Allele Frequency Calculator

What "allele frequency" actually measures

An allele is one of the two copies of a gene that every diploid individual carries — one from each parent. The frequency of an allele is the share of all gene copies in the population that happen to be that variant. If 1 in 50 of those copies were the cystic-fibrosis variant, the allele frequency is 0.02.

Two facts matter for the calculator: an allele frequency always sits between 0 and 1, and across a single gene the frequencies of all variants must sum to 1. For a two-allele system that's the familiar p + q = 1.

The Hardy-Weinberg equation

Under random mating, no selection and a large population, genotype frequencies are predicted by squaring the allele-frequency equation. That gives the three classic terms — homozygous dominant, heterozygous (carrier), and homozygous recessive (affected):

• p — Frequency of the dominant (wild-type) allele, conventionally A
• q — Frequency of the recessive allele, conventionally a
• p² — Share homozygous dominant (AA) — unaffected non-carriers
• 2pq — Share heterozygous (Aa) — phenotypically healthy carriers
• q² — Share homozygous recessive (aa) — affected by the condition

Going from disease prevalence to allele frequencies

The calculator works backwards from the only number you usually have: disease prevalence. Every affected person is homozygous recessive, so prevalence equals q². Square-root to get q, subtract from 1 to get p, then plug both into 2pq to find the carrier rate.

Worked example with a 1-in-10,000 condition:

• q² = 0.0001 → q = 0.01
• p = 1 − 0.01 = 0.99
• 2pq = 2 × 0.99 × 0.01 ≈ 0.0198 — about 1 carrier in 50

The carrier rate is the surprise: rare diseases produce many more carriers than affected individuals. A 1-in-a-million condition still yields a 1-in-500 carrier rate.

Reading the result responsibly

Hardy-Weinberg is a model with assumptions that get violated in real human populations. Three sanity checks before quoting a carrier rate.

1. Match the prevalence to the population — Cystic fibrosis hits about 1 in 2,500 Northern Europeans but only around 1 in 17,000 African Americans. Plugging the wrong prevalence misses the carrier rate by an order of magnitude.
2. Founder populations break the model — Ashkenazi Jewish, Finnish and French-Canadian populations carry several recessive variants well above general-population rates. For counselling, use ethnicity-specific prevalence figures.
3. Consanguinity inflates homozygotes — Relatives share rare alleles, so the homozygous frequency rises above q². Hardy-Weinberg silently assumes mating is random.