gnomAD Variants Tracks
Genome Aggregation Database (gnomAD) Genome and Exome Variants tracks   (All Variation tracks)

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gnomAD v3.1  Genome Aggregation Database (gnomAD) Genome Variants v3.1  Source data version: Release 3.1 (October 29, 2020)
gnomAD v3  Genome Aggregation Database (gnomAD) Genome Variants v3  Source data version: Release 3.0 (October 16, 2019)
gnomAD v2  Genome Aggregation Database (gnomAD) Genome and Exome Variants v2.1  Source data version: Release 2.1.1 (March 6, 2019)


The gnomAD v3.1 track shows variants from 76,156 whole genomes (and no exomes), all mapped to the GRCh38/hg38 reference sequence. 4,454 genomes were added to the number of genomes in the previous v3 release. For more detailed information on gnomAD v3.1, see the related blog post.

The gnomAD v2 tracks show variants from 125,748 exomes and 15,708 whole genomes, all mapped to the GRCh37/hg19 reference sequence and lifted to the GRCh38/hg38 assembly. The data originate from 141,456 unrelated individuals sequenced as part of various population-genetic and disease-specific studies collected by the Genome Aggregation Database (gnomAD), release 2.1.1. Raw data from all studies have been reprocessed through a unified pipeline and jointly variant-called to increase consistency across projects. For more information on the processing pipeline and population annotations, see the following blog post and the 2.1.1 README.

gnomAD v2 data are based on the GRCh37/hg19 assembly. These tracks display the GRCh38/hg38 lift-over provided by gnomAD on their downloads site.

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.

Display Conventions and Configuration

gnomAD v3.1

By default, a maximum of 50,000 variants can be displayed at a time (before applying the filters described below), before the track switches to dense display mode.

Mouse hover on an item will display many details about each variant, including the affected gene(s), the variant type, and annotation (missense, synonymous, etc).

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

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


Label Options

By default, variants are labeled according to their chromosomal position followed by the reference and alternate alleles, for example "chr1:1234-1235 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 these tracks:

  • 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 version 85 (GENCODE v19).
  • Variant Type: Used to exclude/include variants according to the type of variation, as annotated by VEP v85.
There is one additional configurable filter on the minimum minor allele frequency.

gnomAD v2.1.1

The gnomAD v2.1.1 track follows the standard display and configuration options available for VCF tracks, briefly explained below.
  • In mode, a vertical line is drawn at the position of each variant.
  • In mode, "ref" and "alt" alleles are displayed to the left of a vertical line with colored portions corresponding to allele counts. Hovering the mouse pointer over a variant pops up a display of alleles and counts.
  • Filtering Options

    Four filters are available for these tracks, the same as the underlying VCF:

    • AC0: Allele Count 0 after filtering out low confidence genotypes (GQ < 20; DP < 10; and AB < 0.2 for het calls))
    • InbreedingCoeff: Inbreeding Coefficient < -0.3
    • RF: Used to exclude/include variants that failed Random Forest filtering thresholds of 0.055272738028512555, 0.20641025579497013 (probabilities of being a true positive variant) for SNPs, indels)
    • Pass: Variant passes all 3 filters

    There are two additional filters available, one for the minimum minor allele frequency, and a configurable filter on the QUAL score.

    UCSC Methods

    For the v3.1 update, In order to cut down on the amount of displayed data, the following variant types have been filtered out, but are still viewable in the gnomAD browser:

    • Regulatory Region Variants
    • Downstream/Upstream Gene Variants
    • Transcription Factor Binding Site Variants

    For the full steps used to create the track at UCSC, please see the section denoted "gnomAD v3.1 update" in the hg38 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). Variant VCFs can be found in the vcf/ subdirectory. The v3.1 update files are in a special directory as they have been transformed from the underlying VCF.

    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.


    Thanks to the Genome Aggregation Database Consortium for making these data available. The data are released under the ODC Open Database License (OBdL) as described here.


    Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alfoldi J, Wang Q, Collins RL, Laricchia KM, Ganna A, Birnbaum DP et al. Variation across 141,456 human exomes and genomes reveals the spectrum of loss-of-function intolerance across human protein-coding genes. doi:

    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