[ensembl-dev] HGVS shift in GRCh37 and GRCh38

Andrew Parton aparton at ebi.ac.uk
Tue Dec 4 10:29:40 GMT 2018


Hi,

Thank you for this issue report. I’ve taken a look over the last couple of days, and it’s definitely a bug. When VEP looks for the sequences flanking the variant, it takes a chunk of 100 bases at either side, and it doesn’t expand correctly if the indel covers a larger area then that. So for example, 17:g.16029315_16029366del shifts correctly, while 17:g.16029315_16029421del does not.

We’re currently making significant improvements to our HGVS 3’ shifting code, which will resolve this issue, however this is currently scheduled for release in March 2019.

Thanks for reporting this one, and if there’s anything else we can do to help please let us know.

Kind Regards,
Andrew



> On 28 Nov 2018, at 10:13, Bhavana Harsha <bh4 at sanger.ac.uk> wrote:
> 
> Hello,
> 
> We’ve come across something strange in VEP.
> 
> For the GRCh37 variant 17:g.16029315_16029421del, VEP returns the following transcript annotation:
> HGVSg: 17:g.16029316_16029422del
> HGVSc: ENST00000395851.1:c.1609_1634+81del
> HGVSc-offset = 0
> HGVSg-offset = 1
> 
> When we lift-over the genomic variant to GRCh38 (using the Ensembl API) and run VEP we get the following annotation for the same transcript:
> Input: 17:g.16126002_16126108del
> HGVSg: 17:g.16126003_16126109del
> HGVSc: ENST00000395851.5:c.1609_1634+81del
> HGVSc-offset = -1
> HGVSg-offset = 1
> 
> 
> Why does it shift the genomic syntax by 1 position in both the assemblies? 
> Shouldn’t GRCh37 VEP have shifted it by 2 bases or have I missed something here?
> 
> We’re on campus and I’m happy to meet to explain this further, if needed.
> 
> 
> 
> Regards,
> Bhavana
> 
> 
> 
> 
> 
> 
> 
> ---------------------------------------------
> Bhavana Harsha
> Senior Bioinformatician
> COSMIC
> Wellcome Trust Sanger Institute
> Hinxton, UK
> CB10 1SA
> 
> 
> 
> 
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