[ensembl-dev] gnomAD MAFs not returned over the REST API for some variants

[Helen Schuilenburg]

Hi Jonathan

The VEP REST endpoint only returns the gnomAD exome frequency data. It 
does not return the gnomAD genome frequency data.

That is the reason you are not getting gnomAD frequency data for 
rs901011140.

The gnomAD exome and genome frequency data is available using the 
Ensembl browser and the Perl API.

Population allele frequencies are available using the Variation REST 
endpoint but currently does not include gnomAD frequencies.

https://grch37.rest.ensembl.org/documentation/info/variation_id
https://grch37.rest.ensembl.org/variation/human/rs116035550?content-type=application/json;pops=1

We are planning to include gnomAD frequency data in the Variation REST 
endpoint in the next release of the REST API.

Regards
Helen

On 17/05/2018 09:56, Jonathan Stoppani wrote:
> Hello,
>
> I'm trying to retrieve the allele frequencies for different variants 
> and for different databases.
> I'm using the /vep/human/id/ REST endpoint and it mostly works fine.
>
> I have, however, trouble retrieving the gnomAD frequencies for some 
> variants. Interestingly, the web interface reports them as we would 
> expect, but they are not present in the JSON payload returned by the 
> REST API call.
>
> One such example:
>
> Variant identifier: rs901011140
> Variant location: 1:955277
>
> Variant data on gnomAD: 
> http://gnomad.broadinstitute.org/variant/1-955277-G-C
> Note that they don't have the dbSNP identifier on file (not found in 
> dbSNP).
>
> Variant data on Ensembl web: 
> http://grch37.ensembl.org/Homo_sapiens/Variation/Population?v=rs901011140
> Note that the AFs are correctly mirroring what's being reported on gnomAD.
>
> Variant data fetched over the REST API: 
> http://grch37.rest.ensembl.org/vep/human/id/rs901011140?content-type=application/json
> Note that MAFs are not being returned at all.
>
> Am I doing something wrong? Are the AFs not being returned on the API 
> endpoint for a particular reason?
>
> Thank you very much for your help!
>
> Best,
> Jonathan
>
> P.S.: GRCh38 yields the same results:
> http://rest.ensembl.org/vep/human/id/rs901011140?content-type=application/json
> http://www.ensembl.org/Homo_sapiens/Variation/Population?v=rs901011140
>
>
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