Genetics · BEGINNER LESSON
Minor allele frequency
Minor allele frequency (MAF) is the relative frequency of the less common allele at a genetic locus in a population, usually used when a locus has two alleles. It is a proportion, even though some texts loosely call it a frequency count.
What it is
An allele is a version of a gene at a specific locus, or position, in the genome. When a locus has two alleles, the one found less often in the population is called the minor allele, and minor allele frequency is the proportion of all copies at that locus that are that minor allele. This term is used mainly for diallelic markers, meaning markers with two alleles.
[1] Genetic Terminology - PMC - NIH [2] 1.3 [3] A tutorial on conducting genome‐wide association studies
How it is measured and used
MAF is based on counting how many allele copies of each type are present in a population sample and turning that into a relative frequency. In genetics, this helps describe how common a variant is. Some authors use MAF to separate rarer variants from more common ones, for example by applying thresholds such as 1% or 5% in study quality control. In association studies, low-MAF markers are often filtered because there may be too little statistical power to detect an effect, and they can be more prone to genotyping errors.
[1] Genetic Terminology - PMC - NIH [2] 1.3 [3] A tutorial on conducting genome‐wide association studies
Limitations and interpretation
The minor-allele label can change across samples when allele frequencies are near 50%, because the less common allele in one dataset may not be the less common one in another. Also, the idea is most straightforward for two-allele sites; when there are many alleles at a locus, the simple minor-versus-major naming becomes less stable. MAF describes how common an allele is, not whether it is harmful, beneficial, or important.
[1] Genetic Terminology - PMC - NIH [2] 1.3 [3] A tutorial on conducting genome‐wide association studies
SEE THE IDEA
How minor allele frequency is defined
A specific site in the genome being examined.
Two versions are present at that site.
The allele with the smaller population frequency.
The proportion of all allele copies that are the minor allele.
A locus with two alleles is counted in a population sample; the less common allele is identified, and its proportion is reported as MAF.
MAF is a summary of how often the less common allele appears at a site, not a direct measure of biological effect.
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Sources and further reading
This general lesson was generated from public source material. It explains a concept; it does not interpret a private paper or provide medical advice.