differences between GnomAD allele frequencies on the website and when downloading a tsv

[Thomas Pauli]

Hi everyone,

this is probably a minor issue, but for some SNVs I get different allele frequencies in the GnomAD column, depending whether I view the data in patient view, or whether I download the patient view as tsv.

For instance, this patient (https://www.cbioportal.org/patient?sampleId=60&studyId=summit_2018) has a MITF2 T110M mutation. According to the data in patient view, this mutation occurs with an allele frequency of 0.00016 in populations. When I download the tsv it shows a frequency of 0.00018081293486300976. The difference is minor, but it doesn't seem to be a rounding issue, since I'd expect a 0.00018 in patient view instead.

Do you know the reason for the discrepancy? Is the GnomAD data assessed differently when downloading a .tsv file than in patient view?

Best wishes,

Thomas Pauli

[Tali Mazor]

Hi Thomas,

Thanks for letting us know about this - the gnomAD frequency should be the same everywhere. I've created an issue on GitHub where you can track our progress on resolving this: https://github.com/cBioPortal/cbioportal/issues/8956

-Tali

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[Thomas Pauli]

Many thanks Tali,

Best wishes,

Thomas