[ensembl-dev] VEP HGVSp - Delins as substitutions in AA syntax

[Sarah Hunt]

Hi Bhavana,

Thanks for reporting this one. It is fixed in release/89 and will go 
live on our REST server later in the month.

Best wishes,

Sarah


On 02/08/2017 10:20, Bhavana Harsha wrote:
> Hello,
>
> Sorry to be back with what appears to be another bug in the Ensembl 
> Variation API!
> Not sure if you’re aware of this.
>
> The hgvsp syntax for the CDS variant 
> ‘ENST00000304494.5:c.330_331delGGinsAA’ as returned by VEP is
> ‘ENSP00000307101.5:p.TrpGly110TerSer’
>
> According to HGVS rules, the correct AA syntax should be 
> ‘p.Trp110_Gly111delinsTer’ or ‘p.Trp110Ter’. (I’m not sure which is 
> more appropriate here as they both seem correct)
> A substitution of more than one AA should be reported as a delins.
> See the 2nd question in the ‘Q&A’ section.
> http://varnomen.hgvs.org/recommendations/protein/variant/delins/
>
> A simpler example is ‘ENST00000301067.7:c.258_259delGTinsTA’
> VEP hgvsp = ‘ENSP00000301067.7:p.GluLeu86AspMet’
> correct syntax = ‘ENSP00000301067.7:p.Glu86_Leu87delinsAspMet'
>
> I think this is caused by the difference in the definition of the term 
> ’substitution’ between Ensembl and HGVS.
> https://www.ensembl.org/info/genome/variation/index.html
>
>
> Regards,
> Bhavana
>
>
>
>
>
> ---------------------------------------------
> Bhavana Harsha
> Bioinformatician
> COSMIC
> Wellcome Trust Sanger Institute
> Hinxton, UK
> CB10 1SA
>
>
>
>
>
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