gnomAD gnomAD STR Track Settings

Genome Aggregation Database (gnomAD) - Short Tandem Repeat Genotypes at Disease-Associated Loci

Configure track container: Genome Aggregation Database (gnomAD)

Description

The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators at the Broad Institute and collaborating institutions, with the goal of aggregating and harmonizing exome and whole-genome sequencing data from large-scale sequencing projects spanning disease-specific cohorts and population genetics studies. Individuals affected by severe pediatric diseases and first-degree relatives were excluded from the studies. However, some individuals with severe disease may still have remained in the datasets, although probably at an equivalent or lower frequency than observed in the general population. For each variant, gnomAD provides allele frequencies stratified by genetic ancestry group, alongside quality metrics such as depth of coverage and genotype quality scores. The database also supplies sequencing coverage, structural variants, CNVs, and short tandem repeats. Additionally, gnomAD provides non-coding constraint and gene-level constraint metrics — including pLI scores, observed/expected (oe) ratios, and LOEUF values — that quantify intolerance to loss-of-function variation and are widely used to prioritize candidate disease genes. The most current release on hg38 is v4.1, but the older v3 and v2 versions are also available.

The available data tracks are:

gnomAD v4.1 — Shows single nucleotide variants (SNVs) and small insertion/deletion variants of 807,162 individuals, including 730,947 exomes and 76,215 genomes.
gnomAD v3.1.1 — Shows variants from 76,156 whole genomes (and no exomes), all mapped to GRCh38/hg38.
Deprecated: gnomAD v3.1 — Same underlying data as v3.1.1 with older annotations. Do not use; will be removed soon.
gnomAD v3 — Shows variants from 71,702 whole genomes from the v3.0 release.
gnomAD v2 — Shows variants from 125,748 exomes and 15,708 whole genomes, lifted from GRCh37/hg19 to GRCh38/hg38.
gnomAD Mut Constraint — Shows the reduced variation caused by purifying natural selection for 1kbp windows across the genome (based on v3.1.2).
gnomAD Constraint Metrics — Contains per-gene and per-transcript metrics of pathogenicity (LOEUF, pLI, and Z-scores) for v2.1.1, v4, and v4.1.
gnomAD v3 Genome Coverage — Shows various read depth metrics for genome samples from v3.0.1.
gnomAD v4 Exome Coverage — Shows various read depth metrics for exome samples from v4.0.
gnomAD Structural Variants — Shows structural variant calls (variants >=50 nucleotides) from gnomAD v4.1.
gnomAD Rare CNV Variants — Shows rare copy number variants (<1% overall site frequency) from gnomAD v4.1.
gnomAD STR — Shows short tandem repeat genotypes at disease-associated loci from gnomAD v3.1.3.

For questions on the gnomAD data, also see the gnomAD FAQ.

More details on the Variant type(s) can be found on the Sequence Ontology page.

To view the full description, click here.

All tracks in this collection (13)

Display mode: Duplicate track

Show only items with score at or above: (range: 0 to 1000)

Display data as a density graph:

Data schema/format description and download

Related tracks

Tandem Repeat Variation: A collection of population-level STR variation tracks across the genome

Version: gnomAD v3.1.3 STR genotypes (March 2025)
Assembly: Human Dec. 2013 (GRCh38/hg38)
Data last updated at UCSC: 2026-03-12 14:40:52

new Note: Released Apr. 10, 2026

Description

The gnomAD STR track displays short tandem repeat (STR) genotypes at 87 disease-associated loci from the Genome Aggregation Database (gnomAD) v3.1.3. The data include individual-level STR genotypes from 18,511 whole-genome sequenced samples across 10 populations, aggregated into per-locus allele frequency distributions.

These loci were selected because tandem repeat expansions at these sites have been reported to cause human genetic diseases, including Huntington disease (HTT), fragile X syndrome (FMR1), Friedreich ataxia (FXN), various spinocerebellar ataxias, myotonic dystrophies, and other neurological and neuromuscular disorders. Most loci (56) have motifs between 3–6 bp, while additional loci have longer motifs of 10–24 bp.

The genotypes were generated using ExpansionHunter v5 on gnomAD v3.1 whole-genome sequencing data (150 bp read lengths). Of the samples, 64% were PCR-free, 13% PCR-plus, and 23% had unknown PCR protocol. ExpansionHunter was selected because it had the best accuracy among existing tools for detecting expansions at disease-associated loci. Results were generated without off-target regions to minimize overestimation of repeat sizes. For each locus, the data show the distribution of repeat allele sizes observed across the gnomAD population, providing a reference for normal and expanded allele ranges. For more details on the methods, see the gnomAD blog post on STR calls.

Display Conventions

Items are colored by the length of the repeat motif:

Red – mononucleotide (period 1)
Blue – dinucleotide (period 2)
Green – trinucleotide (period 3)
Orange – tetranucleotide (period 4)
Purple – pentanucleotide (period 5)
Steel blue – hexanucleotide (period 6)
Gray – longer or complex motifs

Each item is labeled by the gene name. Hovering shows the repeat motif, gene, total sample count, and number passing quality filters. Clicking an item links to the corresponding gnomAD STR locus page with interactive allele frequency histograms and detailed population breakdowns.

The detail page for each locus shows:

Motif(s) – the repeat unit(s) genotyped at this locus
Samples – total genotyped individuals and number passing filters
Allele distribution – allele sizes and their frequencies
Populations – sample counts per gnomAD population

Methods

The gnomAD STR genotype data file (gnomAD_STR_genotypes__2025_03_17.tsv.gz) was downloaded from the gnomAD downloads page. This file contains individual-level STR genotypes at 87 disease-associated loci generated using ExpansionHunter on gnomAD v3.1.3 whole-genome sequencing data.

For the UCSC Genome Browser track, the individual genotype records (~1.4 million rows) were aggregated per locus to produce summary statistics: total sample count, PASS-filter count, allele size frequency distributions, and per-population sample counts. Coordinates were used as provided (0-based). Some loci include genotypes for multiple motif patterns (e.g., complex repeat structures) and for adjacent repeats; these are represented as separate records.

The 10 populations represented are: African/African American (afr), Admixed American/Latino (amr), Amish (ami), Ashkenazi Jewish (asj), East Asian (eas), Finnish (fin), Middle Eastern (mid), Non-Finnish European (nfe), South Asian (sas), and Other (oth).

Data Access

The raw data can be explored interactively with the Table Browser or the Data Integrator. For automated analysis, the data may be queried from our REST API. The underlying bigBed file can be downloaded from our download server.

The complete gnomAD STR dataset, including individual-level genotypes, is available from the gnomAD downloads page. Interactive locus-level views with allele frequency histograms are available at the gnomAD STR browser.

Credits

Thanks to the gnomAD production team at the Broad Institute for generating and distributing this data.

References

Chen S, Francioli LC, Goodrich JK, Collins RL, Kanai M, Wang Q, Alföldi J, Watts NA, Vittal C, Gauthier LD et al. A genomic mutational constraint map using variation in 76,156 human genomes. Nature. 2024 Jan;625(7993):92-100. PMID: 38057664; PMC: PMC11629659

Dolzhenko E, Deshpande V, Schlesinger F, Krusche P, Petrovski R, Chen S, Emig-Agius D, Gross A, Narzisi G, Bowman B et al. ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions. Bioinformatics. 2019 Nov 1;35(22):4754-4756. PMID: 31134279; PMC: PMC6853681