[ensembl-dev] Incorrect HGVS nomenclature
Emily Perry
emily at ebi.ac.uk
Wed Feb 4 09:02:44 GMT 2015
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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