Missing gnomAD Frequency Values for a Variant in Ensembl VEP

[mrymkdnz]

I ran a variant through Ensembl VEP, and you can view the results here: https://www.ensembl.org/Homo_sapiens/Tools/VEP/Results?tl=uiEVKf6hiWhXE2Og-10660152. However, I noticed that the gnomAD frequency values are missing for this variant.

When I searched for the same variant on the gnomAD website (https://gnomad.broadinstitute.org/variant/7-95316772-A-T?dataset=gnomad_r4), I found that frequency values are present, and the filter status is "PASS."

Could you clarify the reason for this discrepancy? Is there an issue with the data integration between Ensembl VEP and gnomAD, or could there be another explanation for this missing information?

Thank you for your help!

System

• VEP version: v113
• VEP Cache version: 113_GRCh38
• OS: vep launch

  Full VEP command line

  ./vep --af_gnomade --af_gnomadg --appris --biotype --buffer_size 500 --check_existing --distance 5000 --mane --polyphen b --pubmed --regulatory --show_ref_allele --sift b --species homo_sapiens --symbol --transcript_version --tsl --uploaded_allele --cache --input_file [input_data] --output_file [output_file]

[dglemos]

Hi @mrymkdnz, The correct input format is 7 95316772 95316772 A/T. Also, in Ensembl this variant has been flagged because of ambiguity in the allele codes: https://www.ensembl.org/Homo_sapiens/Variation/Explore?db=core;r=7:95316272-95317272;v=rs854560;vdb=variation;vf=480715206 When you run the VEP job you should select the option "Include flagged variants". You can check more details in this job: https://www.ensembl.org/Homo_sapiens/Tools/VEP/Ticket?tl=VWmGwpQeP2DiAv54

[mrymkdnz]

@dglemos Yes, you're right, I made a mistake with the input, thank you. So, if Ensembl VEP flags a variant, does that mean it won't provide information from the gnomad and other databases for that variant?

[dglemos]

If a variant is flagged, VEP will not return co-located variants or their associated data, such as gnomAD data in this case.