[ensembl-dev] variant effect prediction non_synonymous without alleles?

[Graham Ritchie]

Hi Stef,

It looks like you have found a bug in our consequence calculation code! The peptide allele string in this case should be */Q and the consequence should be STOP_LOST (our as yet unreleased new consequence pipeline gets this right). We will endeavour to fix this as soon as we can. For the time being I think you should be able to treat all such results (where there is no reference peptide in the peptide allele string) as STOP_LOST events.

Sorry about this.

Cheers,

Graham


On 23 Dec 2010, at 15:25, mailsvl at fastmail.fm wrote:

> Hi,
> 
> When I use the variant effect predictor (either online or with api) for
> this snv:
> 
> 10_3181003_A/G 10:3181003 ENSG00000107959 ENST00000455371
> NON_SYNONYMOUS_CODING 553 185 /Q rs2279217
> 
> You can see it predicts NON_SYN with only one allele in the change (
> /Q), how is this possible?
> 
> Thanks,
> Stef
> 
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