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Rare Variant

Definition
AI-generated

A rare variant is a genetic variant with low population frequency, commonly defined using a minor allele frequency threshold such as less than 1% or 0.5%.

Topics
Core genetics
Related
Adaptive Burden Test Burden Test Rare Variant Aggregation Test

Why it matters in GWAS

Rare variants are usually poorly captured by standard arrays and often require sequencing, specialized association tests, or aggregation methods to analyze well.

Example usage

"Rare variant burden tests were restricted to predicted damaging coding variants."

Adaptive Burden Test Burden Test Rare Variant Aggregation Test SKAT SKAT-O Common Variant Gene-Based Test Minor Allele Frequency (MAF) Single Nucleotide Variant (SNV) Whole-Exome Sequencing (WES) Whole-Genome Sequencing (WGS)
Related-term network

Click any node to open that term page.

Node order. The current term is first. Next come every page linked from Related terms, in the same top-to-bottom order as that list. Then new terms appear in two-hop layers: for each of those direct neighbors (in that same order), their related terms are appended if not already listed. A third pass does the same for two-hop nodes. The walk stops when a fixed maximum number of nodes is reached.

References

  • Boutry S, Helaers R, et al. (2023). Rare variant association on unrelated individuals in case-control studies using aggregation tests: existing methods and current limitations. Brief Bioinform. https://doi.org/10.1093/bib/bbad412
  • Gibson G. (2012). Rare and common variants: twenty arguments. Nat Rev Genet.
← Randomized controlled trial (RCT) Rare Variant Aggregation Test →

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