What is gnomAD allele frequency
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6 months ago
Eric Wang ▴ 40

Hi, all

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?

Best Eric

AF gnomAD • 1.2k views
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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.

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