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Hum Mutat. 2016 Mar;37(3):235-41. doi: 10.1002/humu.22932. Epub 2016 Jan 5.

dbNSFP v3.0: A One-Stop Database of Functional Predictions and Annotations for Human Nonsynonymous and Splice-Site SNVs.

Liu X1,2, Wu C3, Li C2, Boerwinkle E1,2,4.

Author information

1
Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas.
2
Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas.
3
Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California.
4
Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas.

Abstract

The purpose of the dbNSFP is to provide a one-stop resource for functional predictions and annotations for human nonsynonymous single-nucleotide variants (nsSNVs) and splice-site variants (ssSNVs), and to facilitate the steps of filtering and prioritizing SNVs from a large list of SNVs discovered in an exome-sequencing study. A list of all potential nsSNVs and ssSNVs based on the human reference sequence were created and functional predictions and annotations were curated and compiled for each SNV. Here, we report a recent major update of the database to version 3.0. The SNV list has been rebuilt based on GENCODE 22 and currently the database includes 82,832,027 nsSNVs and ssSNVs. An attached database dbscSNV, which compiled all potential human SNVs within splicing consensus regions and their deleteriousness predictions, add another 15,030,459 potentially functional SNVs. Eleven prediction scores (MetaSVM, MetaLR, CADD, VEST3, PROVEAN, 4× fitCons, fathmm-MKL, and DANN) and allele frequencies from the UK10K cohorts and the Exome Aggregation Consortium (ExAC), among others, have been added. The original seven prediction scores in v2.0 (SIFT, 2× Polyphen2, LRT, MutationTaster, MutationAssessor, and FATHMM) as well as many SNV and gene functional annotations have been updated. dbNSFP v3.0 is freely available at http://sites.google.com/site/jpopgen/dbNSFP.

KEYWORDS:

database; dbNSFP; dbscSNV; functional prediction; nonsynonymous mutation; splice-site mutation

PMID:
26555599
PMCID:
PMC4752381
[Available on 2017-03-01]
DOI:
10.1002/humu.22932
[Indexed for MEDLINE]
Free PMC Article

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