[ensembl-dev] VEP - HGVS syntax coords reversed

[Sarah Hunt]

Hi Bhavana,

Thanks for reporting this one. It will be fixed when we update our REST 
servers for our new release next month. If you are running VEP on the 
command line, you can pick up the fix by updating your copy of the 
ensembl-variation API.

Sorry for the delay in getting back to you - do let us know if you spot 
any other odd cases.

Best wishes,

Sarah

On 10/07/2017 16:23, Bhavana Harsha wrote:
> Hello,
>
> I’m trying to look at the transcript consequences of the following 
> variant:
> 17:g.7577607_7578174del
>
> using the REST API like this:
> http://grch37.rest.ensembl.org/vep/human/hgvs/17:g.7577607_7578174del?content-type=application/json;xref_refseq=1&canonical=1&ccds=1&hgvs=1
>
> This is what I get for one of the transcripts:
> ENST00000269305.4:c.674_672+3delCTGG….
>
> Shouldn’t the correct syntax be ENST00000269305.4:c.*672+3_674*delCTGG..?
>
> (Other transcript consequences for this variant appear to have a 
> similar issue - ENST00000504290.1:n.556_554+3delCTGGT…)
>
> I get the same result using the VEP web interface.
>
>
>
> Regards,
> Bhavana
>
>
>
>
>
>
> ---------------------------------------------
> Bhavana Harsha
> Bioinformatician
> COSMIC
> Wellcome Trust Sanger Institute
> Hinxton, UK
> CB10 1SA
>
>
>
>
>
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