I need Help with the percentage of participants having a certain allele


I have hypothesized that there are more mutations in promoter regions of BRAF in patients with malignant melanoma than healthy individuals.

To test this, I have calculated the percentage of individuals (frequency) that carry a particular allele in 300 malignant melanoma participants from Genomics England. I then did subset gnomAD biobank controls for the same genomic coordinates (BRAF promoter regions). I am going to do chi-square test, so I must calculate the percentage of individuals (frequency) carrying that allele in gnomAD as well.

In gnomAD vcf file for chromosome 7, I see AC, AN, nhomo, but I am not sure how to calculate the percentage of individuals (frequency) each allele.

In Googling I found, gnomAD population frequency could be calculated by AC-nhomo/(AN/2) . However, I am not able to understand the logic here.

Could you please help me with an intuition?

Thanks for any clue


Allele frequency information is available in our VCFs under the name AF:

##INFO=<ID=AF,Number=A,Type=Float,Description="Alternate allele frequency">

Please note that the gnomAD production team is a small team with limited bandwidth, and we are unable to provide bioinformatics support.