Minor allele frequency

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Minor allele frequency (MAF) is the frequency at which the second most common allele occurs in a given population.

Single nucleotide polymorphisms (SNPs) with a minor allele frequency of 0.05 (5%) or greater were targeted by the HapMap project.[1]

MAF is widely used in population genetics studies because it provides information to differentiate between common and rare variants in the population. As an example, a 2015 study sequenced the whole genomes of 2,120 Sardinian individuals. The authors classified the variants found in the study in three classes according to their MAF. It was observed that rare variants (MAF < 0.05) appeared more frequently in coding regions than common variants (MAF > 0.05) in this population.[2]

How to interpret MAF data[edit]

1. Introduce the reference of a SNP of interest, as an example: rs429358, in a database (dbSNP or other).

2. Find MAF/MinorAlleleCount link. MAF/MinorAlleleCount: C=0.1506/754 (1000 Genomes)[3]; where C is the minor allele for that particular locus; 0.1506 is the frequency of the C allele (MAF), i.e. 15% within the 1000 Genomes database; and 754 is the number of times this SNP has been observed in the population of the study.

See also[edit]


  1. ^ The International HapMap Consortium (2005). "A haplotype map of the human genome". Nature. 437 (7063): 1299–1320. doi:10.1038/nature04226. PMC 1880871. PMID 16255080.
  2. ^ Sidore, C., y colaboradores (2015). "Genome sequencing elucidates Sardinian genetic architecture and augments association analyses for lipid and blood inflammatory markers". Nature Genetics. 47: 1272–1281. doi:10.1038/ng.3368. PMC 4627508. PMID 26366554.CS1 maint: Multiple names: authors list (link)
  3. ^ National Center for Biotechnology Information: New SNP Attributes