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Dear VEP developers, </p>
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<p>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.</p>
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<p>The variant is located on chromosome 7, position 74193668 and changes the G to an A.
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<p>Here is the link to gnomAD: <a href="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</a></p>
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<p>And here is the annotation of VEP: </p>
<p><a href="https://www.ensembl.org/Multi/Tools/VEP/Ticket?tl=dIJTZhzghOPHidSp">https://www.ensembl.org/Multi/Tools/VEP/Ticket?tl=dIJTZhzghOPHidSp</a><br>
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<p>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.
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<p>Is there possibly an obvious explanation for this behavior that I have overlooked? Or is it actually a bug?</p>
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<p>I'm looking very much forward to your reply!</p>
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<p>Best regards</p>
<p>Tim Jeske<br>
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