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Minor Allele Frequency (MAF)

  • Short definition: The frequency of the less common allele at a genetic locus in a given population or dataset. For a biallelic site with allele frequencies p and q, MAF = min(p, q). Reported as a fraction or percentage.

Why "minor" allele frequency

  • "Minor" specifies the less common allele, ensuring the metric is bounded in [0, 0.5] for biallelic variants and is comparable across studies and populations even when the reference/alt designation differs.
  • By definition, for biallelic sites MAF = min(p, q) and for multiallelic sites it is the frequency of the second most common allele; therefore MAF ≤ 0.5. The "reference" allele is not guaranteed to be the major allele in a population.
  • Some databases/browsers report the alternate allele frequency (relative to the reference allele), which can be close to 1.0 if the reference allele is rare or absent in that population. This does not imply MAF is 1.0; it reflects that the alternate allele is common while the reference allele is rare. See NCBI Variation Viewer FAQ and gnomAD/ExAC notes.

How it’s calculated (quick intuition)

  • Count each allele copy across individuals, compute allele frequencies, then take the smaller frequency as MAF.
  • Example: If allele A is 0.92 and allele a is 0.08 in a cohort, MAF = 0.08 (8%). If the cohort differs (A=0.55, a=0.45), MAF = 0.45.

Practical uses

  • Variant filtering and study design (e.g., keep MAF > 5% for common-variant GWAS; < 1% or < 0.1% for rare-variant analyses).
  • Interpreting clinical significance and population differences; MAF helps distinguish common polymorphisms from rare/ultrarare variants.

References