Description

The Genome Aggregation Database (gnomAD) - Genome and Exome Variants tracks show single nucleotide variants (SNVs) and small insertion/deletion variants of <50 nucleotides (indels) from 125,748 exomes and 15,708 whole genomes of unrelated individuals, short variant release 2.1.1. For more information on the processing pipeline and population annotations, see the following blog post and the 2.1.1 README.

There are two tracks making up this data set:

1. gnomAD Exome Variants: short variants of 125,748 exomes, release 2.1.1.
2. gnomAD Genome Variants: short variants of 15,708 genomes, release 2.1.1.

VCF files were downloaded according to the gnomAD instructions and transformed into one bigBed file per data set, as described in UCSC Methods.

Display Conventions and Configuration

Display conventions

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

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 these tracks:

1. 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.
2. 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).
3. Variant Type: Used to exclude/include variants according to the type of variation, as annotated by VEP v85.

As an individual variant can possess multiple FILTER and Variant Type values, it is important to select any options of interest (or rather deselect if trying to filter out variants from the display).

Annotations from the Loss-of-function curation results have been added where appropriate to variants in both the exomes and genomes data.

For the full steps used to create the track at UCSC, please see the section denoted "gnomAD v2.1.1 update" in the hg19 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 or downloaded as files from our download server, subject to the conditions set forth by the gnomAD consortium (see below). Please refer to our mailing list archives for questions or our Data Access FAQ for more information.

More information about using and understanding the gnomAD data can be found in the gnomAD FAQ site.

Credits

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

References

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 18;536(7616):285-91. PMID: 27535533; PMC: PMC5018207

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

Collins RL, Brand H, Karczewski KJ, Zhao X, Alföldi J, Francioli LC, Khera AV, Lowther C, Gauthier LD, Wang H et al. A structural variation reference for medical and population genetics. Nature. 2020 May;581(7809):444-451. PMID: 32461652; PMC: PMC7334194

Cummings BB, Karczewski KJ, Kosmicki JA, Seaby EG, Watts NA, Singer-Berk M, Mudge JM, Karjalainen J, Satterstrom FK, O'Donnell-Luria AH et al. Transcript expression-aware annotation improves rare variant interpretation. Nature. 2020 May;581(7809):452-458. PMID: 32461655; PMC: PMC7334198