[ensembl-dev] Incorrect HGVS nomenclature

[Vasisht Tadigotla]

Hi Emily,

It’s the position on the RefSeq transcript (1043_1044) and the reading frame that are off by one. I got a clarification in a separate email that for this RefSeq transcript there is an insertion that’s not present in the reference. 

Regards,
Vasisht

On February 4, 2015 at 4:02:59 AM, Emily Perry (emily at ebi.ac.uk) wrote:

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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