HGVD: Human Genetic Variation Database update 2026 with sequencing of 4344 genetically diverse Japanese individuals

Allele-frequency database integrating 1,209 exomes and 3,135 Japanese genomes, structural variants and tandem-repeat distributions

HGVD, a free Japanese allele-frequency resource launched in 2013, moves to version 3.1. It integrates 1,209 exomes with whole-genome sequencing of 3,135 Japanese individuals selected by principal component analysis to span genetic diversity, providing aggregate statistics for 4,344 individuals, plus genotyping data (3,248 individuals) and eQTL (300 individuals). Frequencies are browsable on GRCh37, GRCh38 and T2T-CHM13, with non-GRCh37 tracks generated by liftOver, and a graph-genome-ready structural-variant release is downloadable. The new pathSTR portal reports population distributions for 68 medically relevant tandem-repeat loci, derived with STRdust from Oxford Nanopore data of 1,019 individuals of the 1000 Genomes Project.

Synthesis written by Geno'X. For the full original abstract, please refer to the source publication.

Useful for interpreting rare and pharmacogenomic variants in patients of Japanese or East Asian ancestry, populations underrepresented in European-dominated databases. The long-read distributions for the 68 repeat loci are the most reusable part outside Japan, since they come from 1000 Genomes Project individuals; the GRCh38 and T2T tracks derived by liftOver call for caution in poorly converted regions.

Analysis by Dr Thibaut Benquey