VariantGnomadStat.vue'
 import VariantClinvarStat from '@/components/variant/VariantClinvarStat.vue'
-import {type AlleleGroup, type AlleleMember, confidenceBadge} from '@/lib/allele-grouping'
+import {type AlleleGroup, confidenceBadge, titleMember} from '@/lib/allele-grouping'
 import {assayLevelDisplay} from '@/lib/measurement-types'
 import type {components} from '@/schema/openapi'
 
@@ -124,13 +127,15 @@ type AlleleAnnotations = components['schemas']['AlleleAnnotations']
 type AlleleIdentity = components['schemas']['AlleleIdentity']
 type SequenceLevel = components['schemas']['SequenceLevel']
 
-type LedgerRole = 'page' | 'measured' | 'other'
+type LedgerRole = 'page' | 'selected' | 'other'
 type LedgerEntry = {group: AlleleGroup; role: LedgerRole}
 
 /**
  * Combined clinical/population + related-alleles ledger. Presents the whole equivalence class in one
- * place, at every level, with a *uniform* card per allele group: this variant (X) leads, the measured
- * allele (Y) follows when the selection assayed a different allele, and the rest collapse underneath.
+ * place, at every level, with a *uniform* card per allele group: your variant (X) leads, the selected
+ * measurement's variant (Y) follows when it differs, and the rest collapse underneath. Badges keep two
+ * axes apart: "Measured" is a page-wide fact about a variant; only the derived labels are relative to the
+ * selection.
  * Every card renders the same three-cell facts grid — molecular consequence, then
  * {@link VariantGnomadStat}/{@link VariantClinvarStat} keyed to that group's own digests — mirroring
  * {@link VariantDetailPanel}'s facts grid on the score-set page, so the only thing split out elsewhere on
@@ -148,6 +153,8 @@ export default defineComponent({
   props: {
     // Every allele group in the selected measurement's equivalence class.
     groups: {type: Array as PropType<AlleleGroup[]>, default: () => []},
+    // Digests of every allele that has a measurement of its own on the page (see useVariantLookup).
+    measuredDigests: {type: Array as PropType<string[]>, default: () => []},
     // Raw alleles/annotations from the selected measurement detail — the stat components resolve each
     // group's subject out of these maps by digest.
     alleles: {type: Object as PropType<Record<string, AlleleIdentity>>, default: () => ({})},
@@ -168,31 +175,38 @@ export default defineComponent({
     pageGroup(): AlleleGroup | null {
       return this.groups.find((g) => g.pageRoot) ?? null
     },
-    // The measured allele's group, pinned only when it differs from the page variant's (otherwise the lead
-    // card already is it).
-    pinnedMeasured(): AlleleGroup | null {
-      const measured = this.groups.find((g) => g.measured) ?? null
-      return measured && measured !== this.pageGroup ? measured : null
+    // Digests measured anywhere on the page, as a Set for lookup.
+    measuredSet(): ReadonlySet<string> {
+      return new Set(this.measuredDigests)
     },
-    // Everything that is neither the page variant nor the pinned measured allele.
+    // The selected measurement's variant, pinned only when it differs from the page variant (otherwise the
+    // lead card already is it).
+    pinnedSelected(): AlleleGroup | null {
+      const selected = this.groups.find((g) => g.measured) ?? null
+      return selected && selected !== this.pageGroup ? selected : null
+    },
+    // Everything that is neither the page variant nor the selected measurement's variant. Variants with a
+    // measurement of their own sort first (stable), so the collapsed remainder leads with what has a card above.
     otherGroups(): AlleleGroup[] {
-      return this.groups.filter((g) => g !== this.pageGroup && g !== this.pinnedMeasured)
+      const others = this.groups.filter((g) => g !== this.pageGroup && g !== this.pinnedSelected)
+      const isMeasured = (g: AlleleGroup) => g.members.some((m) => this.measuredSet.has(m.digest))
+      return [...others.filter(isMeasured), ...others.filter((g) => !isMeasured(g))]
     },
-    // The ordered render list: page variant, then the measured allele, then the rest (collapsed). Roles
-    // drive badge + emphasis, and are assigned from what a group *is* — a group is never given the `page`
-    // role as a stand-in. When the page variant is absent the list simply leads with the measured allele
-    // under its own badge, rather than labelling it "Your variant" and asserting an identity it lacks.
+    // The ordered render list: page variant, then the selected measurement's variant, then the rest
+    // (collapsed). Roles drive emphasis, and are assigned from what a group *is* — a group is never given the
+    // `page` role as a stand-in. When the page variant is absent the list simply leads with the selected
+    // variant under its own badge, rather than labelling it "Your variant" and asserting an identity it lacks.
     entries(): LedgerEntry[] {
       const list: LedgerEntry[] = []
       if (this.pageGroup) list.push({group: this.pageGroup, role: 'page'})
-      if (this.pinnedMeasured) list.push({group: this.pinnedMeasured, role: 'measured'})
+      if (this.pinnedSelected) list.push({group: this.pinnedSelected, role: 'selected'})
       for (const g of this.otherGroups) list.push({group: g, role: 'other'})
       return list
     },
-    // Whether any entry is pinned. When nothing is (no page variant and no measured allele in this
+    // Whether any entry is pinned. When nothing is (no page variant and no selected variant in this
     // envelope), the collapsed rows are all there is, so they must not start hidden behind the toggle.
     hasPinnedEntry(): boolean {
-      return this.pageGroup != null || this.pinnedMeasured != null
+      return this.pageGroup != null || this.pinnedSelected != null
     }
   },
 
@@ -204,35 +218,29 @@ export default defineComponent({
     groupLevel(group: AlleleGroup): SequenceLevel | null {
       return (this.titleMember(group)?.level ?? null) as SequenceLevel | null
     },
-    // The single member whose HGVS titles the card. A projection pair holds the same allele in two
-    // coordinate frames (genomic + cDNA). Lead with cDNA (community-preferred), then protein, then genomic.
-    titleMember(group: AlleleGroup): AlleleMember | null {
-      return (
-        group.members.find((m) => m.level === 'cdna') ??
-        group.members.find((m) => m.level === 'protein') ??
-        group.members[0] ??
-        null
-      )
-    },
+    titleMember,
     allHgvsTitle(group: AlleleGroup): string {
       return group.members.map((m) => `${this.levelLabel(m.level)}: ${m.hgvs || '—'}`).join('  ·  ')
     },
-    // "page" gets its own fixed subject badge — deliberately distinct from the confidence-axis colors used
-    // everywhere else, so "Your variant" (the page's subject) and "Measured" (what was assayed) are
-    // never confused. Every other role reads its label/class off the shared confidence axis, so those
-    // badges match the same Key entry used throughout the app.
-    roleBadge(entry: LedgerEntry): {label: string; class: string} {
-      if (entry.role === 'page') return {label: 'Your variant', class: 'bg-subject/15 text-subject'}
-      const badge = confidenceBadge(entry.group)
+    // The page variant leads with its fixed subject badge — deliberately distinct from the confidence-axis
+    // colors, so "Your variant" (the page's subject) and "Measured" (what was assayed) are never confused —
+    // followed by its standing on the measurement axis: Selected measurement, Measured (has a card of its own
+    // above), or derived relative to the selection. Every other role gets that badge alone.
+    roleBadges(entry: LedgerEntry): {label: string; class: string; term: string}[] {
+      const confidence = confidenceBadge(entry.group, this.measuredSet)
+      const confidenceEntry = confidence && {label: confidence.label, class: confidence.class, term: 'confidence'}
+      if (entry.role === 'page') {
+        const subject = {label: 'Your variant', class: 'bg-subject/15 text-subject', term: 'your-variant'}
+        return confidenceEntry ? [subject, confidenceEntry] : [subject]
+      }
       // No derivation and not measured: the API recorded no relationship (pre-reverse-translation data, or
       // a classification gap). "Unclassified" says so, rather than the old "Related" asserting one that wasn't.
-      return badge
-        ? {label: badge.label, class: badge.class}
-        : {label: 'Unclassified', class: 'bg-border-light text-text-muted'}
+      return [confidenceEntry ?? {label: 'Unclassified', class: 'bg-border-light text-text-muted', term: 'confidence'}]
     },
     cardClass(role: LedgerRole): string {
       if (role === 'page') return 'border-2 border-subject/40 bg-subject/[0.05]'
-      if (role === 'measured') return 'border border-sage/30 bg-sage/[0.03]'
+      // Echoes the selected measurement card's sage border above, tying the two together.
+      if (role === 'selected') return 'border-2 border-sage/60 bg-sage/[0.04]'
       return 'border border-border-light bg-surface'
     },
     levelLabel(level: string | null | undefined): string {
diff --git a/src/components/variant/MvMeasurementCard.vue b/src/components/variant/MvMeasurementCard.vue
index f796258f..8f4fe019 100644
--- a/src/components/variant/MvMeasurementCard.vue
+++ b/src/components/variant/MvMeasurementCard.vue
@@ -20,7 +20,7 @@
         {{ levelLabel }}
       </span>
       <span
-        v-key-term="relationship === 'direct' ? 'your-variant' : 'relationship'"
+        v-key-term="'relationship'"
         class="inline-block rounded-sm px-2 py-0.5 text-[10px] font-semibold uppercase tracking-[0.3px]"
         :class="relationshipClass"
       >
@@ -34,15 +34,15 @@
     <!-- Assay facts -->
     <div class="flex flex-col gap-[3px] text-xs-minus text-text-muted">
       <div class="flex items-baseline gap-1">
-        <span class="fact-label min-w-[80px] shrink-0 font-semibold text-[#aaa]">Assay type</span>
+        <span class="fact-label min-w-[125px] shrink-0 font-semibold text-[#aaa]">Assay type</span>
         <span class="text-text-secondary">{{ assayType || 'Not specified' }}</span>
       </div>
       <div class="flex items-baseline gap-1">
-        <span class="fact-label min-w-[80px] shrink-0 font-semibold text-[#aaa]">Mechanism</span>
+        <span class="fact-label min-w-[125px] shrink-0 font-semibold text-[#aaa]">Molecular mechanism</span>
         <span class="text-text-secondary">{{ mechanism || 'Not specified' }}</span>
       </div>
       <div class="flex items-baseline gap-1">
-        <span class="fact-label min-w-[80px] shrink-0 font-semibold text-[#aaa]">Model system</span>
+        <span class="fact-label min-w-[125px] shrink-0 font-semibold text-[#aaa]">Model system</span>
         <span class="text-text-secondary">{{ modelSystem || 'Not specified' }}</span>
       </div>
     </div>
@@ -53,7 +53,7 @@
         <strong class="font-mono font-bold text-text-secondary">{{ formatScore(score) }}</strong>
       </div>
       <div v-if="classification || evidenceCode" class="mt-1.5">
-        <span class="mb-1 block text-[10px] font-bold uppercase tracking-[0.3px] text-[#aaa]">Classified as</span>
+        <span class="mb-1 block text-[10px] font-bold uppercase tracking-[0.3px] text-[#aaa]">Functional impact</span>
         <div class="flex flex-wrap items-center gap-1.5">
           <MvClassificationTag v-if="classification" :classification="classification" />
           <MvEvidenceTag v-if="evidenceCode" :code="evidenceCode" />
@@ -94,7 +94,7 @@ export default defineComponent({
     loading: {type: Boolean, default: false},
     // The assayed level (AnnotationLayer: protein/cdna/genomic) — drives the level badge.
     assayLevel: {type: [String, null] as PropType<string | null>, default: null},
-    // How the measurement relates to the queried ClinGen allele (direct / RT-related).
+    // Whether the measurement assayed the queried ClinGen allele itself (direct) or a related one (indirect).
     relationship: {type: String as PropType<MeasurementRelationship>, required: true},
     // Score set attributes displayed on the card body.
     scoreSetTitle: {type: String, default: ''},
diff --git a/src/components/variant/VariantClinvarStat.vue b/src/components/variant/VariantClinvarStat.vue
index 5f005ddd..36db81d2 100644
--- a/src/components/variant/VariantClinvarStat.vue
+++ b/src/components/variant/VariantClinvarStat.vue
@@ -12,13 +12,13 @@
     <template v-else-if="headline.kind === 'call'">
       <MvClinvarSummary :clinvar="headline.clinvar" :show-provenance="showHeadlineProvenance" />
       <span v-if="headline.note === 'soft-conflicting'" class="text-xs italic text-text-muted">
-        ClinVar marks a record with the same protein consequence as conflicting.
+        ClinVar marks a record with the same protein change as conflicting.
       </span>
       <span v-else-if="headline.note === 'soft-vus'" class="text-xs italic text-text-muted">
-        ClinVar marks a record with the same protein consequence as uncertain.
+        ClinVar marks a record with the same protein change as uncertain.
       </span>
       <span v-else-if="headline.note === 'concordant'" class="text-xs italic text-text-muted">
-        Representative of concordant records with the same protein consequence.
+        Representative of concordant records with the same protein change.
       </span>
     </template>
     <!-- No usable call, but a ClinVar record exists on an allele (a `-`, e.g. a somatic/oncogenicity-only
@@ -32,7 +32,7 @@
     <!-- Nucleotide measurement with no ClinVar record of its own: be explicit rather than borrow a related
          allele's call. Related records (if any) are offered below as context, not promoted to a call. -->
     <span v-else-if="headline.kind === 'absent'" class="stat-value text-sm italic text-text-muted">
-      No ClinVar record for this allele
+      No ClinVar record for this variant
     </span>
     <span v-else class="stat-value">—</span>
 
@@ -179,8 +179,8 @@ export default defineComponent({
     },
     underlyingClinvarNote(): string {
       return this.isProjectedHeadline
-        ? 'This allele has no ClinVar record. The classification above is inferred from these nucleotide variants that encode the same protein change and does not represent a ClinVar assertion for this allele.'
-        : 'Other variants with the same protein consequence that also carry ClinVar records.'
+        ? 'This variant has no ClinVar record. The classification above is inferred from these nucleotide variants that encode the same protein change and does not represent a ClinVar assertion for this variant.'
+        : 'Other variants with the same protein change that also carry ClinVar records.'
     }
   },
 
diff --git a/src/components/variant/VariantDetailPanel.vue b/src/components/variant/VariantDetailPanel.vue
index a8345bb9..fb9381d6 100644
--- a/src/components/variant/VariantDetailPanel.vue
+++ b/src/components/variant/VariantDetailPanel.vue
@@ -44,7 +44,7 @@
       >
         <VariantConsequenceStat :vep="consequence" />
         <div class="stat">
-          <span v-key-term="'functional-impact'" class="stat-label">Classification</span>
+          <span v-key-term="'functional-impact'" class="stat-label">Functional impact</span>
           <span v-if="selectedClassification" class="flex flex-wrap items-center gap-1.5">
             <span
               v-key-term="'functional-impact'"
diff --git a/src/components/variant/VariantGnomadStat.vue b/src/components/variant/VariantGnomadStat.vue
index eecc8eea..20d3b627 100644
--- a/src/components/variant/VariantGnomadStat.vue
+++ b/src/components/variant/VariantGnomadStat.vue
@@ -143,7 +143,7 @@ export default defineComponent({
           ? 'The frequency of any variants in gnomAD which can encode this protein change. This assay does not establish which one underlies the measurement.'
           : 'Frequencies of any variants in gnomAD which can encode this protein change. This assay does not establish which of them underlie the measurement.'
       }
-      return 'Other variants with the same protein consequence that also have gnomAD frequencies.'
+      return 'Other variants with the same protein change that also have gnomAD frequencies.'
     }
   },
 
diff --git a/src/composables/use-variant-lookup.ts b/src/composables/use-variant-lookup.ts
index 3c797ae2..f6d4b095 100644
--- a/src/composables/use-variant-lookup.ts
+++ b/src/composables/use-variant-lookup.ts
@@ -42,6 +42,10 @@ export interface UseVariantLookupReturn extends UseMeasurementSelectionReturn {
   // The selected measurement's own status as one of the active calibration's controls, if it was used as one.
   selectedVariantControlStatus: ComputedRef<CalibrationControlStatus | null>
 
+  // Digests of every allele that has a measurement of its own in the list — the page-wide notion of
+  // "measured", independent of which measurement is selected. Fills in as detail prefetches resolve.
+  measuredDigests: ComputedRef<Set<string>>
+
   // Per-measurement helpers (for measurement cards)
   getKeyword: (scoreSetUrn: string | null | undefined, key: string) => string | null
 
@@ -127,6 +131,19 @@ export function useVariantLookup(
   const cache = useMeasurementCache(asOf)
   const selection = useMeasurementSelection(variants, filteredVariants, highlightUrn, cache)
 
+  // An allele is "measured" if any measurement's envelope flags it as that measurement's focus. Read from
+  // the prefetched details, so it is stable as the selection changes (unlike `isFocus` on one envelope).
+  const measuredDigests = computed(() => {
+    const digests = new Set<string>()
+    for (const m of variants.value) {
+      const alleles = cache.variantDetails.value[m.variantUrn]?.alleles ?? {}
+      for (const [digest, identity] of Object.entries(alleles)) {
+        if (identity.isFocus) digests.add(digest)
+      }
+    }
+    return digests
+  })
+
   // The selected variant's own status as one of the active calibration's controls, if it was used
   // as one — distinct from `calibrationResolution`, which classifies the variant by score.
   const selectedVariantControlStatus = computed<CalibrationControlStatus | null>(() => {
@@ -285,6 +302,7 @@ export function useVariantLookup(
     proteinCount,
     filteredVariants,
     selectedVariantControlStatus,
+    measuredDigests,
     getKeyword,
     geneName,
     uniqueAssayCount,
diff --git a/src/glossary.ts b/src/glossary.ts
index 358cf107..0148906d 100644
--- a/src/glossary.ts
+++ b/src/glossary.ts
@@ -5,11 +5,18 @@ import {ACMG_KEY_SECTION} from '@/lib/acmg'
 import {CONFIDENCE_KEY_SECTION} from '@/lib/allele-grouping'
 import {CLINICAL_SIGNIFICANCE_KEY_SECTION, INFERRED_CONTROL_KEY_SECTION} from '@/lib/clinvar-controls'
 import {FUNCTIONAL_IMPACT_KEY_SECTION} from '@/lib/functional-impact'
-import {AS_OF_KEY_SECTION, CONSEQUENCE_KEY_SECTION, THIS_VARIANT_KEY_SECTION, SUPERSEDED_KEY_SECTION} from '@/lib/glossary-prose'
+import {
+  AS_OF_KEY_SECTION,
+  CALIBRATION_KEY_SECTION,
+  CONSEQUENCE_KEY_SECTION,
+  NMD_KEY_SECTION,
+  THIS_VARIANT_KEY_SECTION,
+  SUPERSEDED_KEY_SECTION
+} from '@/lib/glossary-prose'
 import {POPULATION_KEY_SECTION} from '@/lib/gnomad'
 import {ASSAY_LEVEL_KEY_SECTION, RELATIONSHIP_KEY_SECTION} from '@/lib/measurement-types'
 
-export const GLOSSARY_DOCS_URL = `${config.appBaseUrl}/docs/mavedb/getting-started/key-concepts.html`
+export const GLOSSARY_DOCS_URL = `${config.appBaseUrl}/docs/mavedb/interpreting-annotated-variants.html`
 
 export const GLOSSARY_SECTIONS: KeySection[] = [
   THIS_VARIANT_KEY_SECTION,
@@ -19,10 +26,12 @@ export const GLOSSARY_SECTIONS: KeySection[] = [
   COORDINATE_FRAME_KEY_SECTION,
   CONSEQUENCE_KEY_SECTION,
   FUNCTIONAL_IMPACT_KEY_SECTION,
+  CALIBRATION_KEY_SECTION,
   ACMG_KEY_SECTION,
   POPULATION_KEY_SECTION,
   CLINICAL_SIGNIFICANCE_KEY_SECTION,
   INFERRED_CONTROL_KEY_SECTION,
+  NMD_KEY_SECTION,
   AS_OF_KEY_SECTION,
   SUPERSEDED_KEY_SECTION
 ]
diff --git a/src/lib/allele-grouping.test.ts b/src/lib/allele-grouping.test.ts
index c998d379..d3de98d6 100644
--- a/src/lib/allele-grouping.test.ts
+++ b/src/lib/allele-grouping.test.ts
@@ -1,6 +1,12 @@
 import {describe, expect, it} from 'vitest'
 
-import {ALLELE_CONFIDENCE, confidenceBadge, groupAlleles, type GroupAllelesInput} from '@/lib/allele-grouping'
+import {
+  ALLELE_CONFIDENCE,
+  confidenceBadge,
+  groupAlleles,
+  titleMember,
+  type GroupAllelesInput
+} from '@/lib/allele-grouping'
 import type {components} from '@/schema/openapi'
 
 type AlleleIdentity = components['schemas']['AlleleIdentity']
@@ -19,6 +25,8 @@ function run(overrides: Partial<GroupAllelesInput>) {
   })
 }
 
+const none: ReadonlySet<string> = new Set()
+
 describe('groupAlleles — projection pairing + confidence', () => {
   // Nucleotide (cdna) assay: the measured cdna folds into its pair's group with its genomic projection;
   // the protein apex is a deterministic projection, unpaired.
@@ -129,16 +137,24 @@ describe('groupAlleles — projection pairing + confidence', () => {
     expect(groups[0].measured).toBe(false)
   })
 
-  it('badges measured over derivation, maps projection→Resolved / convergent→Convergent / candidate→Candidate, else null', () => {
-    // `measured` wins even if a derivation is also present (a stray measured member still reads "Measured").
-    expect(confidenceBadge({measured: true, derivation: 'projection'})).toBe(ALLELE_CONFIDENCE.measured)
-    expect(confidenceBadge({measured: false, derivation: 'projection'})).toBe(ALLELE_CONFIDENCE.projection)
+  it('badges selected over derivation, maps projection→Resolved / convergent→Convergent / candidate→Candidate, else null', () => {
+    // The selected measurement's variant wins even if a derivation is also present.
+    expect(confidenceBadge({measured: true, derivation: 'projection', members: []}, none)).toBe(
+      ALLELE_CONFIDENCE.selected
+    )
+    expect(confidenceBadge({measured: false, derivation: 'projection', members: []}, none)).toBe(
+      ALLELE_CONFIDENCE.projection
+    )
     // A synonymous cousin under a nucleotide assay: a distinct change sharing the consequence, not ambiguous.
-    expect(confidenceBadge({measured: false, derivation: 'convergent'})).toBe(ALLELE_CONFIDENCE.convergent)
+    expect(confidenceBadge({measured: false, derivation: 'convergent', members: []}, none)).toBe(
+      ALLELE_CONFIDENCE.convergent
+    )
     // The protein-assay reverse-translation fan-out: genuinely ambiguous.
-    expect(confidenceBadge({measured: false, derivation: 'candidate'})).toBe(ALLELE_CONFIDENCE.candidate)
+    expect(confidenceBadge({measured: false, derivation: 'candidate', members: []}, none)).toBe(
+      ALLELE_CONFIDENCE.candidate
+    )
     // The focus/measured allele carries no derivation; on its own (measured false) it has no badge.
-    expect(confidenceBadge({measured: false, derivation: null})).toBeNull()
+    expect(confidenceBadge({measured: false, derivation: null, members: []}, none)).toBeNull()
     // The user-facing labels are decoupled from the enum keys.
     expect(ALLELE_CONFIDENCE.projection.label).toBe('Resolved')
     expect(ALLELE_CONFIDENCE.convergent.label).toBe('Convergent')
@@ -157,3 +173,38 @@ describe('groupAlleles — projection pairing + confidence', () => {
     expect(groups[0].clingenLinks).toEqual([])
   })
 })
+
+describe('titleMember', () => {
+  it('leads a projection pair with its cDNA member', () => {
+    const [pair] = run({
+      alleles: {
+        c: {level: 'cdna', hgvs: 'NM_x:c.6C>T', relation: null, isFocus: true, projectionOf: 'g'},
+        g: {level: 'genomic', hgvs: 'NC_x:g.100C>T', relation: null, isFocus: false, projectionOf: 'c'}
+      }
+    })
+    expect(titleMember(pair)?.hgvs).toBe('NM_x:c.6C>T')
+  })
+
+  it('falls back to protein, then the first member', () => {
+    const [protein] = run({alleles: {p: {level: 'protein', hgvs: 'NP_x:p.Leu2Phe', relation: null, isFocus: true}}})
+    expect(titleMember(protein)?.hgvs).toBe('NP_x:p.Leu2Phe')
+    expect(titleMember({members: []})).toBeNull()
+  })
+})
+
+describe('confidenceBadge — page-wide measured', () => {
+  const [pair] = run({
+    alleles: {
+      c: {level: 'cdna', hgvs: 'NM_x:c.6C>T', relation: null, isFocus: false, derivation: 'convergent', projectionOf: 'g'},
+      g: {level: 'genomic', hgvs: 'NC_x:g.100C>T', relation: null, isFocus: false, derivation: 'convergent', projectionOf: 'c'}
+    }
+  })
+
+  it('reads Measured for a variant measured elsewhere, overriding its relative derivation', () => {
+    expect(confidenceBadge(pair, new Set(['g']))).toBe(ALLELE_CONFIDENCE.measured)
+  })
+
+  it('falls back to the relative derivation when no member is measured anywhere', () => {
+    expect(confidenceBadge(pair, new Set(['other']))).toBe(ALLELE_CONFIDENCE.convergent)
+  })
+})
diff --git a/src/lib/allele-grouping.ts b/src/lib/allele-grouping.ts
index 3ddaa393..f204a883 100644
--- a/src/lib/allele-grouping.ts
+++ b/src/lib/allele-grouping.ts
@@ -70,21 +70,28 @@ export interface ConfidenceBadge {
 // separate tokens so they can diverge without touching this file. Insertion order is the drawer's
 // display order.
 export const ALLELE_CONFIDENCE: Record<string, ConfidenceBadge> = {
+  // Solid where `measured` is tinted: the selection is a state of the page, `measured` a fact about a variant.
+  selected: {
+    label: 'Selected measurement',
+    class: 'bg-measured text-white',
+    definition: 'The variant assayed by the measurement you have selected.'
+  },
   measured: {
     label: 'Measured',
     class: 'bg-measured-light text-measured',
-    definition: 'Directly measured in this assay.'
+    definition: 'Has a measurement of its own on this page, whichever measurement is selected.'
   },
   projection: {
     label: 'Resolved',
     class: 'bg-resolved-light text-resolved',
-    definition: 'Derived from the measured allele. The same change expressed at an un-measured coordinate level.'
+    definition:
+      "Derived from the selected measurement's variant: the same change expressed at an un-measured coordinate level."
   },
   convergent: {
     label: 'Convergent',
     class: 'bg-convergent-light text-convergent',
     definition:
-      'A different nucleotide change than what was measured, which happens to produce the same protein change as the measured variant.'
+      "A different nucleotide change than the selected measurement's variant, which happens to produce the same protein change."
   },
   candidate: {
     label: 'Candidate',
@@ -96,16 +103,39 @@ export const ALLELE_CONFIDENCE: Record<string, ConfidenceBadge> = {
 
 export const CONFIDENCE_KEY_SECTION: KeySection = {
   id: 'confidence',
-  title: 'How a coordinate was established',
+  title: 'Measured and derived variants',
+  gloss: 'Whether a variant has a measurement of its own, or how it relates to the selected one.',
   terms: Object.values(ALLELE_CONFIDENCE).map((c) => ({label: c.label, definition: c.definition, class: c.class}))
 }
 
-/** Confidence badge for a group: `measured` wins, else the derived state; null when neither applies. */
-export function confidenceBadge(group: Pick<AlleleGroup, 'measured' | 'derivation'>): ConfidenceBadge | null {
-  if (group.measured) return ALLELE_CONFIDENCE.measured
+/**
+ * Badge for a group, strongest claim first: the selected measurement's own variant, then any variant with a
+ * measurement of its own (`measuredDigests`, page-wide), else its derived state relative to the selected
+ * measurement; null when none applies. Measured-ness is a fact about the variant, so it never flips as the
+ * selection moves — only the derived labels are relative.
+ */
+export function confidenceBadge(
+  group: Pick<AlleleGroup, 'measured' | 'derivation' | 'members'>,
+  measuredDigests: ReadonlySet<string>
+): ConfidenceBadge | null {
+  if (group.measured) return ALLELE_CONFIDENCE.selected
+  if (group.members.some((m) => measuredDigests.has(m.digest))) return ALLELE_CONFIDENCE.measured
   return group.derivation ? (ALLELE_CONFIDENCE[group.derivation] ?? null) : null
 }
 
+/**
+ * The member whose HGVS titles a group. A projection pair holds one change in two coordinate frames
+ * (genomic + coding); lead with cDNA (community-preferred), then protein, then genomic.
+ */
+export function titleMember(group: Pick<AlleleGroup, 'members'>): AlleleMember | null {
+  return (
+    group.members.find((m) => m.level === 'cdna') ??
+    group.members.find((m) => m.level === 'protein') ??
+    group.members[0] ??
+    null
+  )
+}
+
 // ── GROUPING: collapse a variant's alleles into rendered groups ──
 
 export interface GroupAllelesInput {
diff --git a/src/lib/clinvar-controls.ts b/src/lib/clinvar-controls.ts
index b62e2e09..61df64bd 100644
--- a/src/lib/clinvar-controls.ts
+++ b/src/lib/clinvar-controls.ts
@@ -28,7 +28,7 @@ export const INFERRED_CONTROL_KEY_SECTION: KeySection = {
     {
       label: 'Inferred call',
       definition:
-        'A ClinVar call inferred from a related allele with the same protein consequence — shown only when the assayed variant has no ClinVar record of its own.'
+        'A ClinVar call inferred from a related variant with the same protein change — shown only when the assayed variant has no ClinVar record of its own.'
     }
   ]
 }
diff --git a/src/lib/glossary-prose.ts b/src/lib/glossary-prose.ts
index 4e3904ff..6ac2d999 100644
--- a/src/lib/glossary-prose.ts
+++ b/src/lib/glossary-prose.ts
@@ -1,18 +1,15 @@
 import type {KeySection} from '@/composables/use-key-drawer'
 
-// Single source for the "Your variant" concept — the page's own subject allele — wherever it's badged:
-// the allele ledger's page-role entry (MvAlleleLedger) and a measurement's direct-relationship badge
-// (MvMeasurementCard) are the same fact from two objects, so they share this one definition rather than
-// each carrying their own. Leads GLOSSARY_SECTIONS (glossary.ts): establishing the subject first lets
-// "Relationship to your variant" read naturally right after it — how other results relate to the thing
-// this section just defined.
+// Single source for the "Your variant" concept — the page's own subject variant — as badged on the allele
+// ledger's page-role entry (MvAlleleLedger). Leads GLOSSARY_SECTIONS (glossary.ts): establishing the subject
+// first lets "Direct and indirect measurements" read naturally right after it.
 export const THIS_VARIANT_KEY_SECTION: KeySection = {
   id: 'your-variant',
   title: 'Your variant',
   terms: [
     {
       label: 'Your variant',
-      definition: 'The allele this page is about.',
+      definition: 'The variant this page is about.',
       class: 'bg-subject/15 text-subject'
     }
   ]
@@ -29,6 +26,34 @@ export const CONSEQUENCE_KEY_SECTION: KeySection = {
   ]
 }
 
+export const CALIBRATION_KEY_SECTION: KeySection = {
+  id: 'calibration',
+  title: 'Calibration',
+  terms: [
+    {
+      label: 'Calibration',
+      definition:
+        "A score set's score ranges, each tied to a functional impact and, where available, a strength of clinical evidence. This is how a functional score becomes a functional impact and an ACMG code."
+    },
+    {
+      label: 'Calibration control',
+      definition: 'A variant with an established clinical classification, used to derive the calibration.'
+    }
+  ]
+}
+
+export const NMD_KEY_SECTION: KeySection = {
+  id: 'nmd',
+  title: 'NMD',
+  terms: [
+    {
+      label: 'NMD',
+      definition:
+        'Nonsense-mediated decay: a cellular process that destroys transcripts carrying premature stop codons. Assays built on a synthetic cDNA copy of the gene cannot detect variants that act this way.'
+    }
+  ]
+}
+
 export const AS_OF_KEY_SECTION: KeySection = {
   id: 'as-of',
   title: 'As of',
diff --git a/src/lib/measurement-types.test.ts b/src/lib/measurement-types.test.ts
index 338e202e..eb0f8a99 100644
--- a/src/lib/measurement-types.test.ts
+++ b/src/lib/measurement-types.test.ts
@@ -1,6 +1,6 @@
 import {describe, expect, it} from 'vitest'
 
-import {assayLevelBucket, dominantAssayLevel} from '@/lib/measurement-types'
+import {assayLevelBucket, dominantAssayLevel, RELATIONSHIPS, RELATIONSHIP_KEY_SECTION} from '@/lib/measurement-types'
 
 describe('assayLevelBucket', () => {
   it('returns "amino acid" for protein', () => {
@@ -53,3 +53,19 @@ describe('dominantAssayLevel', () => {
     expect(dominantAssayLevel(['cdna', null, 'protein', undefined, 'cdna'])).toBe('cdna')
   })
 })
+
+describe('RELATIONSHIPS', () => {
+  it('flags a direct measurement as Direct', () => {
+    expect(RELATIONSHIPS.direct.label).toBe('Direct')
+  })
+
+  it('flags both related-variant relationships with the same Indirect badge', () => {
+    expect(RELATIONSHIPS.protein_consequence).toEqual(RELATIONSHIPS.nucleotide_encoding)
+    expect(RELATIONSHIPS.protein_consequence.label).toBe('Indirect')
+  })
+
+  it('defines exactly the labels its badges can show in the Key drawer', () => {
+    const badgeLabels = new Set(Object.values(RELATIONSHIPS).map((r) => r.label))
+    expect(new Set(RELATIONSHIP_KEY_SECTION.terms.map((t) => t.label))).toEqual(badgeLabels)
+  })
+})
diff --git a/src/lib/measurement-types.ts b/src/lib/measurement-types.ts
index f228d165..dca3ec7d 100644
--- a/src/lib/measurement-types.ts
+++ b/src/lib/measurement-types.ts
@@ -14,34 +14,34 @@ export function assayLevelBucket(level: string | null | undefined): LevelBucket
 }
 
 /**
- * Single source of truth for the measurement-to-query relationship vocabulary (the RT asymmetry): the
- * card label, an optional chip class, and the Key-drawer gloss. Phrased relative to the page's own variant
- * so the labels self-explain under the "relative to your variant" anchor. Insertion order is display order.
+ * Single source of truth for the measurement-to-query relationship badge (the RT asymmetry). The badge only
+ * flags whether the measurement assayed the page's own variant: `direct`, or `indirect` for both
+ * related-variant relationships. The detail (which related variant, and its HGVS) is stated once, in the
+ * Functional evidence notice, so the vocabulary here stays two words.
  */
-export const RELATIONSHIPS: Record<MeasurementRelationship, {label: string; class?: string; definition?: string}> = {
-  // No `definition`: a direct result is the page's own subject allele — the same concept as the Key
-  // drawer's "Your variant" section (glossary-prose.ts), defined once there rather than twice.
-  direct: {
-    label: 'Your variant',
-    class: 'bg-subject/15 text-subject'
-  },
-  protein_consequence: {
-    label: 'Its protein consequence',
-    definition: 'The result assayed the protein change your variant produces.'
-  },
-  nucleotide_encoding: {
-    label: 'Encodes the protein consequence',
-    definition: 'The result assayed a nucleotide allele that encodes the same protein change as your variant.'
-  }
+export const RELATIONSHIPS: Record<MeasurementRelationship, {label: string; class: string}> = {
+  direct: {label: 'Direct', class: 'bg-subject/15 text-subject'},
+  protein_consequence: {label: 'Indirect', class: 'bg-convergent-light text-convergent'},
+  nucleotide_encoding: {label: 'Indirect', class: 'bg-convergent-light text-convergent'}
 }
 
 export const RELATIONSHIP_KEY_SECTION: KeySection = {
   id: 'relationship',
-  title: 'Relationship to your variant',
-  gloss: 'How each result relates to the allele you searched.',
-  terms: Object.values(RELATIONSHIPS)
-    .filter((r) => r.definition)
-    .map((r) => ({label: r.label, definition: r.definition!, class: r.class}))
+  title: 'Direct and indirect measurements',
+  gloss: 'Whether a measurement assayed your variant itself.',
+  terms: [
+    {
+      label: RELATIONSHIPS.direct.label,
+      definition: 'The measurement assayed your variant itself.',
+      class: RELATIONSHIPS.direct.class
+    },
+    {
+      label: RELATIONSHIPS.protein_consequence.label,
+      definition:
+        'The measurement assayed a related variant instead: the protein change your variant produces, or a nucleotide variant that encodes the same protein change. Its score stands in for your variant rather than measuring it directly.',
+      class: RELATIONSHIPS.protein_consequence.class
+    }
+  ]
 }
 
 /**