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a bug of HGVS nomenclature(protein level) #560

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xiechangxiao opened this issue Sep 4, 2024 · 0 comments
Open

a bug of HGVS nomenclature(protein level) #560

xiechangxiao opened this issue Sep 4, 2024 · 0 comments

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@xiechangxiao
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The results of snpeff are not consistent with the HGVS nomenclature(protein level).

CMD:
java -jar /Packages/snpEff_5.2c/snpEff/snpEff.jar -noStats -no PROTEIN_STRUCTURAL_INTERACTION_LOCUS -no-downstream -no-intergenic -no NEXT_PROT -hgvs1LetterAa -hgvsTrId hg19 caller.vcf >tmp.vcf

version:
5.2c

the snpeff result:
chr5 236676 . GGG AGA . NM5.25;PASS;v3 ANN=AGA|missense_variant|MODERATE|SDHA|SDHA|transcript|NM_004168.4|protein_coding|10/15|NM_004168.4:c.1394_1396delGGGinsAGA|NM_004168.4:p.RA465QT|1430/2693|1394/1995|465/664|

I think the correct result is p.R465_A466delinsQT, not p.RA465QT

Explanation on the HGVS website(https://hgvs-nomenclature.org/stable/recommendations/protein/substitution/#discussion):

image
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