dbNSFP - Releases

Current Release:

dbNSFP v5.3.1 (January 1, 2026) (README v5.3.1a, README v5.3.1c)

Added popEVE scores, derived from a deep generative model combining evolutionary and human population data to estimate variant deleteriousness on a proteome-wide scale (Thanks to the Marks lab at Harvard Medical School, doi: https://doi.org/10.1038/s41588-025-02400-1)
Added hs1(T2T-CHM13 v2.0) reference genome coordinates
Added support for hs1(T2T-CHM13 v2.0) coordinate search in the search_dbNSFP annotation program and the dbNSFP web service

History Releases

dbNSFP v5.3 (October 6, 2025) (README v5.3a, README v5.3c, Change Log)

Rebuilt variant set based on GENCODE release 49 (Ensembl release 115, September 2025), which significantly expanded human protein-coding transcripts using long-read sequencing data.
Added MisFit scores v1.5.1, a novel method to estimate missense fitness effects using a graphical model (thanks to Dr. Yufeng Shen from Columbia University, doi: 10.1038/s41467-025-59937-2).
Added GERP_92_mammals conservation score to replace GERP_91_mammals score.
Added gene constraint measures from gnomAD v4.1: gnomAD_lof.oe, gnomAD_LOEUF, gnomAD_mis.oe, and gnomAD_MOEUF.
Removed allele frequencies for the non-PASS variants in Regeneron Genetics Center Million Exome data.
Fixed a format issue in a small portion of Interpro_domain data.
Other updated datasets include: ClinVar, GWAS Catalog, InterPro, ClinGen, GenCC, Gene Ontology, HGNC, HPO, IntAct, MGI, OMIM, Orphanet, UniProt, Ensembl, RefSeq, and ZFIN.

Rebuilt variant set for all possible nsSNVs and ssSNVs based on latest GENCODE release 48 (Ensembl v114).
Added MutPred2 to replace MutPred v1.2 scores, included in both a and c branch (Thanks to Drs. Timothy Bergquist and Vikas Pejaver from MSMU).
Updated ESM1b scores to include more missense mutations (Thanks to Drs. Po-Yu Lin and Nadav Brandes from NYU).
Added GenCC gene annotations.
Updated following resources to their current versions: ancestral alleles, ClinVar, dbSNP, GWAS catalog, InterPro, ClinGen, Gene Ontology, HGNC, HPO, IntAct, MGI, OMIM, UniProt, RefSeq and ZFIN.

dbNSFP v5.1 (March 21, 2025) (Highlights, README v5.1a, Change Log)

Rebuilt variant set for all possible nsSNVs and ssSNVs based on latest GENCODE release 47 (Ensembl v113).
Added Allele frequencies from All of Us (250k genomes) and Regeneron Genetics Center Million Exome (RGC-ME) (Thanks to Moez Dawood and Dr. Richard Gibbs from HGSC at Baylor College of Medicine).
- Please note RGC-ME allele frequency data is only available in v5.1a for academia use only.
Added dbNSFP_POPMAX_AF/AC etc. based on all population allele frequency columns curated in dbNSFP.
Updated MutationTaster2021 to include more missense mutations (Thanks to Franziska Fritz and Dr. Dominik Seelow from Berlin Institute of Health).
Other updated resources include Clinvar, GWAS catalog, OMIM, Orphanet, ClinGen Dosage Sensitivity, Interpro, HGNC, Uniprot, IntAct, Gene Ontology, MGI, ZFIN, UniParc, RefSeq, MANE, and HPO.
Provided dbNSFP files in a format ready to use with Ensembl Variant Effect Predictor (VEP) (Thanks to Dr. Jamie Allen from EMBL-EBI) and SnpSift.

dbNSFP v5.1.1c (April 24, 2025) (README v5.1.1c)

ClinPred, REVEL and PHACTboost have been added to the dbNSFP commercial branch (Thanks to Drs. Jacek Majewski, Weiva Sieh and Ogün Adebali).

dbNSFP v5.0 (January 1, 2025) README

Fully rebuilt based on GENCODE release 46/Ensembl 112
Transcripts annotations from the MANE project has been added.
Allele frequencies from TOPMed freeze8, and gnomAD exome controls, non-neuro, and non-cancer subsets from v2.1.1 have been added.
Allele frequencies from gnomAD have been updated to v4.1 joint data set (genome+exome).
bStatistic, ancestral alleles, and ClinVar have been updated.
MutationTaster has been updated to MutationTaster2021.
The gene table has also been rebuilt. ClinGen Dosage Sensitivity and Humnan Protein Atlas consensus gene expression levels have been added.
HGNC, Uniprot, IntAct, GWAS catalog, Interpro, Gene Ontology, ConsensusPathDB, HPO, mouse homolog genes, zebrafish homolog genes, HPO, OMIM, Orphanet have been updated.
The egenetics and GNF/Atlas expression, gene interactions and SORVA statistic have been retired.
LRT, FATHMM, fathmm-MKL, fitCons, LINSIGHT, GenoCanyon, EVE, Siphy scores, allele frequencies from ESP, ExAC, UK10K, and GTEx, eQTLGen and Geuvadis eQTLs have been retired.

For versions (1.x - 4.x), please refer to legacy dbNSFP website here.

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