[ensembl-dev] Missing AF annotation

[Andrew Parton]

Hi,

I’ve had a quick look at this variant, and there are a couple of factors at play here:

On GRCh37 then the variant has been flagged as failed - http://grch37.ensembl.org/Homo_sapiens/Variation/Explore?v=rs10614;vdb=variation <http://grch37.ensembl.org/Homo_sapiens/Variation/Explore?v=rs10614;vdb=variation> - however this status is changing for Ensembl 100, which is scheduled for release at the end of April, so the frequencies should appear then. If you’re interested, you can read more about failed variants here: https://www.ensembl.org/info/genome/variation/prediction/variant_quality.html <https://www.ensembl.org/info/genome/variation/prediction/variant_quality.html>
The VEP ticket you’ve attached is using GRCh38 - you can find web VEP for GRCh37 at http://grch37.ensembl.org/Tools/VEP <http://grch37.ensembl.org/Tools/VEP>
You can include failed variants in your annotations with both web VEP and command line VEP. On the web, clicking the ‘include flagged variants’ checkbox will include these variants in your annotations (see http://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Results?tl=XKZlzw60sPRnr8HF-6129418 <http://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Results?tl=XKZlzw60sPRnr8HF-6129418>), and you can use the option ‘—failed 1’ to include these within your command line output.

Kind Regards,
Andrew

> On 17 Apr 2020, at 15:38, Jeske, Tim <Tim.Jeske at med.uni-muenchen.de> wrote:
> 
> Dear VEP developers, 
> 
> I found a frequent variant for which VEP does not correctly report allele frequencies (neither 1000G, nor ESP, nor gnomAD). I've tested both online and command line VEP for GRCh37.
> 
> The variant is located on chromosome 7, position 74193668 and changes the G to an A. 
> Here is the link to gnomAD: https://gnomad.broadinstitute.org/variant/7-74193668-G-A?dataset=gnomad_r2_1 <https://gnomad.broadinstitute.org/variant/7-74193668-G-A?dataset=gnomad_r2_1>
> 
> And here is the annotation of VEP:
> https://www.ensembl.org/Multi/Tools/VEP/Ticket?tl=dIJTZhzghOPHidSp <https://www.ensembl.org/Multi/Tools/VEP/Ticket?tl=dIJTZhzghOPHidSp>
> 
> VEP does not report any AF for the variant and thus it's easily considered as a very rare variants although it's highly frequent.
> 
> Is there possibly an obvious explanation for this behavior that I have overlooked? Or is it actually a bug?
> 
> I'm looking very much forward to your reply!
> 
> Best regards
> Tim Jeske
> 
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