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
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.
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
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.
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.
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
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.
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.
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.