What is gnomAD allele frequency? How to calculate the population allele frequency of a variant in gnomAD? What is the difference between VAF, MAF, and gnomAD AF?
In the gnomAD database, do AF and MAF represent the same meaning?
The confusion occurs due to the fact that there are two variant frequencies: one is the frequency of the variant in a populaiton, another is the allele balance for the particular variant in a particular sample.
Allele frequency in GnomAD = allele count / number of alleles (number of times the variant was called, 1 if heterozygous 2 if homozygous, divided by overall number of alleles available for evaluation). It can be restricted by a population.
VAF: "VAF is the percentage of sequence reads observed matching a specific DNA variant divided by the overall coverage at that locus". So in general it is a property of a variant in a particular sample. E.g. for a position X in the particular sample 45% of reads show a nucleotide T, and 55% shows a nucleotide G. VAF of T variant is 45%.
mAF: minor allele frequency, it can be used as to denote a population frequency of the less frequent variant, as well as the T in the abovementioned example.
MAF: major allele frequency.
This notation is not fixed. For GnomAD I could not find which VAF and MAF you refer to, when I download a table of variants they provide allele frequency only in "populational" sense.
Thank you for your answer.
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