diff --git a/server/src/resolvers/getVariantsResolver/utils/annotateCadd.ts b/server/src/resolvers/getVariantsResolver/utils/annotateCadd.ts index 903f55c6..d1be1213 100644 --- a/server/src/resolvers/getVariantsResolver/utils/annotateCadd.ts +++ b/server/src/resolvers/getVariantsResolver/utils/annotateCadd.ts @@ -28,7 +28,7 @@ const annotate = timeit('annotateCadd')( if (key in annotationKeys) { /* eslint-disable-next-line @typescript-eslint/no-unused-vars */ - const { aaAlt, aaPos, aaRef, cdnaPos, chrom, pos, alt, ref, ...rest } = annotationKeys[key]; + const { aaAlt, aaPos, aaRef, cdsPos, chrom, pos, alt, ref, ...rest } = annotationKeys[key]; response.variant.info = { ...response.variant.info, aaChange: @@ -42,7 +42,8 @@ const annotate = timeit('annotateCadd')( aaAlt === aaRef ? '=' : AMINO_ACID_MAPPING[aaAlt] }` : 'NA', - cdna: alt && cdnaPos && cdnaPos !== 'NA' && ref ? `c.${cdnaPos}${ref}>${alt}` : 'NA', + // uses CDSpos instead of cDNApos + cdna: alt && cdsPos && cdsPos !== 'NA' && ref ? `c.${cdsPos}${ref}>${alt}` : 'NA', ...rest, }; } diff --git a/server/src/resolvers/getVariantsResolver/utils/fetchCaddAnnotations.ts b/server/src/resolvers/getVariantsResolver/utils/fetchCaddAnnotations.ts index 3f4a2c13..07591ea3 100644 --- a/server/src/resolvers/getVariantsResolver/utils/fetchCaddAnnotations.ts +++ b/server/src/resolvers/getVariantsResolver/utils/fetchCaddAnnotations.ts @@ -69,7 +69,8 @@ const _getAnnotations = async (position: string, assemblyId: string) => { oAA: 17 nAA: 18 FeatureID: 20 - cDNApos: 25 + cDNApos: 25 // deprecated for use in OSMP + CDSpos: 27 // replaces cDNApos protpos: 29 spliceAI-acc-gain: 94 (GRCh37) 109 (GRCh38) spliceAI-acc-loss: 95 (GRCh37) 110 (GRCh38) @@ -95,7 +96,7 @@ const _formatAnnotations = (annotations: string[], assemblyId: string) => { ['aaRef', 16], ['aaAlt', 17], ['transcript', 19], - ['cdnaPos', 24], + ['cdsPos', 26], // actually CDSpos ['aaPos', 28], ['phred', assemblyId === 'GRCh37' ? 115 : 133], ]; diff --git a/server/src/types.ts b/server/src/types.ts index 72d368be..5260dab8 100644 --- a/server/src/types.ts +++ b/server/src/types.ts @@ -264,7 +264,7 @@ export interface CaddAnnotation extends VariantCoordinate { aaAlt: string; aaPos: string; aaRef: string; - cdnaPos: string; + cdsPos: string; consequence: string; consScore: number; phred: number;