gnomAD gnomAD v4.1 Track Settings

Genome Aggregation Database (gnomAD) Genome and Exome Variants v4.1

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: Reset to defaults

Minor Allele Frequency Filter:

Filter items by: (select multiple categories and items - Help)

FILTER tags from VCF	Annotation type: pLoF, missense, synonymous, or other	Variant type(s)
Match if all one or more match		Match if all one or more match

Label: dbSnp rsID gnomAD display name

Display data as a density graph:

List subtracks: only selected/visible all
	Squish	gnomAD v4.1 Genomes	Genome Aggregation Database (gnomAD) Genome Variants v4.1	Data format
	Squish	gnomAD v4.1 Exomes	Genome Aggregation Database (gnomAD) Exomes Variants v4.1	Data format

Version: Release v4.1 (April 19, 2024)
Assembly: Human Dec. 2013 (GRCh38/hg38)

Description

GnomAD 4 used the whole-genome data from gnomAD 3 and added more exomes. The current v4.1 release includes a fix for the allele number issue. The v4.1 track shows variants from 807,162 individuals, including 730,947 exomes and 76,215 genomes. This includes the 76,156 genomes from the gnomAD v3.1.2 release as well as new exome data from 416,555 UK Biobank individuals. For more detailed information on gnomAD v4.1, see the related blog post.

Display Conventions and Configuration

Following the conventions on the gnomAD browser, items are shaded according to their Annotation type:

pLoF
Missense
Synonymous
Other

Mouse hover on an item will display the following details about each variant:

Position
Total Allele Frequency (TotalAF)
Genes
Annotation
FILTER tags from VCF (FILTER)
Population with maximum AF (PopMaxAF)
Homozygous Individuals
Homozygous Individuals in XX samples (chrX and chrY only)
Hemizygous Individuals (chrX and chrY only)

Clicking on an item will display additional details on the variant, including a population frequency table showing allele count in each sub-population.

Label Options

To maintain consistency with the gnomAD website, variants are by default labeled according to their chromosomal start position followed by the reference and alternate alleles, for example "chr1-1234-T-CAG". dbSNP rsID's are also available as an additional label, if the variant is present in dbSnp.

Filtering Options

Three filters are available for this track:

FILTER: Used to exclude/include variants that failed Random Forest (RF), Inbreeding Coefficient (Inbreeding Coeff), or Allele Count (AC0) filters. The PASS option is used to include/exclude variants that pass all of the RF, InbreedingCoeff, and AC0 filters, as denoted in the original VCF.
Annotation type: Used to exclude/include variants that are annotated as Probability Loss of Function (pLoF), Missense, Synonymous, or Other, as annotated by VEP.
Variant Type: Used to exclude/include variants according to the type of variation, as annotated by VEP.

There is one additional configurable filter on the minimum minor allele frequency.

UCSC Methods

The gnomAD v4.1 data is unfiltered.

For the full steps used to create the gnomAD tracks at UCSC, please see the hg38 gnomad makedoc.

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, and the genome annotations are stored in files that can be downloaded from our download server, subject to the conditions set forth by the gnomAD consortium (see below).

The underlying bigBed only contains enough information necessary to use the track in the browser. The extra data like VEP annotations and CADD scores are available in the same directory as the bigBed but in the files details.tab.gz and details.tab.gz.gzi. The details.tab.gz contains the gzip compressed extra data in JSON format, and the .gzi file is available to speed searching of this data. Each variant has an associated md5sum in the name field of the bigBed which can be used along with the _dataOffset and _dataLen fields to get the associated external data. For example:

# find an item of interest, the last two fields are _dataOffset and _dataLen:
bigBedToBed genomes.bb stdout | head -4 | tail -1
chr1    12416    12417    854246d79dc5d02dcdbd5f5438542b6e    [..omitted..]    67293    902

# use _dataOffset and _dataLen (add one to _dataLen for the newline character):
bgzip -b 67293 -s 903 gnomad.v4.1.genomes.details.tab.gz
854246d79dc5d02dcdbd5f5438542b6e    {"DDX11L1": {"cons": ["non_coding_transcript_variant"...

The data can also be found directly from the gnomAD downloads page. Please refer to our mailing list archives for questions, or our Data Access FAQ for more information.

Credits

Thanks to the Genome Aggregation Database Consortium for making these data available. The data are released under the Creative Commons Zero Public Domain Dedication as described here.

Please note that some annotations within the provided files may have restrictions on usage. See here for more information.

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

Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alföldi J, Wang Q, Collins RL, Laricchia KM, Ganna A, Birnbaum DP et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature. 2020 May;581(7809):434-443. PMID: 32461654; PMC: PMC7334197

Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, O'Donnell-Luria AH, Ware JS, Hill AJ, Cummings BB et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature. 2016 Aug 17;536(7616):285-91. PMID: 27535533; PMC: PMC5018207