Variant allele frequency versus population frequency

General
1

Hi
I have downloaded vcf file for chromosome 1 from gnomad v3.1.2 from which I did subset biobank/controls samples (non-finnish) .

For each variant, I want to compare my gnomAD vcf with vcf files of colon cancer patients for the same Genomic coordinates to see if I have more variants in Cancer patients that gnomAD as a control.

For my comparision, shall I use variant allele frequency (AF) ### column in my gnomAD aata or I must calculate population frequency by this formula AC-nhomo/(AN/2) ???

I read

Allele frequency is NOT equivalent to the percentage of individuals that carry the allele, but is a suitable value for expressing the frequency of a variant in the general population. The number of individuals carrying a variant will depend on the number of heterozygous and homozygous individuals but can be calculated from the data provided in the variant table.

Please, somebody help me with this definitions

2

Hello,

The gnomAD production team is a small team with limited bandwidth, and we are unable to provide bioinformatics support.

Note that we defined variant allele frequency in the Genetic ancestry blog post:

A variant’s frequency is defined by the number of copies of an allele divided by the total number of chromosomes examined.

Best,
Katherine