[ensembl-dev] Incorrect HGVS nomenclature

[Emily Perry]

Hi Vasisht

I'm not entirely sure I understand your question. A CAG>C change in the 
genome is equivalent to a CTG>G change or CT deletion in a negative 
strand gene or transcript. What annotation is the VEP giving you that 
you believe to be incorrect?

All the best

Emily

On 03/02/2015 23:27, Vasisht Tadigotla wrote:
> Hi,
>
> I’m annotating a variant using GRCh37 and the VEP in the v78 release 
> and the HGVS annotation of the refseq transcripts doesn’t seem to 
> match up to the sequences for those transcripts.
>
> The variant is in SLC37A4 (chr11:g.118895980CAG>C), the HGVS 
> annotations are NM_001467.5:c.1043_1044delCT 
> and NP_001458.1:p.Pro348ArgfsTer? and the amino acid is being 
> annotated as CCT/C.  The aa change is the same for all refseq 
> transcripts in the annotation.
>
> The count seems to be off by one - it’s a CTG/G change. The local 
> sequence context is GCC CTG TTT with the TG being deleted.
>
> The correct HGVS description is  NM_001467.5:c.1042_1043delCT  and the 
> protein is p.Leu348Valfs*53. This is annotated correctly in the 
> Ensembl transcripts - 
> ENST00000545985.1:c.1042_1043delCT, ENSP00000475241.1:p.Leu348ValfsTer53.
>
> The following options were used for the annotation:
>
> —offline —everything —merged
>
> The same issue exists with the web version of VEP:
>
> http://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Results?db=core;tl=Ba08mzoDSO2008gG-584627
>
>
> Thanks,
> Vasisht
>
>
>
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-- 
Dr Emily Perry (Pritchard)
Ensembl Outreach Officer

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK

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