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Protocols

gnomAD specifications

Information


Unique identifier OMICS_17729
Name gnomAD
Alternative name Genome Aggregation Database
Restrictions to use None
Community driven Yes
User data submission Not allowed
Version 2.0
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Additional information


the gnomAD browser is available from: https://github.com/macarthur-lab/gnomad_browser

gnomAD citations

 (78)
call_split

Case Report: Identification of an HNF1B p.Arg527Gln mutation in a Maltese patient with atypical early onset diabetes and diabetic nephropathy

2018
PMCID: 5952643
PMID: 29764441
DOI: 10.1186/s12902-018-0257-z
call_split See protocol

[…] likelihood model to report alleles and Phred-scaled confidence values []. Variants (SNVs and indels) were called with SAMTools, with reference to public databases including dbSNP and 1000Genomes and gnomAD []. Analysis was performed with preference to variants located in genes implicated in atypical non-autoimmune forms of diabetes and early-onset obesity. The prioritized candidate gene list was […]

library_books

High‐throughput discovery of functional disordered regions: investigation of transactivation domains

2018
Mol Syst Biol
PMCID: 5949888
PMID: 29759983
DOI: 10.15252/msb.20188190

[…] the natural human population and in cancer genomes do not confer survival in our assay for TAD functionality. For instance, the W30R in EKLF4 (allele frequency in the human population of 1.3 × 10−5; gnomAD database) and the E135K mutation in ESX, which is prevalent in esophageal adenocarcinoma (allele frequency of 0.37 from cBioPortal), may lead to loss of TAD activity in these transcription fact […]

library_books

Incorporating epilepsy genetics into clinical practice: a 360°evaluation

2018
PMCID: 5945675
PMID: 29760947
DOI: 10.1038/s41525-018-0052-9

[…] ated in an internally developed pipeline. Included in this evaluation were literature and database searches like Human Gene Mutation Database (HGMD), Exome Aggregation Consortium (ExAC) database, the Genome Aggregation Database (gnomAD). Synonymous variants and variants in autosomal dominant genes which had been observed more than three times or in homo-/hemizygous state in the ExAC/gnomAD databas […]

library_books

Genetic analyses in a cohort of 191 pulmonary arterial hypertension patients

2018
PMCID: 5944100
PMID: 29743074
DOI: 10.1186/s12931-018-0789-9

[…] e identified using the GATK HaplotypeCaller program (http://www.broadinstitute.org/gsa/wiki/index.php/Home_Page) and further annotated with comprehensive ANNOVAR software for their frequencies in the Genome Aggregation Database (gnomAD) for the pathogenicity and splicing-altering prediction of single nucleotide variants in the dbNSFP database, which included results from SIFT, Ployphen-2, Mutation […]

library_books

CHRNE compound heterozygous mutations in congenital myasthenic syndrome

2018
PMCID: 5944527
PMID: 29702980
DOI: 10.1097/MD.0000000000010347

[…] >T (p.R99X) was a nonsense mutation that had not yet been reported, but it was found in the GnomAD database of unaffected individuals, just one time (as a heterozygote, never as a homozygote) (http://gnomad.broadinstitute.org/variant/17–4805561-G-A). The nonsense mutation may lead to premature termination of protein translation. The I-TASSER server generated vastly different 3D atomic models based […]

library_books

Delineation of the genetic and clinical spectrum of Phelan McDermid syndrome caused by SHANK3 point mutations

2018
Mol Autism
PMCID: 5921983
PMID: 29719671
DOI: 10.1186/s13229-018-0205-9

[…] her two parents). In addition to a nonsense mutation, individual S13 carries a missense variant (p.Ser1291Leu) absent in the mother but present in the unaffected sister and in four individuals in the Genome Aggregation Database (gnomAD), suggesting it is likely benign, despite being predicted as damaging by several in silico tools (Additional file : Table S3). All other mutations are absent from t […]

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gnomAD funding source(s)
This work was supported by NIGMS R01 GM104371 and by NIDDK U54 DK105566.

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