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SCRUM-5928 fix missing attributes: nucleotide change, cross references #1751

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Merged
cmpich merged 3 commits into from
Apr 14, 2026
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Merged

SCRUM-5928 fix missing attributes: nucleotide change, cross references #1751

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SCRUM-5928 fix missing attributes: nucleotide change, cross references
cmpich Apr 14, 2026
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cmpich Apr 14, 2026
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Merge branch 'stage' into SCRUM-5829
cmpich Apr 14, 2026
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23 changes: 18 additions & 5 deletions src/containers/allelePage/VariantSummaryCuration.jsx
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,15 @@ const VariantSummaryCuration = ({ variant: variantData, variantId }) => {

const consequencesAnchor = variantId ? '#variant-molecular-consequences' : sectionAnchor(cvgla?.hgvs);

const { taxon: species, variantType: type, references, crossReferences, relatedNotes: notes } = variant || {};
const {
taxon: species,
variantType: type,
references,
crossReferences: variantCrossRefs,
relatedNotes: notes,
} = variant || {};
const crossReferences =
variantCrossRefs?.length > 0 ? variantCrossRefs : [variantData?.allele?.dataProviderCrossReference].filter(Boolean);

const variantLocationObj = cvgla?.variantGenomicLocationAssociationObject;

Expand All @@ -40,17 +48,22 @@ const VariantSummaryCuration = ({ variant: variantData, variantId }) => {

const assembly = variantLocationObj?.genomeAssembly?.primaryExternalId;

const nucleotideChange = variant?.nucleotideChange;
const referenceSequence = cvgla?.referenceSequence;
const variantSequence = cvgla?.variantSequence;
const nucleotideChange =
variant?.nucleotideChange ||
(referenceSequence && variantSequence ? `${referenceSequence}>${variantSequence}` : null) ||
cvgla?.hgvs?.match(/g\.\d+(?:_\d+)?(.+)$/)?.[1] ||
null;

const consequence = cvgla?.mostSevereConsequence?.vepConsequences?.[0]?.name;

const hgvsC = cvgla?.hgvsC;
const hgvsP = cvgla?.hgvsP;
const predictedVariantConsequences = cvgla?.predictedVariantConsequences;

const hgvsC = cvgla?.hgvsC || predictedVariantConsequences?.map((pvc) => pvc.hgvsCodingNomenclature).filter(Boolean);
const hgvsP = cvgla?.hgvsP || predictedVariantConsequences?.map((pvc) => pvc.hgvsProteinNomenclature).filter(Boolean);

const overlapGenes = cvgla?.overlapGenes;
const predictedVariantConsequences = cvgla?.predictedVariantConsequences;

const genomeLocation = getVariantGenomeLocation(variantData);
return (
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