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Rare vs Low-frequency vs Common variants

Terms
Rare Variant Low-frequency variant Common Variant Minor Allele Frequency (MAF)
Definition

These labels partition allele frequency in a reference population (often via MAF cutoffs). Rare variants are the least common; common variants are frequent enough for standard array GWAS; low-frequency sits between—often defined by study-specific thresholds (e.g. 1–5% MAF).

Topics
Core genetics GWAS

How they differ

Rare Low-frequency Common
Typical MAF Often below ~1% (sometimes 0.5% or 0.1% in definitions). Often ~1%–5% (study-dependent). Often above ~1% or 5% (arrays and imputation focus).
GWAS reality Poorly tagged by array; WGS/WES, burden tests, SKAT. Needs larger N than common SNPs; frequency-aware tests. Standard SNP association and meta-analysis workhorses.
Interpretation Stronger per-allele effects possible; population-specific. Middle ground for power and detection. Polygenic architecture often dominated by common SNP signal.

Rule of thumb: Always check the paper’s explicit MAF filters; rare vs common boundaries are not universal. The same variant can be “common” in one population and rare in another.

References

  • Gibson G. (2012). Rare and common variants: twenty arguments. Nat Rev Genet.
  • Bomba L, et al. (2017). The impact of rare variation on complex traits. Cell.