Minor allele frequency

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

SNPs with a minor allele frequency of 0.05 or greater were targeted by the HapMap project.[1]

It 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 recent study sequenced the whole genomes of 2,120 Sardinian individuals. The authors classified the variants found in the study in three classes according to the frequency of the MAF. It was observed that rare variants (MAF <0.005) 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]

3. what do those numbers mean?:

a. C, is the minor allele for that particular locus

b. 0.1506, is the frequency of the C allele (MAF), it means 15% within the 1000 Genomes database.

c. 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. PMC 1880871Freely accessible. PMID 16255080. doi:10.1038/nature04226. 
  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. PMC 4627508Freely accessible. PMID 26366554. doi:10.1038/ng.3368. 
  3. ^ National Center for Biotechnology Information: New SNP Attributes