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Incorrect translation for unaffected stop codon #83

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federkasten opened this issue Nov 30, 2023 · 0 comments · Fixed by #81 or #86
Closed

Incorrect translation for unaffected stop codon #83

federkasten opened this issue Nov 30, 2023 · 0 comments · Fixed by #81 or #86
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@federkasten
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In hg38 reference genome, chr3 149520808 C CTTAA translates to NM_015472.6:c.1199_1200insTTAA and p.*402*ext*9.

The resulting protein change is p.=, as the stop codon at position 401 is unaffected.

UCSC

Repro 🐛

(require '[varity.vcf-to-hgvs :as v2h]) 
(v2h/vcf-variant->protein-hgvs {:chr "chr3" :pos 149520808 :ref "C" :alt "CTTAA"} "/path/to/hg38.fa" "/pat/to//ncbiRefSeq_hg38_20210909.txt.gz") ;=> (#clj-hgvs/hgvs "p.*402*ext*9")
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