[ensembl-dev] Incorrect HGVSp start coordinate for certain delins variants

[Sarah Hunt]

Hi Reece,

Thanks for the detailed bug report. The fix you suggest will not have
unwanted impact so has been added to CVS for branch 71.

Best wishes,
Sarah
On Tue, May 14, 2013 at 5:48 AM, Reece Hart <reece at harts.net> wrote:

> Hi-
>
> VEP 2.8 and VEP 71 appear to have a bug in which the start coordinate for
> protein HGVSp effects are repeated for certain delins variants.
>
>  For example, with this VCF line as input:
>   3 10191482 CVID1003553 A ATTT 60 PASS
> VEP 2.3 correctly returns
>    HGVSp=ENSP00000256474.2:p.Lys159delinsIleX
>   HGVSp=ENSP00000344757.2:p.Lys118delinsIleX
> for two transcripts, whereas VEP 2.8 and VEP 71 each return
>   HGVSp=ENSP00000256474.2:p.Lys159159delinsIleX
>    HGVSp=ENSP00000344757.2:p.Lys118118delinsIleX
> (two coding transcripts)
>
> Notice that the start coordinates, 159 and 118, are repeated VEP 2.8 and
> 71.
>
>
> More examples:
>  5 112175315 CVID1010109 T TAAA 60 PASS
> 9 98238379 CVID6007616 AT ACTGCTGC 60 PASS
> 10 43610045 CVID4000412 AG ATTCT 60 PASS
> 10 89711990 CVID4000640 TTCC TATAAAT 60 PASS
> 17 7578202 CVID6007473 AC AACCA 60 PASS
> 17 78063675 CVID6004403 A ATGT 60 PASS
>
>
> The error appears to be in TranscriptVariationAllele.pm:794:
>
> $hgvs_notation->{'hgvs'} .= $ref_pep_first . $hgvs_notation->{start} .
> $hgvs_notation->{end} . $hgvs_notation->{type} . $hgvs_notation->{alt} ;
>
> Having both $ref_pep_first and $hgvs_notation->{start} has the effect of
> repeating the starting coordinate. Removing $hgvs_notation->{start} from
> the above line solves this problem for these cases, but I'm unsure that I
> fully understand the logic that is implemented in _get_hgvs_protein_format
> or the impact of this change on other cases.
>
>
> -Reece
>
>
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