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<p>Hi Jonathan<br>
<br>
The VEP REST endpoint only returns the gnomAD exome frequency
data. It does not return the gnomAD genome frequency data.</p>
<p>That is the reason you are not getting gnomAD frequency data for
rs901011140.</p>
<p>The gnomAD exome and genome frequency data is available using the
Ensembl browser and the Perl API.<br>
<br>
Population allele frequencies are available using the Variation
REST endpoint but currently does not include gnomAD frequencies.</p>
<p><a class="moz-txt-link-freetext" href="https://grch37.rest.ensembl.org/documentation/info/variation_id">https://grch37.rest.ensembl.org/documentation/info/variation_id</a><br>
<a class="moz-txt-link-freetext" href="https://grch37.rest.ensembl.org/variation/human/rs116035550?content-type=application/json;pops=1">https://grch37.rest.ensembl.org/variation/human/rs116035550?content-type=application/json;pops=1</a><br>
<br>
We are planning to include gnomAD frequency data in the Variation
REST endpoint in the next release of the REST API.<br>
</p>
Regards<br>
Helen <br>
<br>
<div class="moz-cite-prefix">On 17/05/2018 09:56, Jonathan Stoppani
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAFzCN1tzinvRA0gjWYmHK+U1AULxRMjkqRHAc9Om4iM97cDgmQ@mail.gmail.com">
<div dir="ltr">Hello,
<div><br>
</div>
<div>I'm trying to retrieve the allele frequencies for different
variants and for different databases.</div>
<div>I'm using the /vep/human/id/ REST endpoint and it mostly
works fine.</div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>One such example:</div>
<div><br>
</div>
<div>Variant identifier: rs901011140</div>
<div>Variant location: 1:955277<br>
</div>
<div><br>
</div>
<div>Variant data on gnomAD: <a
href="http://gnomad.broadinstitute.org/variant/1-955277-G-C"
moz-do-not-send="true">http://gnomad.broadinstitute.org/variant/1-955277-G-C</a></div>
<div>Note that they don't have the dbSNP identifier on file (<font
face="monospace, monospace">not found in dbSNP</font>).</div>
<div><br>
</div>
<div>Variant data on Ensembl web: <a
href="http://grch37.ensembl.org/Homo_sapiens/Variation/Population?v=rs901011140"
moz-do-not-send="true">http://grch37.ensembl.org/Homo_sapiens/Variation/Population?v=rs901011140</a></div>
<div>Note that the AFs are correctly mirroring what's being
reported on gnomAD.<br class="gmail-Apple-interchange-newline">
<br>
</div>
<div>Variant data fetched over the REST API: <a
href="http://grch37.rest.ensembl.org/vep/human/id/rs901011140?content-type=application/json"
moz-do-not-send="true">http://grch37.rest.ensembl.org/vep/human/id/rs901011140?content-type=application/json</a></div>
<div>Note that MAFs are not being returned at all.</div>
<div><br>
</div>
<div>Am I doing something wrong? Are the AFs not being returned
on the API endpoint for a particular reason?</div>
<div><br>
</div>
<div>Thank you very much for your help!</div>
<div><br>
</div>
<div>Best,</div>
<div>Jonathan</div>
<div><br>
</div>
<div>P.S.: GRCh38 yields the same results:</div>
<div><a
href="http://rest.ensembl.org/vep/human/id/rs901011140?content-type=application/json"
moz-do-not-send="true">http://rest.ensembl.org/vep/human/id/rs901011140?content-type=application/json</a><br>
</div>
<div><a
href="http://www.ensembl.org/Homo_sapiens/Variation/Population?v=rs901011140"
moz-do-not-send="true">http://www.ensembl.org/Homo_sapiens/Variation/Population?v=rs901011140</a><br>
</div>
</div>
<br>
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<br>
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