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

By Xiaoming Liu, Chunlei Wu, Chang Li, Eric Boerwinkle. 2016

928 citations recorded by the source corpus.

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.

Subfields: Genetics, Molecular Biology

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Citations in the corpus

CADD: predicting the deleteriousness of variants throughout the human genome (2018, positive): “In addition, our SNV scores are available through a number of third-party sources, such as dbNSFP (48), as a plug-in for Ensembl VEP, ANNOVAR (49), SeattleSeq (50), ExAC / gnomAD (8) and PopViz (51).”
Using deep mutational scanning to benchmark variant effect predictors and identify disease mutations (2020, methodology): “We also made use of the dbNSFP (Liu et al , 2016) database of pre-calculated predictions from multiple VEPs for the human genome (downloaded 2020-02-12).”
Variation Interpretation Predictors: Principles, Types, Performance, and Choice (2016, background): “0) contains results for 14 predictors, altogether for 83 million variants [Liu et al., 2016].”
The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies (2017, neutral): “0 dataset (Liu et al. 2016).”