Grpmax faf value in gnomAD VCF files

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1

There are new ACMG guidelines, and they include the use of FAF grpmax data from gnomAD (see: https://zifornd.com/blogs/how-acmg-guidelines-and-gnomad-are-aligning-to-simplify-variant-interpretation/). These guidelines require the use of Grpmax Filtering AF data, as displayed in the gnomAD browser.

Where can this data be found in the downloadable gnomAD VCF files? When checking specific variants, I wasn’t able to identify the corresponding INFO field. For example, in gnomAD v4.1, for chr21:5031919 (REF: TAAAA, ALT: T) the Grpmax Filtering AF shown in the browser is 0.001377, while in the VCF fafmax_faf95_max = 0.00144208.

How can this data be extracted from the VCF files, both for gnomAD v4.1 and for gnomAD v3.1.2?

2

Hi,

Can you clarify where you are obtaining the value of 0.001377 from? As shown in the browser, the fafmax_faf95 value for chr21-5031919-TAAAA-T is 0.001442 for genomes, 0.001628 for exomes, and 0.001599 combined. These values are also stated in the joint VCF as fafmax_faf95_max_exomes, fafmax_faf95_max_genomes, fafmax_faf95_max_joint, or in the separate VCFs as fafmax_faf95_max.

3

Sorry, my mistake. I accidentally checked the data in the v3.1.2 browser, where the Grpmax filtering AF is 0.001377 (matching the value in the v3.1.2 VCF), but then tried to find it in the v4.1 VCF. Apologies for the confusion.