Allele Frequency

• Note: For the population-level frequency of the less common allele, see Minor Allele Frequency (MAF).

• Allele Frequency is the proportion of all chromosome copies in a population that carry a specific allele at a given locus; expressed as a fraction or percentage. For diploid autosomes, it’s the count of the allele divided by 2 × number of individuals.

Why the name “allele frequency”

• Allele: an alternative form of a gene (or variant) at a locus.
• Frequency: a population-level measure—how often that allele occurs among all copies of the locus in the gene pool, not how often a genotype occurs. In simple two-allele systems, frequencies are often denoted p and q with p + q = 1.

How it’s calculated (quick intuition)

• Autosomal diploid case: frequency(allele A) = number of A copies / (2 × N individuals).
• Example: If 10 people have 15 A alleles and 5 a alleles across their 20 chromosomes, f(A) = 15/20 = 0.75 and f(a) = 0.25.

Real‑life examples and uses

• Variant filtering: Studies filter by minor allele frequency (MAF) to distinguish common vs rare variants (e.g., keep MAF > 5% for common-variant GWAS; < 1% for rare-variant analyses).
• Population differences: Comparing allele frequencies across populations reveals effects of selection, drift, migration, and demographic history.
• Clinical and public health: Frequencies help interpret disease-associated and pharmacogenomic variants and guide screening strategies.

See also

• Minor allele frequency (MAF)

References

• Nature Scitable: “Allele frequency”
• Khan Academy: “Allele frequency & the gene pool”
• Wikipedia: “Allele frequency”
• Wikipedia: “Minor allele frequency”
• Biology LibreTexts: “Allele and Genotype Frequencies”