The dbNSFP is an integrated database of functional predictions from multiple algorithms for the comprehensive collection of human non-synonymous SNPs (NSs). Its current version (ver 1.1) is based on CCDS version 20090327 and includes a total of 75,931,005 NSs. It compiles prediction scores from four prediction algorithms (SIFT, Polyphen2, LRT and MutationTaster), two conservation scores (PhyloP and GERP++) and other related information. 

    We welcome developers of functional prediction methods to provide their predictions and scores to the database. Please contact Dr. Liu (xmliu.uth{a}gmail.com) for details. 

    dbNSFP v1.0 can be downloaded from here. A README file is here. More details about the database can be found in our paper. 
    A companion Java program called search_dbNSFP.class can be downloaded from here and used for local queries.
    
    dbNSFP v1.1 added the following entries: rs numbers from UniSNP (a cleaned version of dbSNP build 129), allele frequency recorded in dbSNP, allele frequency reported by 1000 Genomes Project, alternative gene names, descriptive gene name, database cross references (gene IDs of HGNC, MIM, Ensembl and HPRD). The unziped database is 18Gb.
    dbNSFP v1.1 can be downloaded from here. A README file is here. 
    A companion Java program called search_dbNSFP11.class can be downloaded from here and used for local queries.
    

    dbNSFP v1.2 added GERP++ neutral rates and RS scores. It can be downloaded from here (including readme and the corresponding java search program). A README file is here.
    dbNSFP v1.3 added Uniprot ID, accession number and amino acid position based on the Polyphen-2 annotations. Users can now search amino acid change directly referring to a Uniprot ID or accession number. dbNSFP v1.3 can be downloaded from here (including readme and the corresponding java search program). A README file is here.

    Update (Nov. 10, 2011): A bug was found in the conpanion search program for dbNSFP v1.3, which causes invalid search using AA mutations with Uniprot ID or accession number. Please use the updated search program. The search program in the  dbNSFP v1.3 zip file has been updated.

    dbNSFP_light is a light version of dbNSFP, which contains less annotation entries but some additional 9,285,316 NSs that are not in CCDS version 20090327.

    dbNSFP_light v1.0 can be downloaded from here. A README file is here. Scores of PhyloP, SIFT, Polyphen2, LRT and MutationTaster are included but missing data are not imputed. Prediction of LRT and MutationTaster are also included, as well as the omega estimated by LRT. A companion Java program called search_dbNSFP_light.class can be downloaded from here and used for local queries. Mirrors in mainland China: dbNSFP_light v1.0, README file and search_dbNSFP_light.

    dbNSFP_light v1.1 added GERP++ neutral rates and RS scores. It can be downloaded from here (including readme and the corresponding java search program). A README file is here.

    dbNSFP_light v1.2 added Uniprot ID, accession number and amino acid position based on the Polyphen-2 annotations. Users can now search amino acid change directly referring to a Uniprot ID or accession number. dbNSFP_light v1.2 can be downloaded from here (including readme and the corresponding java search program). A README file is here.

    dbNSFP_light v1.3 updated SIFT scores (August, 2011 version) and Polyphen-2 scores (May, 2011 version). SIFT: 7,097,009 scores added, 48,011,111 updated. Polyphen-2: 2,136,757 scores added, 53,712,654 updated. Uniprot ID, accession number and amino acid position based on the Polyphen-2 annotations have been updated too. It can be downloaded from here (including readme and the corresponding java search program). A README file is here.

    NEW (April 11, 2012): The long waited dbNSFP v2.0 is on the horizon now. The new database is rebuilt based on the Gencode release 9 / Ensembl version 64. The default coordinate is hg19, but hg18 is still supported. There will be two parts of the database: one focuses on variant annotation and the other focuses on gene annotation. The variant sub-database is now open for beta test and can be downloaded from here. A README file is here. SIFT, Polyphen-2 and MutationTaster scores are updated. Please note that now all scores are RAW scores, without imputation and transformation. One more conservation score, SiPhy, is added along with other new annotations such as the protein functional domains, the allele frequencies observed in the 1000 Genomes phase 1 data and the NHLBI's Exome Sequencing Project data, etc. Bug reports are very welcome.
    

    If you use dbNSFP or dbNSFP_light, please cite our paper: Liu X, Jian X, and Boerwinkle E. 2011. dbNSFP: a lightweight database of human non-synonymous SNPs and their functional predictions. Human Mutation. 32:894-899.