dbNSFP version 4.9a Release: August 8, 2024 Major sources: Variant determination: Gencode release 29/Ensembl 94, released October, 2018 (hg38) Functional predictions: SIFT ensembl 66, released Jan, 2015 http://provean.jcvi.org/index.php SIFT4G 2.4, released Nov. 1, 2016 http://sift.bii.a-star.edu.sg/sift4g/public//Homo_sapiens/ PROVEAN 1.1 ensembl 66, released Jan, 2015 http://provean.jcvi.org/index.php Polyphen-2 v2.2.2, released Feb, 2012 http://genetics.bwh.harvard.edu/pph2/ LRT, released November, 2009 http://www.genetics.wustl.edu/jflab/lrt_query.html MutationTaster 2, data retrieved in 2015 http://www.mutationtaster.org/ MutationAssessor release 3, http://mutationassessor.org/ FATHMM v2.3, http://fathmm.biocompute.org.uk fathmm-MKL, http://fathmm.biocompute.org.uk/fathmmMKL.htm fathmm-XF, http://fathmm.biocompute.org.uk/fathmm-xf/ CADD v1.7, http://cadd.gs.washington.edu/ VEST v4.0, http://karchinlab.org/apps/appVest.html fitCons v1.01, http://compgen.bscb.cornell.edu/fitCons/ LINSIGHT, http://compgen.cshl.edu/~yihuang/LINSIGHT/ DANN, https://cbcl.ics.uci.edu/public_data/DANN/ MetaSVM and MetaLR, doi: 10.1093/hmg/ddu733 GenoCanyon v1.0.3, http://genocanyon.med.yale.edu/index.html Eigen & Eigen PC v1.1, http://www.columbia.edu/~ii2135/eigen.html M-CAP v1.3, http://bejerano.stanford.edu/MCAP/ REVEL release May 3, 2021, https://sites.google.com/site/revelgenomics/ MutPred v1.2, http://mutpred.mutdb.org/ MVP 1.0, https://github.com/ShenLab/missense MPC release1, ftp://ftp.broadinstitute.org/pub/ExAC_release/release1/regional_missense_constraint/ PrimateAI, https://github.com/Illumina/PrimateAI deogen2, https://deogen2.mutaframe.com/ ALoFT 1.0, http://aloft.gersteinlab.org/ BayesDel v1, http://fengbj-laboratory.org/BayesDel/BayesDel.html ClinPred, https://sites.google.com/site/clinpred/home LIST-S2 Release: 2019_10, https://precomputed.list-s2.msl.ubc.ca/ MetaRNN v1.0, http://www.liulab.science/metarnn.html gMVP, https://github.com/ShenLab/gMVP/ VARITY, http://varity.varianteffect.org/ ESM1b, https://huggingface.co/spaces/ntranoslab/esm_variants/tree/main EVE, https://evemodel.org/ AlphaMissense, https://console.cloud.google.com/storage/browser/dm_alphamissense PHACTboost, https://github.com/CompGenomeLab/PHACTboost MutFormer, https://github.com/WGLab/mutformer MutScore, https://iob-genetic.shinyapps.io/mutscore/ Conservation scores: phyloP100way_vertebrate (hg38) http://hgdownload.soe.ucsc.edu/goldenPath/hg38/phyloP100way/ phyloP470way_mammalian (hg38) https://hgdownload.soe.ucsc.edu/goldenPath/hg38/phyloP470way/ phyloP17way_primate (hg38) http://hgdownload.soe.ucsc.edu/goldenPath/hg38/phyloP17way/ phastCons100way_vertebrate (hg38) http://hgdownload.soe.ucsc.edu/goldenPath/hg38/phastCons100way/ phastCons470way_mammalian (hg38) https://hgdownload.cse.ucsc.edu/goldenpath/hg38/phastCons470way/ phastCons17way_primate (hg38) http://hgdownload.soe.ucsc.edu/goldenPath/hg38/phastCons17way/ GERP++ http://mendel.stanford.edu/SidowLab/downloads/gerp/ GERP_91_mammals https://ftp.ensembl.org/pub/current_compara/conservation_scores/91_mammals.gerp_conservation_score/ SiPhy https://www.broadinstitute.org/mammals-models/29-mammals-project-supplementary-info bStatistic http://cadd.gs.washington.edu/ Other variant annotation sources: Interpro v71 http://www.ebi.ac.uk/interpro/ 1000 Genomes project http://www.1000genomes.org/ ESP http://evs.gs.washington.edu/EVS/ dbSNP b156 (hg38) https://ftp.ncbi.nih.gov/snp/archive/b156/VCF/GCF_000001405.40.gz clinvar release 20240805 (hg38) ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/ ExAC v0.3 http://exac.broadinstitute.org/ gnomAD exome v4.0.0 http://gnomad.broadinstitute.org/downloads gnomAD genome v4.0.0 http://gnomad.broadinstitute.org/downloads ALFA (Allele Frequency Aggregator) release 2 https://www.ncbi.nlm.nih.gov/snp/docs/gsr/alfa/ UK10K COHORT http://www.uk10k.org/studies/cohorts.html Ancestral alleles (hg38) ftp://ftp.ensembl.org/pub/release-93/fasta/ancestral_alleles/homo_sapiens_ancestor_GRCh38.tar.gz Altai Neanderthal genotypes: http://cdna.eva.mpg.de/neandertal/Vindija/VCF/Altai/ Denisova genotypes: http://cdna.eva.mpg.de/neandertal/Vindija/VCF/Denisova/ Vindija33.19 genotypes: http://cdna.eva.mpg.de/neandertal/Vindija/VCF/Vindija33.19/ Chagyrskaya genotype: http://cdna.eva.mpg.de/neandertal/Chagyrskaya/VCF/ GTEx v8 https://www.gtexportal.org/home/datasets Geuvadis https://www.ebi.ac.uk/Tools/geuvadis-das/ eQTLGen 2019-12-23 https://www.eqtlgen.org/phase1.html Other gene annotation sources: HGNC, downloaded on October 21, 2018 Uniprot, Release 2019_01 IntAct, downloaded on November 30, 2018 GWAS catalog, r2018-11-26 egenetics and GNF/Atlas expression data, downloaded from BioMart on Oct. 1, 2013 BioGRID, version 3.5.167 Haploinsufficiency probability data, from doi:10.1371/journal.pgen.1001154 Recessive probability data, from DOI:10.1126/science.1215040 Residual Variation Intolerance Score (RVIS), v3 http://genic-intolerance.org/ Genome-wide haploinsufficiency score (GHIS), from doi: 10.1093/nar/gkv474 ExAC Functional Gene Constraint, from release0.3.1 ExAC CNV gene score, from release0.3.1 GO, downloaded on December 6, 2018 ConsensusPathDB, Release 33 Essential genes, from doi:10.1371/journal.pgen.1003484, doi: 10.1126/science.aac7041, doi: 10.1016/j.cell.2015.11.015, doi: 10.1126/science.aac7557, doi:10.1371/journal.pcbi.1002886 Mouse genes, from Mouse Genome Informatics (MGI), 6.13 Zebrafish genes, from The Zebrafish Information Network (ZFIN), downloaded on December 7,2018 KEGG pathway, from http://www.openbioinformatics.org/gengen/tutorial_calculate_gsea.html BioCarta pathway, from http://www.openbioinformatics.org/gengen/tutorial_calculate_gsea.html GDI, from doi: 10.1073/pnas.1518646112 LoFtool, from DOI:10.1093/bioinformatics/btv602 SORVA, from doi: 10.1101/103218 HIPred, from doi:10.1093/bioinformatics/btx028 HPO, data release 20200608, https://hpo.jax.org/app/download/annotation Files: dbNSFP4.9a_variant.chr<#>.gz - gzipped dbNSFP variant database files by chromosomes dbNSFP4.9_gene.gz - gzipped dbNSFP gene database file dbNSFP4.9_gene.complete.gz - gzipped dbNSFP gene database file with complete interaction columns dbNSFP4.9a.readme.txt - this file search_dbNSFP49a.jar - companion GUI Java program for searching dbNSFP4.9a search_dbNSFP49a.class - companion command-line Java program for searching dbNSFP4.9a LICENSE.txt - the license for using the source code search_dbNSFP49a.readme.pdf - README file for search_dbNSFP48a.class tryhg19.in - an example input file with hg19 genome positions tryhg18.in - an example input file with hg18 genome positions tryhg38.in - an example input file with hg38 genome positions try.vcf - an example of vcf input file Description: The dbNSFP is an integrated database of functional annotations from multiple sources for the comprehensive collection of human non-synonymous SNPs (nsSNVs). Its current version includes a total of 84,013,490 nsSNVs and ssSNVs (splice site SNVs). It compiles prediction scores from 32 prediction algorithms (SIFT, SIFT4G, Polyphen2-HDIV, Polyphen2-HVAR, LRT, MutationTaster2, MutationAssessor, FATHMM, MetaSVM, MetaLR, CADD, VEST4, PROVEAN, FATHMM-MKL coding, FATHMM-XF coding, fitCons, LINSIGHT, DANN, GenoCanyon, Eigen, Eigen-PC, M-CAP, REVEL, MutPred, MVP, MPC, PrimateAI, GEOGEN2, BayesDel, ClinPred, LIST-S2, ALoFT), 9 conservation scores (bStatistic, phyloP100way_vertebrate, phyloP30way_mammal, phyloP17way_primate, phastCons100way_vertebrate, phastCons30way_mammal, phastCons17way_primate, GERP++ and SiPhy) and other function annotations. Since version 2.0, dbNSFP is separated into two parts, dbNSFP_variant and dbNSFP_gene. As their names indicate, the former focuses on variant annotations (including prediction scores and conservation scores), and the latter focuses on gene annotations. Since version 2.6, dbscSNV is added as an attached database, which includes all potential human SNVs within splicing consensus regions (−3 to +8 at the 5’ splice site and −12 to +2 at the 3’ splice site), i.e. scSNVs, and predictions for their potential of altering splicing. Since version 3, two branches of dbNSFP are provided: "a" branch is suitable for academic use, which includes all the resources, and "c" branch is suitable for commercial use, which does not include Polyphen2, VEST, REVEL, CADD, LINSIGHT, GenoCanyon. Columns of dbNSFP_variant: 1 chr: chromosome number 2 pos(1-based): physical position on the chromosome as to hg38 (1-based coordinate). For mitochondrial SNV, this position refers to the rCRS (GenBank: NC_012920). 3 ref: reference nucleotide allele (as on the + strand) 4 alt: alternative nucleotide allele (as on the + strand) 5 aaref: reference amino acid "." if the variant is a splicing site SNP (2bp on each end of an intron) 6 aaalt: alternative amino acid "." if the variant is a splicing site SNP (2bp on each end of an intron) 7 rs_dbSNP: rs number from dbSNP 8 hg19_chr: chromosome as to hg19, "." means missing 9 hg19_pos(1-based): physical position on the chromosome as to hg19 (1-based coordinate). For mitochondrial SNV, this position refers to a YRI sequence (GenBank: AF347015) 10 hg18_chr: chromosome as to hg18, "." means missing 11 hg18_pos(1-based): physical position on the chromosome as to hg18 (1-based coordinate) For mitochondrial SNV, this position refers to a YRI sequence (GenBank: AF347015) 12 aapos: amino acid position as to the protein. "-1" if the variant is a splicing site SNP (2bp on each end of an intron). Multiple entries separated by ";", corresponding to Ensembl_proteinid 13 genename: gene name; if the nsSNV can be assigned to multiple genes, gene names are separated by ";" 14 Ensembl_geneid: Ensembl gene id 15 Ensembl_transcriptid: Ensembl transcript ids (Multiple entries separated by ";") 16 Ensembl_proteinid: Ensembl protein ids Multiple entries separated by ";", corresponding to Ensembl_transcriptids 17 Uniprot_acc: Uniprot accession number matching the Ensembl_proteinid Multiple entries separated by ";". 18 Uniprot_entry: Uniprot entry ID matching the Ensembl_proteinid Multiple entries separated by ";". 19 HGVSc_ANNOVAR: HGVS coding variant presentation from ANNOVAR Multiple entries separated by ";", corresponds to Ensembl_transcriptid 20 HGVSp_ANNOVAR: HGVS protein variant presentation from ANNOVAR Multiple entries separated by ";", corresponds to Ensembl_proteinid 21 HGVSc_snpEff: HGVS coding variant presentation from snpEff Multiple entries separated by ";", corresponds to Ensembl_transcriptid 22 HGVSp_snpEff: HGVS protein variant presentation from snpEff Multiple entries separated by ";", corresponds to Ensembl_proteinid 23 HGVSc_VEP: HGVS coding variant presentation from VEP Multiple entries separated by ";", corresponds to Ensembl_transcriptid 24 HGVSp_VEP: HGVS protein variant presentation from VEP Multiple entries separated by ";", corresponds to Ensembl_proteinid 25 APPRIS: APPRIS annotation for the transcripts matching Ensembl_transcriptid Multiple entries separated by ";". Potential values: principal1, principal2, principal3, principal4, principal5, alternative1, alternative2. See https://useast.ensembl.org/info/genome/genebuild/transcript_quality_tags.html 26 GENCODE_basic: Whether the transcript belongs to GENCODE_basic (5' and 3' complete transcripts). Multiple entries separated by ";", matching Ensembl_transcriptid. See https://useast.ensembl.org/info/genome/genebuild/transcript_quality_tags.html 27 TSL: Transcript Support Level. Multiple entries separated by ";", matching Ensembl_transcriptid. Potential values: 1 to 5, NA. See https://useast.ensembl.org/info/genome/genebuild/transcript_quality_tags.html 28 VEP_canonical: canonical transcript used in Ensembl. Multiple entries separated by ";", matching Ensembl_transcriptid. See https://useast.ensembl.org/Help/Glossary?id=521 29 cds_strand: coding sequence (CDS) strand (+ or -) 30 refcodon: reference codon 31 codonpos: position on the codon (1, 2 or 3) 32 codon_degeneracy: degenerate type (0, 2 or 3) 33 Ancestral_allele: ancestral allele based on 8 primates EPO. Ancestral alleles by Ensembl 84. The following comes from its original README file: ACTG - high-confidence call, ancestral state supported by the other two sequences actg - low-confidence call, ancestral state supported by one sequence only N - failure, the ancestral state is not supported by any other sequence - - the extant species contains an insertion at this position . - no coverage in the alignment 34 AltaiNeandertal: genotype of a deep sequenced Altai Neanderthal 35 Denisova: genotype of a deep sequenced Denisova 36 VindijiaNeandertal: genotype of a deep sequenced Vindijia Neandertal 37 ChagyrskayaNeandertal: genotype of a deep sequenced Chagyrskaya Neandertal 38 SIFT_score: SIFT score (SIFTori). Scores range from 0 to 1. The smaller the score the more likely the SNP has damaging effect. Multiple scores separated by ";", corresponding to Ensembl_proteinid. 39 SIFT_converted_rankscore: SIFTori scores were first converted to SIFTnew=1-SIFTori, then ranked among all SIFTnew scores in dbNSFP. The rankscore is the ratio of the rank the SIFTnew score over the total number of SIFTnew scores in dbNSFP. If there are multiple scores, only the most damaging (largest) rankscore is presented. The rankscores range from 0.00964 to 0.91255. 40 SIFT_pred: If SIFTori is smaller than 0.05 (rankscore>0.39575) the corresponding nsSNV is predicted as "D(amaging)"; otherwise it is predicted as "T(olerated)". Multiple predictions separated by ";" 41 SIFT4G_score: SIFT 4G score (SIFT4G). Scores range from 0 to 1. The smaller the score the more likely the SNP has damaging effect. Multiple scores separated by ",", corresponding to Ensembl_transcriptid 42 SIFT4G_converted_rankscore: SIFT4G scores were first converted to SIFT4Gnew=1-SIFT4G, then ranked among all SIFT4Gnew scores in dbNSFP. The rankscore is the ratio of the rank the SIFT4Gnew score over the total number of SIFT4Gnew scores in dbNSFP. If there are multiple scores, only the most damaging (largest) rankscore is presented. 43 SIFT4G_pred: If SIFT4G is < 0.05 the corresponding nsSNV is predicted as "D(amaging)"; otherwise it is predicted as "T(olerated)". Multiple scores separated by ",", corresponding to Ensembl_transcriptid 44 Polyphen2_HDIV_score: Polyphen2 score based on HumDiv, i.e. hdiv_prob. The score ranges from 0 to 1. Multiple entries separated by ";", corresponding to Uniprot_acc. 45 Polyphen2_HDIV_rankscore: Polyphen2 HDIV scores were first ranked among all HDIV scores in dbNSFP. The rankscore is the ratio of the rank the score over the total number of the scores in dbNSFP. If there are multiple scores, only the most damaging (largest) rankscore is presented. The scores range from 0.03061 to 0.91137. 46 Polyphen2_HDIV_pred: Polyphen2 prediction based on HumDiv, "D" ("probably damaging", HDIV score in [0.957,1] or rankscore in [0.55859,0.91137]), "P" ("possibly damaging", HDIV score in [0.454,0.956] or rankscore in [0.37043,0.55681]) and "B" ("benign", HDIV score in [0,0.452] or rankscore in [0.03061,0.36974]). Score cutoff for binary classification is 0.5 for HDIV score or 0.38028 for rankscore, i.e. the prediction is "neutral" if the HDIV score is smaller than 0.5 (rankscore is smaller than 0.38028), and "deleterious" if the HDIV score is larger than 0.5 (rankscore is larger than 0.38028). Multiple entries are separated by ";", corresponding to Uniprot_acc. 47 Polyphen2_HVAR_score: Polyphen2 score based on HumVar, i.e. hvar_prob. The score ranges from 0 to 1. Multiple entries separated by ";", corresponding to Uniprot_acc. 48 Polyphen2_HVAR_rankscore: Polyphen2 HVAR scores were first ranked among all HVAR scores in dbNSFP. The rankscore is the ratio of the rank the score over the total number of the scores in dbNSFP. If there are multiple scores, only the most damaging (largest) rankscore is presented. The scores range from 0.01493 to 0.97581. 49 Polyphen2_HVAR_pred: Polyphen2 prediction based on HumVar, "D" ("probably damaging", HVAR score in [0.909,1] or rankscore in [0.65694,0.97581]), "P" ("possibly damaging", HVAR in [0.447,0.908] or rankscore in [0.47121,0.65622]) and "B" ("benign", HVAR score in [0,0.446] or rankscore in [0.01493,0.47076]). Score cutoff for binary classification is 0.5 for HVAR score or 0.48762 for rankscore, i.e. the prediction is "neutral" if the HVAR score is smaller than 0.5 (rankscore is smaller than 0.48762), and "deleterious" if the HVAR score is larger than 0.5 (rankscore is larger than 0.48762). Multiple entries are separated by ";", corresponding to Uniprot_acc. 50 LRT_score: The original LRT two-sided p-value (LRTori), ranges from 0 to 1. 51 LRT_converted_rankscore: LRTori scores were first converted as LRTnew=1-LRTori*0.5 if Omega<1, or LRTnew=LRTori*0.5 if Omega>=1. Then LRTnew scores were ranked among all LRTnew scores in dbNSFP. The rankscore is the ratio of the rank over the total number of the scores in dbNSFP. The scores range from 0.00162 to 0.8433. 52 LRT_pred: LRT prediction, D(eleterious), N(eutral) or U(nknown), which is not solely determined by the score. 53 LRT_Omega: estimated nonsynonymous-to-synonymous-rate ratio (Omega, reported by LRT) 54 MutationTaster_score: MutationTaster p-value (MTori), ranges from 0 to 1. Multiple scores are separated by ";". Information on corresponding transcript(s) can be found by querying http://www.mutationtaster.org/ChrPos.html 55 MutationTaster_converted_rankscore: The MTori scores were first converted. If the prediction is "A" or "D" MTnew=MTori; if the prediction is "N" or "P", MTnew=1-MTori. Then MTnew scores were ranked among all MTnew scores in dbNSFP. If there are multiple scores of a SNV, only the largest MTnew was used in ranking. The rankscore is the ratio of the rank of the score over the total number of MTnew scores in dbNSFP. The scores range from 0.08979 to 0.81001. 56 MutationTaster_pred: MutationTaster prediction, "A" ("disease_causing_automatic"), "D" ("disease_causing"), "N" ("polymorphism") or "P" ("polymorphism_automatic"). The score cutoff between "D" and "N" is 0.5 for MTnew and 0.31733 for the rankscore. 57 MutationTaster_model: MutationTaster prediction models. 58 MutationTaster_AAE: MutationTaster predicted amino acid change. 59 MutationAssessor_score: MutationAssessor functional impact combined score (MAori). The score ranges from -5.17 to 6.49 in dbNSFP. Multiple entries are separated by ";", corresponding to Uniprot_entry. 60 MutationAssessor_rankscore: MAori scores were ranked among all MAori scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of MAori scores in dbNSFP. The scores range from 0 to 1. 61 MutationAssessor_pred: MutationAssessor's functional impact of a variant - predicted functional, i.e. high ("H") or medium ("M"), or predicted non-functional, i.e. low ("L") or neutral ("N"). The MAori score cutoffs between "H" and "M", "M" and "L", and "L" and "N", are 3.5, 1.935 and 0.8, respectively. The rankscore cutoffs between "H" and "M", "M" and "L", and "L" and "N", are 0.9307, 0.52043 and 0.19675, respectively. 62 FATHMM_score: FATHMM default score (weighted for human inherited-disease mutations with Disease Ontology) (FATHMMori). Scores range from -16.13 to 10.64. The smaller the score the more likely the SNP has damaging effect. Multiple scores separated by ";", corresponding to Ensembl_proteinid. 63 FATHMM_converted_rankscore: FATHMMori scores were first converted to FATHMMnew=1-(FATHMMori+16.13)/26.77, then ranked among all FATHMMnew scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of FATHMMnew scores in dbNSFP. If there are multiple scores, only the most damaging (largest) rankscore is presented. The scores range from 0 to 1. 64 FATHMM_pred: If a FATHMMori score is <=-1.5 (or rankscore >=0.81332) the corresponding nsSNV is predicted as "D(AMAGING)"; otherwise it is predicted as "T(OLERATED)". Multiple predictions separated by ";", corresponding to Ensembl_proteinid. 65 PROVEAN_score: PROVEAN score (PROVEANori). Scores range from -14 to 14. The smaller the score the more likely the SNP has damaging effect. Multiple scores separated by ";", corresponding to Ensembl_proteinid. 66 PROVEAN_converted_rankscore: PROVEANori were first converted to PROVEANnew=1-(PROVEANori+14)/28, then ranked among all PROVEANnew scores in dbNSFP. The rankscore is the ratio of the rank the PROVEANnew score over the total number of PROVEANnew scores in dbNSFP. If there are multiple scores, only the most damaging (largest) rankscore is presented. The scores range from 0 to 1. 67 PROVEAN_pred: If PROVEANori <= -2.5 (rankscore>=0.54382) the corresponding nsSNV is predicted as "D(amaging)"; otherwise it is predicted as "N(eutral)". Multiple predictions separated by ";", corresponding to Ensembl_proteinid. 68 VEST4_score: VEST 4.0 score. Score ranges from 0 to 1. The larger the score the more likely the mutation may cause functional change. Multiple scores separated by ";", corresponding to Ensembl_transcriptid. Please note this score is free for non-commercial use. For more details please refer to http://wiki.chasmsoftware.org/index.php/SoftwareLicense. Commercial users should contact the Johns Hopkins Technology Transfer office. 69 VEST4_rankscore: VEST4 scores were ranked among all VEST4 scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of VEST4 scores in dbNSFP. In case there are multiple scores for the same variant, the largest score (most damaging) is presented. The scores range from 0 to 1. Please note VEST score is free for non-commercial use. For more details please refer to http://wiki.chasmsoftware.org/index.php/SoftwareLicense. Commercial users should contact the Johns Hopkins Technology Transfer office. 70 MetaSVM_score: Our support vector machine (SVM) based ensemble prediction score, which incorporated 10 scores (SIFT, PolyPhen-2 HDIV, PolyPhen-2 HVAR, GERP++, MutationTaster, Mutation Assessor, FATHMM, LRT, SiPhy, PhyloP) and the maximum frequency observed in the 1000 genomes populations. Larger value means the SNV is more likely to be damaging. Scores range from -2 to 3 in dbNSFP. 71 MetaSVM_rankscore: MetaSVM scores were ranked among all MetaSVM scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of MetaSVM scores in dbNSFP. The scores range from 0 to 1. 72 MetaSVM_pred: Prediction of our SVM based ensemble prediction score,"T(olerated)" or "D(amaging)". The score cutoff between "D" and "T" is 0. The rankscore cutoff between "D" and "T" is 0.82257. 73 MetaLR_score: Our logistic regression (LR) based ensemble prediction score, which incorporated 10 scores (SIFT, PolyPhen-2 HDIV, PolyPhen-2 HVAR, GERP++, MutationTaster, Mutation Assessor, FATHMM, LRT, SiPhy, PhyloP) and the maximum frequency observed in the 1000 genomes populations. Larger value means the SNV is more likely to be damaging. Scores range from 0 to 1. 74 MetaLR_rankscore: MetaLR scores were ranked among all MetaLR scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of MetaLR scores in dbNSFP. The scores range from 0 to 1. 75 MetaLR_pred: Prediction of our MetaLR based ensemble prediction score,"T(olerated)" or "D(amaging)". The score cutoff between "D" and "T" is 0.5. The rankscore cutoff between "D" and "T" is 0.81101. 76 Reliability_index: Number of observed component scores (except the maximum frequency in the 1000 genomes populations) for MetaSVM and MetaLR. Ranges from 1 to 10. As MetaSVM and MetaLR scores are calculated based on imputed data, the less missing component scores, the higher the reliability of the scores and predictions. 77 MetaRNN_score: Our recurrent neural network (RNN) based ensemble prediction score, which incorporated 16 scores (SIFT, Polyphen2_HDIV, Polyphen2_HVAR, MutationAssessor, PROVEAN, VEST4, M-CAP, REVEL, MutPred, MVP, PrimateAI, DEOGEN2, CADD, fathmm-XF, Eigen and GenoCanyon), 8 conservation scores (GERP, phyloP100way_vertebrate, phyloP30way_mammalian, phyloP17way_primate, phastCons100way_vertebrate, phastCons30way_mammalian, phastCons17way_primate and SiPhy), and allele frequency information from the 1000 Genomes Project (1000GP), ExAC, and gnomAD. Larger value means the SNV is more likely to be damaging. Scores range from 0 to 1. 78 MetaRNN_rankscore: MetaRNN scores were ranked among all MetaRNN scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of MetaRNN scores in dbNSFP. The scores range from 0 to 1. 79 MetaRNN_pred: Prediction of our MetaRNN based ensemble prediction score,"T(olerated)" or "D(amaging)". The score cutoff between "D" and "T" is 0.5. The rankscore cutoff between "D" and "T" is 0.6149. 80 M-CAP_score: M-CAP is hybrid ensemble score (details in DOI: 10.1038/ng.3703). Scores range from 0 to 1. The larger the score the more likely the SNP has damaging effect. 81 M-CAP_rankscore: M-CAP scores were ranked among all M-CAP scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of M-CAP scores in dbNSFP. 82 M-CAP_pred: Prediction of M-CAP score based on the authors' recommendation, "T(olerated)" or "D(amaging)". The score cutoff between "D" and "T" is 0.025. 83 REVEL_score: REVEL is an ensemble score based on 13 individual scores for predicting the pathogenicity of missense variants. Scores range from 0 to 1. The larger the score the more likely the SNP has damaging effect. "REVEL scores are freely available for non-commercial use. For other uses, please contact Weiva Sieh" (weiva.sieh@mssm.edu) Multiple entries are separated by ";", corresponding to Ensembl_transcriptid. 84 REVEL_rankscore: REVEL scores were ranked among all REVEL scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of REVEL scores in dbNSFP. 85 MutPred_score: General MutPred score. Scores range from 0 to 1. The larger the score the more likely the SNP has damaging effect. 86 MutPred_rankscore: MutPred scores were ranked among all MutPred scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of MutPred scores in dbNSFP. 87 MutPred_protID: UniProt accession or Ensembl transcript ID used for MutPred_score calculation. 88 MutPred_AAchange: Amino acid change used for MutPred_score calculation. 89 MutPred_Top5features: Top 5 features (molecular mechanisms of disease) as predicted by MutPred with p values. MutPred_score > 0.5 and p < 0.05 are referred to as actionable hypotheses. MutPred_score > 0.75 and p < 0.05 are referred to as confident hypotheses. MutPred_score > 0.75 and p < 0.01 are referred to as very confident hypotheses. 90 MVP_score: A pathogenicity prediction score for missense variants using deep learning approach. The range of MVP score is from 0 to 1. The larger the score, the more likely the variant is pathogenic. The authors suggest thresholds of 0.7 and 0.75 for separating damaging vs tolerant variants in constrained genes (ExAC pLI >=0.5) and non-constrained genes (ExAC pLI<0.5), respectively. Details see doi: http://dx.doi.org/10.1101/259390 Multiple entries are separated by ";", corresponding to Ensembl_transcriptid. 91 MVP_rankscore: MVP scores were ranked among all MVP scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of MVP scores in dbNSFP. 92 gMVP_score: A pathogenicity prediction score for missense variants using a graph attention neural network model. The range of gMVP score is from 0 to 1. The larger the score, the more likely the variant is pathogenic. Details see doi: https://www.nature.com/articles/s42256-022-00561-w Multiple entries are separated by ";", corresponding to Ensembl_transcriptid. 93 gMVP_rankscore: gMVP scores were ranked among all gMVP scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of gMVP scores in dbNSFP. 94 MPC_score: A deleteriousness prediction score for missense variants based on regional missense constraint. The range of MPC score is 0 to 5. The larger the score, the more likely the variant is pathogenic. Details see doi: http://dx.doi.org/10.1101/148353. Multiple entries are separated by ";", corresponding to Ensembl_transcriptid. 95 MPC_rankscore: MPC scores were ranked among all MPC scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of MPC scores in dbNSFP. 96 PrimateAI_score: A pathogenicity prediction score for missense variants based on common variants of non-human primate species using a deep neural network. The range of PrimateAI score is 0 to 1. The larger the score, the more likely the variant is pathogenic. The authors suggest a threshold of 0.803 for separating damaging vs tolerant variants. Details see https://doi.org/10.1038/s41588-018-0167-z 97 PrimateAI_rankscore: PrimateAI scores were ranked among all PrimateAI scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of PrimateAI scores in dbNSFP. 98 PrimateAI_pred: Prediction of PrimateAI score based on the authors' recommendation, "T(olerated)" or "D(amaging)". The score cutoff between "D" and "T" is 0.803. 99 DEOGEN2_score: A deleteriousness prediction score "which incorporates heterogeneous information about the molecular effects of the variants, the domains involved, the relevance of the gene and the interactions in which it participates". It ranges from 0 to 1. The larger the score, the more likely the variant is deleterious. The authors suggest a threshold of 0.5 for separating damaging vs tolerant variants. 100 DEOGEN2_rankscore: DEOGEN2 scores were ranked among all DEOGEN2 scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of DEOGEN2 scores in dbNSFP. 101 DEOGEN2_pred: Prediction of DEOGEN2 score based on the authors' recommendation, "T(olerated)" or "D(amaging)". The score cutoff between "D" and "T" is 0.5. 102 BayesDel_addAF_score: A deleteriousness preidction meta-score for SNVs and indels with inclusion of MaxAF. See https://doi.org/10.1002/humu.23158 for details. The range of the score in dbNSFP is from -1.11707 to 0.750927. The higher the score, the more likely the variant is pathogenic. The author suggested cutoff between deleterious ("D") and tolerated ("T") is 0.0692655. 103 BayesDel_addAF_rankscore: BayesDel_addAF scores were ranked among all BayesDel_addAF scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of BayesDel_addAF scores in dbNSFP. 104 BayesDel_addAF_pred: Prediction of BayesDel_addAF score based on the authors' recommendation, "T(olerated)" or "D(amaging)". The score cutoff between "D" and "T" is 0.0692655. 105 BayesDel_noAF_score: A deleteriousness preidction meta-score for SNVs and indels without inclusion of MaxAF. See https://doi.org/10.1002/humu.23158 for details. The range of the score in dbNSFP is from -1.31914 to 0.840878. The higher the score, the more likely the variant is pathogenic. The author suggested cutoff between deleterious ("D") and tolerated ("T") is -0.0570105. 106 BayesDel_noAF_rankscore: BayesDel_noAF scores were ranked among all BayesDel_noAF scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of BayesDel_noAF scores in dbNSFP. 107 BayesDel_noAF_pred: Prediction of BayesDel_noAF score based on the authors' recommendation, "T(olerated)" or "D(amaging)". The score cutoff between "D" and "T" is -0.0570105. 108 ClinPred_score: A deleteriousness preidction meta-score for nonsynonymous SNVs. See https://doi.org/10.1016/j.ajhg.2018.08.005. for details. The range of the score in dbNSFP is from 0 to 1. The higher the score, the more likely the variant is pathogenic. The author suggested cutoff between deleterious ("D") and tolerated ("T") is 0.5. 109 ClinPred_rankscore: ClinPred scores were ranked among all ClinPred scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of ClinPred scores in dbNSFP. 110 ClinPred_pred: Prediction of ClinPred score based on the authors' recommendation, "T(olerated)" or "D(amaging)". The score cutoff between "D" and "T" is 0.5. 111 LIST-S2_score: A deleteriousness preidction score for nonsynonymous SNVs. See https://doi.org/10.1093/nar/gkaa288. for details. The range of the score in dbNSFP is from 0 to 1. The higher the score, the more likely the variant is pathogenic. The author suggested cutoff between deleterious ("D") and tolerated ("T") is 0.85. 112 LIST-S2_rankscore: LIST-S2 scores were ranked among all LIST-S2 scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of LIST-S2 scores in dbNSFP. 113 LIST-S2_pred: Prediction of LIST-S2 score based on the authors' recommendation, "T(olerated)" or "D(amaging)". The score cutoff between "D" and "T" is 0.85. 114 VARITY_R_score: VARITY_R scores are pathogenicity prediction scores for rare human missense variants. The range of VARITY_R score is from 0 to 1. The larger the score, the more likely the variant is pathogenic. Details see doi: https://doi.org/10.1016/j.ajhg.2021.08.012 115 VARITY_R_rankscore: VARITY_R scores were ranked among all VARITY_R scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of VARITY_R scores in dbNSFP. 116 VARITY_ER_score: VARITY_ER scores are pathogenicity prediction scores for extreme rare human missense variants. The range of VARITY_ER score is from 0 to 1. The larger the score, the more likely the variant is pathogenic. Details see doi: https://doi.org/10.1016/j.ajhg.2021.08.012 117 VARITY_ER_rankscore: VARITY_ER scores were ranked among all VARITY_ER scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of VARITY_ER scores in dbNSFP. 118 VARITY_R_LOO_score: "Same as VARITY_R except the prediction on the variants used for training was made using Leave-One-Variant out." Details see doi: https://doi.org/10.1016/j.ajhg.2021.08.012 119 VARITY_R_LOO_rankscore: VARITY_R_LOO scores were ranked among all VARITY_R_LOO scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of VARITY_R_LOO scores in dbNSFP. 120 VARITY_ER_LOO_score: "Same as VARITY_ER except the prediction on the variants used for training was made using Leave-One-Variant out." Details see https://doi.org/10.1016/j.ajhg.2021.08.012 121 VARITY_ER_LOO_rankscore: VARITY_ER_LOO scores were ranked among all VARITY_ER_LOO scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of VARITY_ER_LOO scores in dbNSFP. 122 ESM1b_score: ESM1b scores are log-likelihood ratio (LLR) scores for predicting the pathogenic effects of coding variants based on a 650-million-parameter protein language model, ESM1b. The range of ESM1b score in dbNSFP is from -24.538 to 6.937. The smaller the score, the more likely the variant is pathogenic. Details see doi: https://doi.org/10.1038/s41588-023-01465-0 123 ESM1b_rankscore: ESM1b scores were firstly negated (i.e., -ESM1b_score), then ranked among all -ESM1b_score scores in dbNSFP. The rankscore is the ratio of the rank of the -ESM1b_score over the total number of scores in dbNSFP. 124 ESM1b_pred: The authors do not recommend a threshold for separating deleterious (D) variants versus tolerated (T) variants. This prediction is based on the threshold of -7.5 described in their paper that yields a true-positive rate of 81% and a true-negative rate of 82% in their ClinVar and HGMD test datasets. 125 EVE_score: EVE is a unsupervised model designed to predict the clinical relevance of human single amino acid variants by examining the sequences of various organisms throughout evolutionary history. The EVE score ranges from 0 to 1. The larger the score, the more likely the variant is pathogenic. Detals see https://doi.org/10.1038/s41586-021-04043-8. 126 EVE_rankscore: EVE scores were ranked among all EVE scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of EVE scores in dbNSFP. 127 EVE_Class10_pred: The EVE classification (B)enign, (U)ncertain, or (P)athogenic when setting 10% as uncertain in a Gaussian mixture model. 128 EVE_Class20_pred: The EVE classification (B)enign, (U)ncertain, or (P)athogenic when setting 20% as uncertain in a Gaussian mixture model. 129 EVE_Class25_pred: The EVE classification (B)enign, (U)ncertain, or (P)athogenic when setting 25% as uncertain in a Gaussian mixture model. 130 EVE_Class30_pred: The EVE classification (B)enign, (U)ncertain, or (P)athogenic when setting 30% as uncertain in a Gaussian mixture model. 131 EVE_Class40_pred: The EVE classification (B)enign, (U)ncertain, or (P)athogenic when setting 40% as uncertain in a Gaussian mixture model. 132 EVE_Class50_pred: The EVE classification (B)enign, (U)ncertain, or (P)athogenic when setting 50% as uncertain in a Gaussian mixture model. 133 EVE_Class60_pred: The EVE classification (B)enign, (U)ncertain, or (P)athogenic when setting 60% as uncertain in a Gaussian mixture model. 134 EVE_Class70_pred: The EVE classification (B)enign, (U)ncertain, or (P)athogenic when setting 70% as uncertain in a Gaussian mixture model. 135 EVE_Class75_pred: The EVE classification (B)enign, (U)ncertain, or (P)athogenic when setting 75% as uncertain in a Gaussian mixture model. 136 EVE_Class80_pred: The EVE classification (B)enign, (U)ncertain, or (P)athogenic when setting 80% as uncertain in a Gaussian mixture model. 137 EVE_Class90_pred: The EVE classification (B)enign, (U)ncertain, or (P)athogenic when setting 90% as uncertain in a Gaussian mixture model. 138 AlphaMissense_score: AlphaMissense is a unsupervised model for predicting the pathogenicity of human missense variants by incorporating structural context of an AlphaFold-derived system. The AlphaMissense score ranges from 0 to 1. The larger the score, the more likely the variant is pathogenic. Details see https://doi.org/10.1126/science.adg7492. License information: Copyright (2023) DeepMind Technologies Limited. All materials are licensed under the Creative Commons Attribution 4.0 International License (CC-BY) (the “License”). You may obtain a copy of the License at: https://creativecommons.org/licenses/by/4.0/legalcode. 139 AlphaMissense_rankscore: AlphaMissense scores were ranked among all AlphaMissense scores in dbNSFP. The rankscore is the ratio of the rank of the AlphaMissense_score over the total number of scores in dbNSFP. 140 AlphaMissense_pred: The AlphaMissense classification of likely (B)enign, (A)mbiguous, or likely (P)athogenic with 90% expected precision estimated from ClinVar for likely benign and likely pathogenic classes. 141 PHACTboost_score: "PHACTboost is a gradiatent boosting tree based classifier that combines PHACT scores with information from multiple sequence alignment, phylogenetic trees, and ancestral reconstruction." The range of the score is from 0 to 1, the larger the score the more likely the variant is pathegenic. Details see https://doi.org/10.1093/molbev/msae136. The authors recommend to use 0.62 as the cutoff for binary prediction (personal communication). 142 PHACTboost_rankscore: PHACTboost scores were ranked among all PHACTboost scores in dbNSFP. The rankscore is the ratio of the rank of the PHACTboost_score over the total number of scores in dbNSFP. 143 MutFormer_score: "MutFormer is an application of the BERT (Bidirectional Encoder Representations from Transformers) NLP (Natural Language Processing) model with an added adaptive vocabulary to protein context, for the purpose of predicting the effect of missense mutations on protein function." The range of the score is from 0 to 1, the larger the score the more likely the variant is pathegenic. Details see https://doi.org/10.1016/j.xinn.2023.100487. The authors recommend to use 0.8838 as the cutoff for binary prediction (personal communication). 144 MutFormer_rankscore: MutFormer scores were ranked among all MutFormer scores in dbNSFP. The rankscore is the ratio of the rank of the MutFormer_score over the total number of scores in dbNSFP. 145 MutScore_score: MutScore is an ensemble score which integerate multiple unsupervised scores for DNA substitutions with additional positional clustering information. The range of the score is from 0 to 1, the larger the score the more likely the variant is pathegenic. Details see https://doi.org/10.1016/j.ajhg.2022.01.006. The authors recommend to use 0.5 as the cutoff for binary prediction (personal communication). 146 MutScore_rankscore: MutScore scores were ranked among all MutScore scores in dbNSFP. The rankscore is the ratio of the rank of the MutScore_score over the total number of scores in dbNSFP. 147 Aloft_Fraction_transcripts_affected: the fraction of the transcripts of the gene affected i.e. No. of transcripts affected by the SNP/Total no. of protein_coding transcripts for the gene multiple values separated by ";", corresponding to Ensembl_proteinid. 148 Aloft_prob_Tolerant: Probability of the SNP being classified as benign by ALoFT multiple values separated by ";", corresponding to Ensembl_proteinid. 149 Aloft_prob_Recessive: Probability of the SNP being classified as recessive disease-causing by ALoFT multiple values separated by ";", corresponding to Ensembl_proteinid. 150 Aloft_prob_Dominant: Probability of the SNP being classified as dominant disease-causing by ALoFT multiple values separated by ";", corresponding to Ensembl_proteinid. 151 Aloft_pred: final classification predicted by ALoFT; values can be Tolerant, Recessive or Dominant multiple values separated by ";", corresponding to Ensembl_proteinid. 152 Aloft_Confidence: Confidence level of Aloft_pred; values can be "High Confidence" (p < 0.05) or "Low Confidence" (p > 0.05) multiple values separated by ";", corresponding to Ensembl_proteinid. 153 CADD_raw: CADD raw score for functional prediction of a SNP. Please refer to Kircher et al. (2014) Nature Genetics 46(3):310-5 for details. The larger the score the more likely the SNP has damaging effect. Scores range from -28.377575 to 25.511592 in dbNSFP. Please note the following copyright statement for CADD: "CADD scores (http://cadd.gs.washington.edu/) are Copyright 2013 University of Washington and Hudson-Alpha Institute for Biotechnology (all rights reserved) but are freely available for all academic, non-commercial applications. For commercial licensing information contact Jennifer McCullar (mccullaj@uw.edu)." 154 CADD_raw_rankscore: CADD raw scores were ranked among all CADD raw scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of CADD raw scores in dbNSFP. Please note the following copyright statement for CADD: "CADD scores (http://cadd.gs.washington.edu/) are Copyright 2013 University of Washington and Hudson-Alpha Institute for Biotechnology (all rights reserved) but are freely available for all academic, non-commercial applications. For commercial licensing information contact Jennifer McCullar (mccullaj@uw.edu)." 155 CADD_phred: CADD phred-like score. This is phred-like rank score based on whole genome CADD raw scores. Please refer to Kircher et al. (2014) Nature Genetics 46(3):310-5 for details. The larger the score the more likely the SNP has damaging effect. Please note the following copyright statement for CADD: "CADD scores (http://cadd.gs.washington.edu/) are Copyright 2013 University of Washington and Hudson-Alpha Institute for Biotechnology (all rights reserved) but are freely available for all academic, non-commercial applications. For commercial licensing information contact Jennifer McCullar (mccullaj@uw.edu)." 156 CADD_raw_hg19: CADD raw score for functional prediction of a SNP using the hg19 model. Please refer to Kircher et al. (2014) Nature Genetics 46(3):310-5 for details. The larger the score the more likely the SNP has damaging effect. Scores range from -9.777566 to 30.05914 in dbNSFP. Please note the following copyright statement for CADD: "CADD scores (http://cadd.gs.washington.edu/) are Copyright 2013 University of Washington and Hudson-Alpha Institute for Biotechnology (all rights reserved) but are freely available for all academic, non-commercial applications. For commercial licensing information contact Jennifer McCullar (mccullaj@uw.edu)." 157 CADD_raw_rankscore_hg19: CADD raw scores were ranked among all CADD_raw_hg19 in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of CADD raw scores in dbNSFP. Please note the following copyright statement for CADD: "CADD scores (http://cadd.gs.washington.edu/) are Copyright 2013 University of Washington and Hudson-Alpha Institute for Biotechnology (all rights reserved) but are freely available for all academic, non-commercial applications. For commercial licensing information contact Jennifer McCullar (mccullaj@uw.edu)." 158 CADD_phred_hg19: CADD phred-like score using the hg19 model. This is phred-like rank score based on whole genome CADD raw scores. Please refer to Kircher et al. (2014) Nature Genetics 46(3):310-5 for details. The larger the score the more likely the SNP has damaging effect. Please note the following copyright statement for CADD: "CADD scores (http://cadd.gs.washington.edu/) are Copyright 2013 University of Washington and Hudson-Alpha Institute for Biotechnology (all rights reserved) but are freely available for all academic, non-commercial applications. For commercial licensing information contact Jennifer McCullar (mccullaj@uw.edu)." 159 DANN_score: DANN is a functional prediction score retrained based on the training data of CADD using deep neural network. Scores range from 0 to 1. A larger number indicate a higher probability to be damaging. More information of this score can be found in doi: 10.1093/bioinformatics/btu703. 160 DANN_rankscore: DANN scores were ranked among all DANN scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of DANN scores in dbNSFP. 161 fathmm-MKL_coding_score: fathmm-MKL p-values. Scores range from 0 to 1. SNVs with scores >0.5 are predicted to be deleterious, and those <0.5 are predicted to be neutral or benign. Scores close to 0 or 1 are with the highest-confidence. Coding scores are trained using 10 groups of features. More details of the score can be found in doi: 10.1093/bioinformatics/btv009. 162 fathmm-MKL_coding_rankscore: fathmm-MKL coding scores were ranked among all fathmm-MKL coding scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of fathmm-MKL coding scores in dbNSFP. 163 fathmm-MKL_coding_pred: If a fathmm-MKL_coding_score is >0.5 (or rankscore >0.28317) the corresponding nsSNV is predicted as "D(AMAGING)"; otherwise it is predicted as "N(EUTRAL)". 164 fathmm-MKL_coding_group: the groups of features (labeled A-J) used to obtained the score. More details can be found in doi: 10.1093/bioinformatics/btv009. 165 fathmm-XF_coding_score: fathmm-XF p-values. Scores range from 0 to 1. SNVs with scores >0.5 are predicted to be deleterious, and those <0.5 are predicted to be neutral or benign. Scores close to 0 or 1 are with the highest-confidence. Coding scores are trained using 10 groups of features. More details of the score can be found in doi: 10.1093/bioinformatics/btx536. 166 fathmm-XF_coding_rankscore: fathmm-XF coding scores were ranked among all fathmm-XF coding scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of fathmm-XF coding scores in dbNSFP. 167 fathmm-XF_coding_pred: If a fathmm-XF_coding_score is >0.5, the corresponding nsSNV is predicted as "D(AMAGING)"; otherwise it is predicted as "N(EUTRAL)". 168 Eigen-raw_coding: Eigen score for coding SNVs. A functional prediction score based on conservation, allele frequencies, and deleteriousness prediction using an unsupervised learning method (doi: 10.1038/ng.3477). 169 Eigen-raw_coding_rankscore: Eigen-raw scores were ranked among all Eigen-raw scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of Eigen-raw scores in dbNSFP. 170 Eigen-phred_coding: Eigen score in phred scale. 171 Eigen-PC-raw_coding: Eigen PC score for genome-wide SNVs. A functional prediction score based on conservation, allele frequencies, deleteriousness prediction (for missense SNVs) and epigenomic signals (for synonymous and non-coding SNVs) using an unsupervised learning method (doi: 10.1038/ng.3477). 172 Eigen-PC-raw_coding_rankscore: Eigen-PC-raw scores were ranked among all Eigen-PC-raw scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of Eigen-PC-raw scores in dbNSFP. 173 Eigen-PC-phred_coding: Eigen PC score in phred scale. 174 GenoCanyon_score: A functional prediction score based on conservation and biochemical annotations using an unsupervised statistical learning. (doi:10.1038/srep10576) 175 GenoCanyon_rankscore: GenoCanyon_score scores were ranked among all integrated fitCons scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of GenoCanyon_score scores in dbNSFP. 176 integrated_fitCons_score: fitCons score predicts the fraction of genomic positions belonging to a specific function class (defined by epigenomic "fingerprint") that are under selective pressure. Scores range from 0 to 1, with a larger score indicating a higher proportion of nucleic sites of the functional class the genomic position belong to are under selective pressure, therefore more likely to be functional important. Integrated (i6) scores are integrated across three cell types (GM12878, H1-hESC and HUVEC). More details can be found in doi:10.1038/ng.3196. 177 integrated_fitCons_rankscore: integrated fitCons scores were ranked among all integrated fitCons scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of integrated fitCons scores in dbNSFP. 178 integrated_confidence_value: 0 - highly significant scores (approx. p<.003); 1 - significant scores (approx. p<.05); 2 - informative scores (approx. p<.25); 3 - other scores (approx. p>=.25). 179 GM12878_fitCons_score: fitCons score predicts the fraction of genomic positions belonging to a specific function class (defined by epigenomic "fingerprint") that are under selective pressure. Scores range from 0 to 1, with a larger score indicating a higher proportion of nucleic sites of the functional class the genomic position belong to are under selective pressure, therefore more likely to be functional important. GM12878 fitCons scores are based on cell type GM12878. More details can be found in doi:10.1038/ng.3196. 180 GM12878_fitCons_rankscore: GM12878 fitCons scores were ranked among all GM12878 fitCons scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of GM12878 fitCons scores in dbNSFP. 181 GM12878_confidence_value: 0 - highly significant scores (approx. p<.003); 1 - significant scores (approx. p<.05); 2 - informative scores (approx. p<.25); 3 - other scores (approx. p>=.25). 182 H1-hESC_fitCons_score: fitCons score predicts the fraction of genomic positions belonging to a specific function class (defined by epigenomic "fingerprint") that are under selective pressure. Scores range from 0 to 1, with a larger score indicating a higher proportion of nucleic sites of the functional class the genomic position belong to are under selective pressure, therefore more likely to be functional important. GM12878 fitCons scores are based on cell type H1-hESC. More details can be found in doi:10.1038/ng.3196. 183 H1-hESC_fitCons_rankscore: H1-hESC fitCons scores were ranked among all H1-hESC fitCons scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of H1-hESC fitCons scores in dbNSFP. 184 H1-hESC_confidence_value: 0 - highly significant scores (approx. p<.003); 1 - significant scores (approx. p<.05); 2 - informative scores (approx. p<.25); 3 - other scores (approx. p>=.25). 185 HUVEC_fitCons_score: fitCons score predicts the fraction of genomic positions belonging to a specific function class (defined by epigenomic "fingerprint") that are under selective pressure. Scores range from 0 to 1, with a larger score indicating a higher proportion of nucleic sites of the functional class the genomic position belong to are under selective pressure, therefore more likely to be functional important. GM12878 fitCons scores are based on cell type HUVEC. More details can be found in doi:10.1038/ng.3196. 186 HUVEC_fitCons_rankscore: HUVEC fitCons scores were ranked among all HUVEC fitCons scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of HUVEC fitCons scores in dbNSFP. 187 HUVEC_confidence_value: 0 - highly significant scores (approx. p<.003); 1 - significant scores (approx. p<.05); 2 - informative scores (approx. p<.25); 3 - other scores (approx. p>=.25). 188 LINSIGHT: "The LINSIGHT score measures the probability of negative selection on noncoding sites" Details refer to doi:10.1038/ng.3810. 189 LINSIGHT_rankscore: LINSIGHT scores were ranked among all LINSIGHT scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of LINSIGHT scores in dbNSFP. 190 GERP++_NR: GERP++ neutral rate 191 GERP++_RS: GERP++ RS score, the larger the score, the more conserved the site. Scores range from -12.3 to 6.17. 192 GERP++_RS_rankscore: GERP++ RS scores were ranked among all GERP++ RS scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of GERP++ RS scores in dbNSFP. 193 GERP_91_mammals: GERP conservation score calculated based on multiple sequence alignments of 91 mammals. 194 GERP_91_mammals_rankscore: GERP (91 mammals) scores were ranked among all GERP (91 mammals) scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of GERP_91_mammals scores in dbNSFP. 195 phyloP100way_vertebrate: phyloP (phylogenetic p-values) conservation score based on the multiple alignments of 100 vertebrate genomes (including human). The larger the score, the more conserved the site. Scores range from -20.0 to 10.003 in dbNSFP. 196 phyloP100way_vertebrate_rankscore: phyloP100way_vertebrate scores were ranked among all phyloP100way_vertebrate scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of phyloP100way_vertebrate scores in dbNSFP. 197 phyloP470way_mammalian: phyloP (phylogenetic p-values) conservation score based on the multiple alignments of 470 mammalian genomes (including human). The larger the score, the more conserved the site. Scores range from -20 to 11.936 in dbNSFP. 198 phyloP470way_mammalian_rankscore: phyloP470way_mammalian scores were ranked among all phyloP470way_mammalian scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of phyloP470way_mammalian scores in dbNSFP. 199 phyloP17way_primate: a conservation score based on 17way alignment primate set, the higher the more conservative. Scores range from -13.362 to 0.756 in dbNSFP. 200 phyloP17way_primate_rankscore: the rank of the phyloP17way_primate score among all phyloP17way_primate scores in dbNSFP. 201 phastCons100way_vertebrate: phastCons conservation score based on the multiple alignments of 100 vertebrate genomes (including human). The larger the score, the more conserved the site. Scores range from 0 to 1. 202 phastCons100way_vertebrate_rankscore: phastCons100way_vertebrate scores were ranked among all phastCons100way_vertebrate scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of phastCons100way_vertebrate scores in dbNSFP. 203 phastCons470way_mammalian: phastCons conservation score based on the multiple alignments of 470 mammalian genomes (including human). The larger the score, the more conserved the site. Scores range from 0 to 1. 204 phastCons470way_mammalian_rankscore: phastCons470way_mammalian scores were ranked among all phastCons470way_mammalian scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of phastCons470way_mammalian scores in dbNSFP. 205 phastCons17way_primate: a conservation score based on 17way alignment primate set, The larger the score, the more conserved the site. Scores range from 0 to 1. 206 phastCons17way_primate_rankscore: the rank of the phastCons17way_primate score among all phastCons17way_primate scores in dbNSFP. 207 SiPhy_29way_pi: The estimated stationary distribution of A, C, G and T at the site, using SiPhy algorithm based on 29 mammals genomes. 208 SiPhy_29way_logOdds: SiPhy score based on 29 mammals genomes. The larger the score, the more conserved the site. Scores range from 0 to 37.9718 in dbNSFP. 209 SiPhy_29way_logOdds_rankscore: SiPhy_29way_logOdds scores were ranked among all SiPhy_29way_logOdds scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of SiPhy_29way_logOdds scores in dbNSFP. 210 bStatistic: Background selection (B) value estimates from doi.org/10.1371/journal.pgen.1000471. Ranges from 0 to 1000. It estimates the expected fraction (*1000) of neutral diversity present at a site. Values close to 0 represent near complete removal of diversity as a result of background selection and values near 1000 indicating absent of background selection. Data from CADD v1.4. 211 bStatistic_converted_rankscore: bStatistic scores were first converted to -bStatistic, then ranked among all -bStatistic scores in dbNSFP. The rankscore is the ratio of the rank of -bStatistic over the total number of -bStatistic scores in dbNSFP. 212 1000Gp3_AC: Alternative allele counts in the whole 1000 genomes phase 3 (1000Gp3) data. 213 1000Gp3_AF: Alternative allele frequency in the whole 1000Gp3 data. 214 1000Gp3_AFR_AC: Alternative allele counts in the 1000Gp3 African descendent samples. 215 1000Gp3_AFR_AF: Alternative allele frequency in the 1000Gp3 African descendent samples. 216 1000Gp3_EUR_AC: Alternative allele counts in the 1000Gp3 European descendent samples. 217 1000Gp3_EUR_AF: Alternative allele frequency in the 1000Gp3 European descendent samples. 218 1000Gp3_AMR_AC: Alternative allele counts in the 1000Gp3 American descendent samples. 219 1000Gp3_AMR_AF: Alternative allele frequency in the 1000Gp3 American descendent samples. 220 1000Gp3_EAS_AC: Alternative allele counts in the 1000Gp3 East Asian descendent samples. 221 1000Gp3_EAS_AF: Alternative allele frequency in the 1000Gp3 East Asian descendent samples. 222 1000Gp3_SAS_AC: Alternative allele counts in the 1000Gp3 South Asian descendent samples. 223 1000Gp3_SAS_AF: Alternative allele frequency in the 1000Gp3 South Asian descendent samples. 224 TWINSUK_AC: Alternative allele count in called genotypes in UK10K TWINSUK cohort. 225 TWINSUK_AF: Alternative allele frequency in called genotypes in UK10K TWINSUK cohort. 226 ALSPAC_AC: Alternative allele count in called genotypes in UK10K ALSPAC cohort. 227 ALSPAC_AF: Alternative allele frequency in called genotypes in UK10K ALSPAC cohort. 228 UK10K_AC: Alternative allele count in combined genotypes in UK10K cohort (TWINSUK+ALSPAC). 229 UK10K_AF: Alternative allele frequency in combined genotypes in UK10K cohort (TWINSUK+ALSPAC). 230 ESP6500_AA_AC: Alternative allele count in the African American samples of the NHLBI GO Exome Sequencing Project (ESP6500 data set). 231 ESP6500_AA_AF: Alternative allele frequency in the African American samples of the NHLBI GO Exome Sequencing Project (ESP6500 data set). 232 ESP6500_EA_AC: Alternative allele count in the European American samples of the NHLBI GO Exome Sequencing Project (ESP6500 data set). 233 ESP6500_EA_AF: Alternative allele frequency in the European American samples of the NHLBI GO Exome Sequencing Project (ESP6500 data set). 234 ExAC_AC: Allele count in total ExAC samples (60,706 samples) 235 ExAC_AF: Allele frequency in total ExAC samples 236 ExAC_Adj_AC: Adjusted Alt allele counts (DP >= 10 & GQ >= 20) in total ExAC samples 237 ExAC_Adj_AF: Adjusted Alt allele frequency (DP >= 10 & GQ >= 20) in total ExAC samples 238 ExAC_AFR_AC: Adjusted Alt allele counts (DP >= 10 & GQ >= 20) in African & African American ExAC samples 239 ExAC_AFR_AF: Adjusted Alt allele frequency (DP >= 10 & GQ >= 20) in African & African American ExAC samples 240 ExAC_AMR_AC: Adjusted Alt allele counts (DP >= 10 & GQ >= 20) in American ExAC samples 241 ExAC_AMR_AF: Adjusted Alt allele frequency (DP >= 10 & GQ >= 20) in American ExAC samples 242 ExAC_EAS_AC: Adjusted Alt allele counts (DP >= 10 & GQ >= 20) in East Asian ExAC samples 243 ExAC_EAS_AF: Adjusted Alt allele frequency (DP >= 10 & GQ >= 20) in East Asian ExAC samples 244 ExAC_FIN_AC: Adjusted Alt allele counts (DP >= 10 & GQ >= 20) in Finnish ExAC samples 245 ExAC_FIN_AF: Adjusted Alt allele frequency (DP >= 10 & GQ >= 20) in Finnish ExAC samples 246 ExAC_NFE_AC: Adjusted Alt allele counts (DP >= 10 & GQ >= 20) in Non-Finnish European ExAC samples 247 ExAC_NFE_AF: Adjusted Alt allele frequency (DP >= 10 & GQ >= 20) in Non-Finnish European ExAC samples 248 ExAC_SAS_AC: Adjusted Alt allele counts (DP >= 10 & GQ >= 20) in South Asian ExAC samples 249 ExAC_SAS_AF: Adjusted Alt allele frequency (DP >= 10 & GQ >= 20) in South Asian ExAC samples 250 ExAC_nonTCGA_AC: Allele count in total ExAC_nonTCGA samples (53,105 samples) 251 ExAC_nonTCGA_AF: Allele frequency in total ExAC_nonTCGA samples 252 ExAC_nonTCGA_Adj_AC: Adjusted Alt allele counts (DP >= 10 & GQ >= 20) in total ExAC_nonTCGA samples 253 ExAC_nonTCGA_Adj_AF: Adjusted Alt allele frequency (DP >= 10 & GQ >= 20) in total ExAC_nonTCGA samples 254 ExAC_nonTCGA_AFR_AC: Adjusted Alt allele counts (DP >= 10 & GQ >= 20) in African & African American ExAC_nonTCGA samples 255 ExAC_nonTCGA_AFR_AF: Adjusted Alt allele frequency (DP >= 10 & GQ >= 20) in African & African American ExAC_nonTCGA samples 256 ExAC_nonTCGA_AMR_AC: Adjusted Alt allele counts (DP >= 10 & GQ >= 20) in American ExAC_nonTCGA samples 257 ExAC_nonTCGA_AMR_AF: Adjusted Alt allele frequency (DP >= 10 & GQ >= 20) in American ExAC_nonTCGA samples 258 ExAC_nonTCGA_EAS_AC: Adjusted Alt allele counts (DP >= 10 & GQ >= 20) in East Asian ExAC_nonTCGA samples 259 ExAC_nonTCGA_EAS_AF: Adjusted Alt allele frequency (DP >= 10 & GQ >= 20) in East Asian ExAC_nonTCGA samples 260 ExAC_nonTCGA_FIN_AC: Adjusted Alt allele counts (DP >= 10 & GQ >= 20) in Finnish ExAC_nonTCGA samples 261 ExAC_nonTCGA_FIN_AF: Adjusted Alt allele frequency (DP >= 10 & GQ >= 20) in Finnish ExAC_nonTCGA samples 262 ExAC_nonTCGA_NFE_AC: Adjusted Alt allele counts (DP >= 10 & GQ >= 20) in Non-Finnish European ExAC_nonTCGA samples 263 ExAC_nonTCGA_NFE_AF: Adjusted Alt allele frequency (DP >= 10 & GQ >= 20) in Non-Finnish European ExAC_nonTCGA samples 264 ExAC_nonTCGA_SAS_AC: Adjusted Alt allele counts (DP >= 10 & GQ >= 20) in South Asian ExAC_nonTCGA samples 265 ExAC_nonTCGA_SAS_AF: Adjusted Alt allele frequency (DP >= 10 & GQ >= 20) in South Asian ExAC_nonTCGA samples 266 ExAC_nonpsych_AC: Allele count in total ExAC_nonpsych samples (45,376 samples) 267 ExAC_nonpsych_AF: Allele frequency in total ExAC_nonpsych samples 268 ExAC_nonpsych_Adj_AC: Adjusted Alt allele counts (DP >= 10 & GQ >= 20) in total ExAC_nonpsych samples 269 ExAC_nonpsych_Adj_AF: Adjusted Alt allele frequency (DP >= 10 & GQ >= 20) in total ExAC_nonpsych samples 270 ExAC_nonpsych_AFR_AC: Adjusted Alt allele counts (DP >= 10 & GQ >= 20) in African & African American ExAC_nonpsych samples 271 ExAC_nonpsych_AFR_AF: Adjusted Alt allele frequency (DP >= 10 & GQ >= 20) in African & African American ExAC_nonpsych samples 272 ExAC_nonpsych_AMR_AC: Adjusted Alt allele counts (DP >= 10 & GQ >= 20) in American ExAC_nonpsych samples 273 ExAC_nonpsych_AMR_AF: Adjusted Alt allele frequency (DP >= 10 & GQ >= 20) in American ExAC_nonpsych samples 274 ExAC_nonpsych_EAS_AC: Adjusted Alt allele counts (DP >= 10 & GQ >= 20) in East Asian ExAC_nonpsych samples 275 ExAC_nonpsych_EAS_AF: Adjusted Alt allele frequency (DP >= 10 & GQ >= 20) in East Asian ExAC_nonpsych samples 276 ExAC_nonpsych_FIN_AC: Adjusted Alt allele counts (DP >= 10 & GQ >= 20) in Finnish ExAC_nonpsych samples 277 ExAC_nonpsych_FIN_AF: Adjusted Alt allele frequency (DP >= 10 & GQ >= 20) in Finnish ExAC_nonpsych samples 278 ExAC_nonpsych_NFE_AC: Adjusted Alt allele counts (DP >= 10 & GQ >= 20) in Non-Finnish European ExAC_nonpsych samples 279 ExAC_nonpsych_NFE_AF: Adjusted Alt allele frequency (DP >= 10 & GQ >= 20) in Non-Finnish European ExAC_nonpsych samples 280 ExAC_nonpsych_SAS_AC: Adjusted Alt allele counts (DP >= 10 & GQ >= 20) in South Asian ExAC_nonpsych samples 281 ExAC_nonpsych_SAS_AF: Adjusted Alt allele frequency (DP >= 10 & GQ >= 20) in South Asian ExAC_nonpsych samples 282 gnomAD_exomes_flag: information from gnomAD exome data indicating whether the variant falling within low-complexity (lcr) or segmental duplication (segdup) or decoy regions. The flag can be either "." for high-quality PASS or not reported/polymorphic in gnomAD exomes, "lcr" for within lcr, "segdup" for within segdup, or "decoy" for with decoy region. 283 gnomAD_exomes_AC: Alternative allele count in the whole gnomAD exome samples v4.0.0 284 gnomAD_exomes_AN: Total allele count in the whole gnomAD exome samples v4.0.0 285 gnomAD_exomes_AF: Alternative allele frequency in the whole gnomAD exome samples v4.0.0 286 gnomAD_exomes_nhomalt: Count of individuals with homozygous alternative allele in the whole gnomAD exome samples v4.0.0 287 gnomAD_exomes_POPMAX_AC: Allele count in the population with the maximum AF 288 gnomAD_exomes_POPMAX_AN: Total number of alleles in the population with the maximum AF 289 gnomAD_exomes_POPMAX_AF: Maximum allele frequency across populations (excluding samples of Ashkenazi, Finnish, and indeterminate ancestry) 290 gnomAD_exomes_POPMAX_nhomalt: Count of homozygous individuals in the population with the maximum allele frequency 291 gnomAD_exomes_AFR_AC: Alternative allele count in the African/African American gnomAD exome samples v4.0.0 292 gnomAD_exomes_AFR_AN: Total allele count in the African/African American gnomAD exome samples v4.0.0 293 gnomAD_exomes_AFR_AF: Alternative allele frequency in the African/African American gnomAD exome samples v4.0.0 294 gnomAD_exomes_AFR_nhomalt: Count of individuals with homozygous alternative allele in the African/African American gnomAD exome samples v4.0.0 295 gnomAD_exomes_AMR_AC: Alternative allele count in the Latino gnomAD exome samples v4.0.0 296 gnomAD_exomes_AMR_AN: Total allele count in the Latino gnomAD exome samples v4.0.0 297 gnomAD_exomes_AMR_AF: Alternative allele frequency in the Latino gnomAD exome samples v4.0.0 298 gnomAD_exomes_AMR_nhomalt: Count of individuals with homozygous alternative allele in the Latino gnomAD exome samples v4.0.0 299 gnomAD_exomes_ASJ_AC: Alternative allele count in the Ashkenazi Jewish gnomAD exome samples v4.0.0 300 gnomAD_exomes_ASJ_AN: Total allele count in the Ashkenazi Jewish gnomAD exome samples v4.0.0 301 gnomAD_exomes_ASJ_AF: Alternative allele frequency in the Ashkenazi Jewish gnomAD exome samples v4.0.0 302 gnomAD_exomes_ASJ_nhomalt: Count of individuals with homozygous alternative allele in the Ashkenazi Jewish gnomAD exome samples v4.0.0 303 gnomAD_exomes_EAS_AC: Alternative allele count in the East Asian gnomAD exome samples v4.0.0 304 gnomAD_exomes_EAS_AN: Total allele count in the East Asian gnomAD exome samples v4.0.0 305 gnomAD_exomes_EAS_AF: Alternative allele frequency in the East Asian gnomAD exome samples v4.0.0 306 gnomAD_exomes_EAS_nhomalt: Count of individuals with homozygous alternative allele in the East Asian gnomAD exome samples v4.0.0 307 gnomAD_exomes_FIN_AC: Alternative allele count in the Finnish gnomAD exome samples v4.0.0 308 gnomAD_exomes_FIN_AN: Total allele count in the Finnish gnomAD exome samples v4.0.0 309 gnomAD_exomes_FIN_AF: Alternative allele frequency in the Finnish gnomAD exome samples v4.0.0 310 gnomAD_exomes_FIN_nhomalt: Count of individuals with homozygous alternative allele in the Finnish gnomAD exome samples v4.0.0 311 gnomAD_exomes_MID_AC: Alternative allele count in the Middle Eastern gnomAD exome samples v4.0.0 312 gnomAD_exomes_MID_AN: Total allele count in the Middle Eastern gnomAD exome samples v4.0.0 313 gnomAD_exomes_MID_AF: Alternative allele frequency in the Middle Eastern gnomAD exome samples v4.0.0 314 gnomAD_exomes_MID_nhomalt: Count of individuals with homozygous alternative allele in the Middle Eastern gnomAD exome samples v4.0.0 315 gnomAD_exomes_NFE_AC: Alternative allele count in the Non-Finnish European gnomAD exome samples v4.0.0 316 gnomAD_exomes_NFE_AN: Total allele count in the Non-Finnish European gnomAD exome samples v4.0.0 317 gnomAD_exomes_NFE_AF: Alternative allele frequency in the Non-Finnish European gnomAD exome samples v4.0.0 318 gnomAD_exomes_NFE_nhomalt: Count of individuals with homozygous alternative allele in the Non-Finnish European gnomAD exome samples v4.0.0 319 gnomAD_exomes_SAS_AC: Alternative allele count in the South Asian gnomAD exome samples v4.0.0 320 gnomAD_exomes_SAS_AN: Total allele count in the South Asian gnomAD exome samples v4.0.0 321 gnomAD_exomes_SAS_AF: Alternative allele frequency in the South Asian gnomAD exome samples v4.0.0 322 gnomAD_exomes_SAS_nhomalt: Count of individuals with homozygous alternative allele in the South Asian gnomAD exome samples v4.0.0 323 gnomAD_exomes_non_ukb_AC: Alternative allele count in the non-UKBiobank subset of whole gnomAD exome samples v4.0.0 324 gnomAD_exomes_non_ukb_AN: Total allele count in the non-UKBiobank subset of whole gnomAD exome samples v4.0.0 325 gnomAD_exomes_non_ukb_AF: Alternative allele frequency in the non-UKBiobank subset of whole gnomAD exome samples v4.0.0 326 gnomAD_exomes_non_ukb_nhomalt: Count of individuals with homozygous alternative allele in the non-UKBiobank subset of whole gnomAD exome samples v4.0.0 327 gnomAD_exomes_non_ukb_AFR_AC: Alternative allele count in the non-UKBiobank subset of African/African American gnomAD exome samples v4.0.0 328 gnomAD_exomes_non_ukb_AFR_AN: Total allele count in the non-UKBiobank subset of African/African American gnomAD exome samples v4.0.0 329 gnomAD_exomes_non_ukb_AFR_AF: Alternative allele frequency in the non-UKBiobank subset of African/African American gnomAD exome samples v4.0.0 330 gnomAD_exomes_non_ukb_AFR_nhomalt: Count of individuals with homozygous alternative allele in the non-UKBiobank subset of African/African American gnomAD exome samples v4.0.0 331 gnomAD_exomes_non_ukb_AMR_AC: Alternative allele count in the non-UKBiobank subset of Latino gnomAD exome samples v4.0.0 332 gnomAD_exomes_non_ukb_AMR_AN: Total allele count in the non-UKBiobank subset of Latino gnomAD exome samples v4.0.0 333 gnomAD_exomes_non_ukb_AMR_AF: Alternative allele frequency in the non-UKBiobank subset of Latino gnomAD exome samples v4.0.0 334 gnomAD_exomes_non_ukb_AMR_nhomalt: Count of individuals with homozygous alternative allele in the non-UKBiobank subset of Latino gnomAD exome samples v4.0.0 335 gnomAD_exomes_non_ukb_ASJ_AC: Alternative allele count in the non-UKBiobank subset of Ashkenazi Jewish gnomAD exome samples v4.0.0 336 gnomAD_exomes_non_ukb_ASJ_AN: Total allele count in the non-UKBiobank subset of Ashkenazi Jewish gnomAD exome samples v4.0.0 337 gnomAD_exomes_non_ukb_ASJ_AF: Alternative allele frequency in the non-UKBiobank subset of Ashkenazi Jewish gnomAD exome samples v4.0.0 338 gnomAD_exomes_non_ukb_ASJ_nhomalt: Count of individuals with homozygous alternative allele in the non-UKBiobank subset of Ashkenazi Jewish gnomAD exome samples v4.0.0 339 gnomAD_exomes_non_ukb_EAS_AC: Alternative allele count in the non-UKBiobank subset of East Asian gnomAD exome samples v4.0.0 340 gnomAD_exomes_non_ukb_EAS_AN: Total allele count in the non-UKBiobank subset of East Asian gnomAD exome samples v4.0.0 341 gnomAD_exomes_non_ukb_EAS_AF: Alternative allele frequency in the non-UKBiobank subset of East Asian gnomAD exome samples v4.0.0 342 gnomAD_exomes_non_ukb_EAS_nhomalt: Count of individuals with homozygous alternative allele in the non-UKBiobank subset of East Asian gnomAD exome samples v4.0.0 343 gnomAD_exomes_non_ukb_FIN_AC: Alternative allele count in the non-UKBiobank subset of Finnish gnomAD exome samples v4.0.0 344 gnomAD_exomes_non_ukb_FIN_AN: Total allele count in the non-UKBiobank subset of Finnish gnomAD exome samples v4.0.0 345 gnomAD_exomes_non_ukb_FIN_AF: Alternative allele frequency in the non-UKBiobank subset of Finnish gnomAD exome samples v4.0.0 346 gnomAD_exomes_non_ukb_FIN_nhomalt: Count of individuals with homozygous alternative allele in the non-UKBiobank subset of Finnish gnomAD exome samples v4.0.0 347 gnomAD_exomes_non_ukb_MID_AC: Alternative allele count in the non-UKBiobank subset of Middle Eastern gnomAD exome samples v4.0.0 348 gnomAD_exomes_non_ukb_MID_AN: Total allele count in the non-UKBiobank subset of Middle Eastern gnomAD exome samples v4.0.0 349 gnomAD_exomes_non_ukb_MID_AF: Alternative allele frequency in the non-UKBiobank subset of Middle Eastern gnomAD exome samples v4.0.0 350 gnomAD_exomes_non_ukb_MID_nhomalt: Count of individuals with homozygous alternative allele in the non-UKBiobank subset of Middle Eastern gnomAD exome samples v4.0.0 351 gnomAD_exomes_non_ukb_NFE_AC: Alternative allele count in the non-UKBiobank subset of Non-Finnish European gnomAD exome samples v4.0.0 352 gnomAD_exomes_non_ukb_NFE_AN: Total allele count in the non-UKBiobank subset of Non-Finnish European gnomAD exome samples v4.0.0 353 gnomAD_exomes_non_ukb_NFE_AF: Alternative allele frequency in the non-UKBiobank subset of Non-Finnish European gnomAD exome samples v4.0.0 354 gnomAD_exomes_non_ukb_NFE_nhomalt: Count of individuals with homozygous alternative allele in the non-UKBiobank subset of Non-Finnish European gnomAD exome samples v4.0.0 355 gnomAD_exomes_non_ukb_SAS_AC: Alternative allele count in the non-UKBiobank subset of South Asian gnomAD exome samples v4.0.0 356 gnomAD_exomes_non_ukb_SAS_AN: Total allele count in the non-UKBiobank subset of South Asian gnomAD exome samples v4.0.0 357 gnomAD_exomes_non_ukb_SAS_AF: Alternative allele frequency in the non-UKBiobank subset of South Asian gnomAD exome samples v4.0.0 358 gnomAD_exomes_non_ukb_SAS_nhomalt: Count of individuals with homozygous alternative allele in the non-UKBiobank subset of South Asian gnomAD exome samples v4.0.0 359 gnomAD_genomes_flag: information from gnomAD genome data indicating whether the variant falling within low-complexity (lcr) or segmental duplication (segdup) or decoy regions. The flag can be either "." for high-quality PASS or not reported/polymorphic in gnomAD exomes, "lcr" for within lcr, "segdup" for within segdup, or "decoy" for with decoy region. 360 gnomAD_genomes_AC: Alternative allele count in the whole gnomAD genome samples v4.0.0 For mtDNA, this is sum of AC_hom ("Allele count restricted to variants with a heteroplasmy level >= 0.95") and AC_het ("Allele count restricted to variants with a heteroplasmy level >= 0.10 and < 0.95") 361 gnomAD_genomes_AN: Total allele count in the whole gnomAD genome samples v4.0.0 362 gnomAD_genomes_AF: Alternative allele frequency in the whole gnomAD genome samples v4.0.0 For mtDNA, this is sum of AF_hom ("Allele frequency restricted to variants with a heteroplasmy level >= 0.95") and AF_het ("Allele frequency restricted to variants with a heteroplasmy level >= 0.10 and < 0.95") 363 gnomAD_genomes_nhomalt: Count of individuals with homozygous alternative allele in the whole gnomAD genome samples v4.0.0 For mtDNA, this is AC_hom ("Allele count restricted to variants with a heteroplasmy level >= 0.95") 364 gnomAD_genomes_POPMAX_AC: Allele count in the population with the maximum AF 365 gnomAD_genomes_POPMAX_AN: Total number of alleles in the population with the maximum AF 366 gnomAD_genomes_POPMAX_AF: Maximum allele frequency across populations (excluding samples of Ashkenazi, Finnish, and indeterminate ancestry) 367 gnomAD_genomes_POPMAX_nhomalt: Count of homozygous individuals in the population with the maximum allele frequency 368 gnomAD_genomes_AFR_AC: Alternative allele count in the African/African American gnomAD genome samples v4.0.0 For mtDNA, this is sum of AC_hom ("Allele count restricted to variants with a heteroplasmy level >= 0.95") and AC_het ("Allele count restricted to variants with a heteroplasmy level >= 0.10 and < 0.95") 369 gnomAD_genomes_AFR_AN: Total allele count in the African/African American gnomAD genome samples v4.0.0 370 gnomAD_genomes_AFR_AF: Alternative allele frequency in the African/African American gnomAD genome samples v4.0.0 For mtDNA, this is sum of AF_hom ("Allele frequency restricted to variants with a heteroplasmy level >= 0.95") and AF_het ("Allele frequency restricted to variants with a heteroplasmy level >= 0.10 and < 0.95") 371 gnomAD_genomes_AFR_nhomalt: Count of individuals with homozygous alternative allele in the African/African American gnomAD genome samples v4.0.0 For mtDNA, this is AC_hom ("Allele count restricted to variants with a heteroplasmy level >= 0.95") 372 gnomAD_genomes_AMI_AC: Alternative allele count in the Amish gnomAD genome samples v4.0.0 For mtDNA, this is sum of AC_hom ("Allele count restricted to variants with a heteroplasmy level >= 0.95") and AC_het ("Allele count restricted to variants with a heteroplasmy level >= 0.10 and < 0.95") 373 gnomAD_genomes_AMI_AN: Total allele count in the Amish gnomAD genome samples v4.0.0 374 gnomAD_genomes_AMI_AF: Alternative allele frequency in the Amish gnomAD genome samples v4.0.0 For mtDNA, this is sum of AF_hom ("Allele frequency restricted to variants with a heteroplasmy level >= 0.95") and AF_het ("Allele frequency restricted to variants with a heteroplasmy level >= 0.10 and < 0.95") 375 gnomAD_genomes_AMI_nhomalt: Count of individuals with homozygous alternative allele in the Amish gnomAD genome samples v4.0.0 For mtDNA, this is AC_hom ("Allele count restricted to variants with a heteroplasmy level >= 0.95") 376 gnomAD_genomes_AMR_AC: Alternative allele count in the Latino gnomAD genome samples v4.0.0 For mtDNA, this is sum of AC_hom ("Allele count restricted to variants with a heteroplasmy level >= 0.95") and AC_het ("Allele count restricted to variants with a heteroplasmy level >= 0.10 and < 0.95") 377 gnomAD_genomes_AMR_AN: Total allele count in the Latino gnomAD genome samples v4.0.0 378 gnomAD_genomes_AMR_AF: Alternative allele frequency in the Latino gnomAD genome samples v4.0.0 For mtDNA, this is sum of AF_hom ("Allele frequency restricted to variants with a heteroplasmy level >= 0.95") and AF_het ("Allele frequency restricted to variants with a heteroplasmy level >= 0.10 and < 0.95") 379 gnomAD_genomes_AMR_nhomalt: Count of individuals with homozygous alternative allele in the Latino gnomAD genome samples v4.0.0 For mtDNA, this is AC_hom ("Allele count restricted to variants with a heteroplasmy level >= 0.95") 380 gnomAD_genomes_ASJ_AC: Alternative allele count in the Ashkenazi Jewish gnomAD genome samples v4.0.0 For mtDNA, this is sum of AC_hom ("Allele count restricted to variants with a heteroplasmy level >= 0.95") and AC_het ("Allele count restricted to variants with a heteroplasmy level >= 0.10 and < 0.95") 381 gnomAD_genomes_ASJ_AN: Total allele count in the Ashkenazi Jewish gnomAD genome samples v4.0.0 382 gnomAD_genomes_ASJ_AF: Alternative allele frequency in the Ashkenazi Jewish gnomAD genome samples v4.0.0 For mtDNA, this is sum of AF_hom ("Allele frequency restricted to variants with a heteroplasmy level >= 0.95") and AF_het ("Allele frequency restricted to variants with a heteroplasmy level >= 0.10 and < 0.95") 383 gnomAD_genomes_ASJ_nhomalt: Count of individuals with homozygous alternative allele in the Ashkenazi Jewish gnomAD genome samples v4.0.0 For mtDNA, this is AC_hom ("Allele count restricted to variants with a heteroplasmy level >= 0.95") 384 gnomAD_genomes_EAS_AC: Alternative allele count in the East Asian gnomAD genome samples v4.0.0 For mtDNA, this is sum of AC_hom ("Allele count restricted to variants with a heteroplasmy level >= 0.95") and AC_het ("Allele count restricted to variants with a heteroplasmy level >= 0.10 and < 0.95") 385 gnomAD_genomes_EAS_AN: Total allele count in the East Asian gnomAD genome samples v4.0.0 386 gnomAD_genomes_EAS_AF: Alternative allele frequency in the East Asian gnomAD genome samples v4.0.0 For mtDNA, this is sum of AF_hom ("Allele frequency restricted to variants with a heteroplasmy level >= 0.95") and AF_het ("Allele frequency restricted to variants with a heteroplasmy level >= 0.10 and < 0.95") 387 gnomAD_genomes_EAS_nhomalt: Count of individuals with homozygous alternative allele in the East Asian gnomAD genome samples v4.0.0 For mtDNA, this is AC_hom ("Allele count restricted to variants with a heteroplasmy level >= 0.95") 388 gnomAD_genomes_FIN_AC: Alternative allele count in the Finnish gnomAD genome samples v4.0.0 For mtDNA, this is sum of AC_hom ("Allele count restricted to variants with a heteroplasmy level >= 0.95") and AC_het ("Allele count restricted to variants with a heteroplasmy level >= 0.10 and < 0.95") 389 gnomAD_genomes_FIN_AN: Total allele count in the Finnish gnomAD genome samples v4.0.0 390 gnomAD_genomes_FIN_AF: Alternative allele frequency in the Finnish gnomAD genome samples v4.0.0 For mtDNA, this is sum of AF_hom ("Allele frequency restricted to variants with a heteroplasmy level >= 0.95") and AF_het ("Allele frequency restricted to variants with a heteroplasmy level >= 0.10 and < 0.95") 391 gnomAD_genomes_FIN_nhomalt: Count of individuals with homozygous alternative allele in the Finnish gnomAD genome samples v4.0.0 For mtDNA, this is AC_hom ("Allele count restricted to variants with a heteroplasmy level >= 0.95") 392 gnomAD_genomes_MID_AC: Alternative allele count in the Middle Eastern gnomAD genome samples v4.0.0 For mtDNA, this is sum of AC_hom ("Allele count restricted to variants with a heteroplasmy level >= 0.95") and AC_het ("Allele count restricted to variants with a heteroplasmy level >= 0.10 and < 0.95") 393 gnomAD_genomes_MID_AN: Total allele count in the Middle Eastern gnomAD genome samples v4.0.0 394 gnomAD_genomes_MID_AF: Alternative allele frequency in the Middle Eastern gnomAD genome samples v4.0.0 For mtDNA, this is sum of AF_hom ("Allele frequency restricted to variants with a heteroplasmy level >= 0.95") and AF_het ("Allele frequency restricted to variants with a heteroplasmy level >= 0.10 and < 0.95") 395 gnomAD_genomes_MID_nhomalt: Count of individuals with homozygous alternative allele in the Middle Eastern gnomAD genome samples v4.0.0 For mtDNA, this is AC_hom ("Allele count restricted to variants with a heteroplasmy level >= 0.95") 396 gnomAD_genomes_NFE_AC: Alternative allele count in the Non-Finnish European gnomAD genome samples v4.0.0 For mtDNA, this is sum of AC_hom ("Allele count restricted to variants with a heteroplasmy level >= 0.95") and AC_het ("Allele count restricted to variants with a heteroplasmy level >= 0.10 and < 0.95") 397 gnomAD_genomes_NFE_AN: Total allele count in the Non-Finnish European gnomAD genome samples v4.0.0 398 gnomAD_genomes_NFE_AF: Alternative allele frequency in the Non-Finnish European gnomAD genome samples v4.0.0 For mtDNA, this is sum of AF_hom ("Allele frequency restricted to variants with a heteroplasmy level >= 0.95") and AF_het ("Allele frequency restricted to variants with a heteroplasmy level >= 0.10 and < 0.95") 399 gnomAD_genomes_NFE_nhomalt: Count of individuals with homozygous alternative allele in the Non-Finnish European gnomAD genome samples v4.0.0 For mtDNA, this is AC_hom ("Allele count restricted to variants with a heteroplasmy level >= 0.95") 400 gnomAD_genomes_SAS_AC: Alternative allele count in the South Asian gnomAD genome samples v4.0.0 For mtDNA, this is sum of AC_hom ("Allele count restricted to variants with a heteroplasmy level >= 0.95") and AC_het ("Allele count restricted to variants with a heteroplasmy level >= 0.10 and < 0.95") 401 gnomAD_genomes_SAS_AN: Total allele count in the South Asian gnomAD genome samples v4.0.0 402 gnomAD_genomes_SAS_AF: Alternative allele frequency in the South Asian gnomAD genome samples v4.0.0 For mtDNA, this is sum of AF_hom ("Allele frequency restricted to variants with a heteroplasmy level >= 0.95") and AF_het ("Allele frequency restricted to variants with a heteroplasmy level >= 0.10 and < 0.95") 403 gnomAD_genomes_SAS_nhomalt: Count of individuals with homozygous alternative allele in the South Asian gnomAD genome samples v4.0.0 For mtDNA, this is AC_hom ("Allele count restricted to variants with a heteroplasmy level >= 0.95") 404 ALFA_European_AC: Alternative allele count of the European samples in the Allele Frequency Aggregator 405 ALFA_European_AN: Total allele count of the European samples in the Allele Frequency Aggregator 406 ALFA_European_AF: Alternative allele frequency of the European samples in the Allele Frequency Aggregator 407 ALFA_African_Others_AC: Alternative allele count of the individuals with African ancestry in the Allele Frequency Aggregator 408 ALFA_African_Others_AN: Total allele count of the individuals with African ancestry in the Allele Frequency Aggregator 409 ALFA_African_Others_AF: Alternative allele frequency of the individuals with African ancestry in the Allele Frequency Aggregator 410 ALFA_East_Asian_AC: Alternative allele count of the East Asian samples in the Allele Frequency Aggregator 411 ALFA_East_Asian_AN: Total allele count of the East Asian samples in the Allele Frequency Aggregator 412 ALFA_East_Asian_AF: Alternative allele frequency of the East Asian samples in the Allele Frequency Aggregator 413 ALFA_African_American_AC: Alternative allele count of the African American samples in the Allele Frequency Aggregator 414 ALFA_African_American_AN: Total allele count of the African American samples in the Allele Frequency Aggregator 415 ALFA_African_American_AF: Alternative allele frequency of the African American samples in the Allele Frequency Aggregator 416 ALFA_Latin_American_1_AC: Alternative allele count of the Latin American individiuals with Afro-Caribbean ancestry in the Allele Frequency Aggregator 417 ALFA_Latin_American_1_AN: Total allele count of the Latin American individiuals with Afro-Caribbean ancestry in the Allele Frequency Aggregator 418 ALFA_Latin_American_1_AF: Alternative allele frequency of the Latin American individiuals with Afro-Caribbean ancestry in the Allele Frequency Aggregator 419 ALFA_Latin_American_2_AC: Alternative allele count of the Latin American individiuals with mostly European and Native American Ancestry in the Allele Frequency Aggregator 420 ALFA_Latin_American_2_AN: Total allele count of the Latin American individiuals with mostly European and Native American Ancestry in the Allele Frequency Aggregator 421 ALFA_Latin_American_2_AF: Alternative allele frequency of the Latin American individiuals with mostly European and Native American Ancestry in the Allele Frequency Aggregator 422 ALFA_Other_Asian_AC: Alternative allele count of the Asian individiuals excluding South or East Asian in the Allele Frequency Aggregator 423 ALFA_Other_Asian_AN: Total allele count of the Asian individiuals excluding South or East Asian in the Allele Frequency Aggregator 424 ALFA_Other_Asian_AF: Alternative allele frequency of the Asian individiuals excluding South or East Asian in the Allele Frequency Aggregator 425 ALFA_South_Asian_AC: Alternative allele count of the South Asian samples in the Allele Frequency Aggregator 426 ALFA_South_Asian_AN: Total allele count of the South Asian samples in the Allele Frequency Aggregator 427 ALFA_South_Asian_AF: Alternative allele frequency of the South Asian samples in the Allele Frequency Aggregator 428 ALFA_Other_AC: Alternative allele count of the samples whose self-reported population is inconsistent with the GRAF-assigned population in the Allele Frequency Aggregator 429 ALFA_Other_AN: Total allele count of the samples whose self-reported population is inconsistent with the GRAF-assigned population in the Allele Frequency Aggregator 430 ALFA_Other_AF: Alternative allele frequency of the samples whose self-reported population is inconsistent with the GRAF-assigned population in the Allele Frequency Aggregator 431 ALFA_African_AC: Alternative allele count of the all African samples (African_Others and African_American) in the Allele Frequency Aggregator 432 ALFA_African_AN: Total allele count of the all African samples (African_Others and African_American) in the Allele Frequency Aggregator 433 ALFA_African_AF: Alternative allele frequency of the all African samples (African_Others and African_American) in the Allele Frequency Aggregator 434 ALFA_Asian_AC: Alternative allele count of the all Asian individuals (East_Asian and Other_Asian, excluding South_Asian) in the Allele Frequency Aggregator 435 ALFA_Asian_AN: Total allele count of the all Asian individuals (East_Asian and Other_Asian, excluding South_Asian) in the Allele Frequency Aggregator 436 ALFA_Asian_AF: Alternative allele frequency of the all Asian individuals (East_Asian and Other_Asian, excluding South_Asian) in the Allele Frequency Aggregator 437 ALFA_Total_AC: Alternative allele count of the total samples in the Allele Frequency Aggregator 438 ALFA_Total_AN: Total allele count of the total samples in the Allele Frequency Aggregator 439 ALFA_Total_AF: Alternative allele frequency of the total samples in the Allele Frequency Aggregator 440 clinvar_id: clinvar variation ID 441 clinvar_clnsig: clinical significance by clinvar Possible values: Benign, Likely_benign, Likely_pathogenic, Pathogenic, drug_response, histocompatibility. A negative score means the score is for the ref allele 442 clinvar_trait: the trait/disease the clinvar_clnsig referring to 443 clinvar_review: ClinVar Review Status summary Possible values: no assertion criteria provided, criteria provided, single submitter, criteria provided, multiple submitters, no conflicts, reviewed by expert panel, practice guideline 444 clinvar_hgvs: variant in HGVS format 445 clinvar_var_source: source of the variant 446 clinvar_MedGen_id: MedGen ID of the trait/disease the clinvar_trait referring to 447 clinvar_OMIM_id: OMIM ID of the trait/disease the clinvar_trait referring to 448 clinvar_Orphanet_id: Orphanet ID of the trait/disease the clinvar_trait referring to 449 Interpro_domain: domain or conserved site on which the variant locates. Domain annotations come from Interpro database. The number in the brackets following a specific domain is the count of times Interpro assigns the variant position to that domain, typically coming from different predicting databases. Multiple entries separated by ";". 450 GTEx_V8_eQTL_gene: target gene of the (significant) eQTL SNP 451 GTEx_V8_eQTL_tissue: tissue type of the expression data with which the eQTL/gene pair is detected 452 GTEx_V8_sQTL_gene: target gene of the (significant) sQTL SNP 453 GTEx_V8_sQTL_tissue: tissue type of the expression data with which the sQTL/gene pair is detected 454 eQTLGen_snp_id: id of the eQTL SNP 455 eQTLGen_gene_id: id of the target gene of the (significant) eQTL SNP 456 eQTLGen_gene_symbol: symbol of the target gene of the (significant) eQTL SNP 457 eQTLGen_cis_or_trans: eQTL type, cis or trans 458 Geuvadis_eQTL_target_gene: Ensembl gene ID of the eQTL associated with, from the Geuvadis project Note 1: Missing data is designated as '.'. Columns of dbNSFP_gene: Gene_name: Gene symbol from HGNC Ensembl_gene: Ensembl gene id (from HGNC) chr: Chromosome number (from HGNC) 459 Gene_old_names: Old gene symbol (from HGNC) 460 Gene_other_names: Other gene names (from HGNC) 461 Uniprot_acc(HGNC/Uniprot): Uniprot acc number (from HGNC and Uniprot) 462 Uniprot_id(HGNC/Uniprot): Uniprot id (from HGNC and Uniprot) 463 Entrez_gene_id: Entrez gene id (from HGNC) 464 CCDS_id: CCDS id (from HGNC) 465 Refseq_id: Refseq gene id (from HGNC) 466 ucsc_id: UCSC gene id (from HGNC) 467 MIM_id: MIM gene id (from HGNC) 468 OMIM_id: MIM gene id from OMIM 469 Gene_full_name: Gene full name (from HGNC) 470 Pathway(Uniprot): Pathway description from Uniprot 471 Pathway(BioCarta)_short: Short name of the Pathway(s) the gene belongs to (from BioCarta) 472 Pathway(BioCarta)_full: Full name(s) of the Pathway(s) the gene belongs to (from BioCarta) 473 Pathway(ConsensusPathDB): Pathway(s) the gene belongs to (from ConsensusPathDB) 474 Pathway(KEGG)_id: ID(s) of the Pathway(s) the gene belongs to (from KEGG) 475 Pathway(KEGG)_full: Full name(s) of the Pathway(s) the gene belongs to (from KEGG) 476 Function_description: Function description of the gene (from Uniprot) 477 Disease_description: Disease(s) the gene caused or associated with (from Uniprot) 478 MIM_phenotype_id: MIM id(s) of the phenotype the gene caused or associated with (from Uniprot) 479 MIM_disease: MIM disease name(s) with MIM id(s) in "[]" (from Uniprot) 480 Orphanet_disorder_id: Orphanet Number of the disorder the gene caused or associated with 481 Orphanet_disorder: Disorder name from Orphanet 482 Orphanet_association_type: the type of association beteen the gene and the disorder 483 Trait_association(GWAS): Trait(s) the gene associated with (from GWAS catalog) 484 HPO_id: ID of the mapped Human Phenotype Ontology. Multiple IDs are separated by ";" 485 HPO_name: Name of the mapped Human Phenotype Ontology. Multiple names are separated by ";" 486 GO_biological_process: GO terms for biological process 487 GO_cellular_component: GO terms for cellular component 488 GO_molecular_function: GO terms for molecular function 489 Tissue_specificity(Uniprot): Tissue specificity description from Uniprot 490 Expression(egenetics): Tissues/organs the gene expressed in (egenetics data from BioMart) 491 Expression(GNF/Atlas): Tissues/organs the gene expressed in (GNF/Atlas data from BioMart) 492 Interactions(IntAct): The number of other genes this gene interacting with (from IntAct). Full information (gene name followed by Pubmed id in "[]") can be found in the ".complete" table 493 Interactions(BioGRID): The number of other genes this gene interacting with (from BioGRID) Full information (gene name followed by Pubmed id in "[]") can be found in the ".complete" table 494 Interactions(ConsensusPathDB): The number of other genes this gene interacting with (from ConsensusPathDB). Full information (gene name followed by interaction confidence in "[]") can be found in the ".complete" table 495 P(HI): Estimated probability of haploinsufficiency of the gene (from doi:10.1371/journal.pgen.1001154) 496 HIPred_score: Estimated probability of haploinsufficiency of the gene (from doi:10.1093/bioinformatics/btx028) 497 HIPred: HIPred prediction of haploinsufficiency of the gene. Y(es) or N(o). (from doi:10.1093/bioinformatics/btx028) 498 GHIS: A score predicting the gene haploinsufficiency. The higher the score the more likely the gene is haploinsufficient. (from doi: 10.1093/nar/gkv474) 499 P(rec): Estimated probability that gene is a recessive disease gene (from DOI:10.1126/science.1215040) 500 Known_rec_info: Known recessive status of the gene (from DOI:10.1126/science.1215040) "lof-tolerant = seen in homozygous state in at least one 1000G individual" "recessive = known OMIM recessive disease" (original annotations from DOI:10.1126/science.1215040) 501 RVIS_EVS: Residual Variation Intolerance Score, a measure of intolerance of mutational burden, the higher the score the more tolerant to mutational burden the gene is. Based on EVS (ESP6500) data. from doi:10.1371/journal.pgen.1003709 502 RVIS_percentile_EVS: The percentile rank of the gene based on RVIS, the higher the percentile the more tolerant to mutational burden the gene is. Based on EVS (ESP6500) data. 503 LoF-FDR_ExAC: "A gene's corresponding FDR p-value for preferential LoF depletion among the ExAC population. Lower FDR corresponds with genes that are increasingly depleted of LoF variants." cited from RVIS document. 504 RVIS_ExAC: "ExAC-based RVIS; setting 'common' MAF filter at 0.05% in at least one of the six individual ethnic strata from ExAC." cited from RVIS document. 505 RVIS_percentile_ExAC: "Genome-Wide percentile for the new ExAC-based RVIS; setting 'common' MAF filter at 0.05% in at least one of the six individual ethnic strata from ExAC." cited from RVIS document. 506 ExAC_pLI: "the probability of being loss-of-function intolerant (intolerant of both heterozygous and homozygous lof variants)" based on ExAC r0.3 data 507 ExAC_pRec: "the probability of being intolerant of homozygous, but not heterozygous lof variants" based on ExAC r0.3 data 508 ExAC_pNull: "the probability of being tolerant of both heterozygous and homozygous lof variants" based on ExAC r0.3 data 509 ExAC_nonTCGA_pLI: "the probability of being loss-of-function intolerant (intolerant of both heterozygous and homozygous lof variants)" based on ExAC r0.3 nonTCGA subset 510 ExAC_nonTCGA_pRec: "the probability of being intolerant of homozygous, but not heterozygous lof variants" based on ExAC r0.3 nonTCGA subset 511 ExAC_nonTCGA_pNull: "the probability of being tolerant of both heterozygous and homozygous lof variants" based on ExAC r0.3 nonTCGA subset 512 ExAC_nonpsych_pLI: "the probability of being loss-of-function intolerant (intolerant of both heterozygous and homozygous lof variants)" based on ExAC r0.3 nonpsych subset 513 ExAC_nonpsych_pRec: "the probability of being intolerant of homozygous, but not heterozygous lof variants" based on ExAC r0.3 nonpsych subset 514 ExAC_nonpsych_pNull: "the probability of being tolerant of both heterozygous and homozygous lof variants" based on ExAC r0.3 nonpsych subset 515 gnomAD_pLI: "the probability of being loss-of-function intolerant (intolerant of both heterozygous and homozygous lof variants)" based on gnomAD 2.1 data 516 gnomAD_pRec: "the probability of being intolerant of homozygous, but not heterozygous lof variants" based on gnomAD 2.1 data 517 gnomAD_pNull: "the probability of being tolerant of both heterozygous and homozygous lof variants" based on gnomAD 2.1 data 518 ExAC_del.score: "Winsorised deletion intolerance z-score" based on ExAC r0.3.1 CNV data 519 ExAC_dup.score: "Winsorised duplication intolerance z-score" based on ExAC r0.3.1 CNV data 520 ExAC_cnv.score: "Winsorised cnv intolerance z-score" based on ExAC r0.3.1 CNV data 521 ExAC_cnv_flag: "Gene is in a known region of recurrent CNVs mediated by tandem segmental duplications and intolerance scores are more likely to be biased or noisy." from ExAC r0.3.1 CNV release 522 GDI: gene damage index score, "a genome-wide, gene-level metric of the mutational damage that has accumulated in the general population" from doi: 10.1073/pnas.1518646112. The higher the score the less likely the gene is to be responsible for monogenic diseases. 523 GDI-Phred: Phred-scaled GDI scores 524 Gene damage prediction (all disease-causing genes): gene damage prediction (low/medium/high) by GDI for all diseases 525 Gene damage prediction (all Mendelian disease-causing genes): gene damage prediction (low/medium/high) by GDI for all Mendelian diseases 526 Gene damage prediction (Mendelian AD disease-causing genes): gene damage prediction (low/medium/high) by GDI for Mendelian autosomal dominant diseases 527 Gene damage prediction (Mendelian AR disease-causing genes): gene damage prediction (low/medium/high) by GDI for Mendelian autosomal recessive diseases 528 Gene damage prediction (all PID disease-causing genes): gene damage prediction (low/medium/high) by GDI for all primary immunodeficiency diseases 529 Gene damage prediction (PID AD disease-causing genes): gene damage prediction (low/medium/high) by GDI for primary immunodeficiency autosomal dominant diseases 530 Gene damage prediction (PID AR disease-causing genes): gene damage prediction (low/medium/high) by GDI for primary immunodeficiency autosomal recessive diseases 531 Gene damage prediction (all cancer disease-causing genes): gene damage prediction (low/medium/high) by GDI for all cancer disease 532 Gene damage prediction (cancer recessive disease-causing genes): gene damage prediction (low/medium/high) by GDI for cancer recessive disease 533 Gene damage prediction (cancer dominant disease-causing genes): gene damage prediction (low/medium/high) by GDI for cancer dominant disease 534 LoFtool_score: a percentile score for gene intolerance to functional change. The lower the score the higher gene intolerance to functional change. For details see doi: 10.1093/bioinformatics/btv602. 535 SORVA_LOF_MAF0.005_HetOrHom: the fraction of individuals in the 1000 Genomes Project data (N=2504) who are either Heterozygote or Homozygote of LOF SNVs whose MAF<0.005. This fraction is from a method for ranking genes based on mutational burden called SORVA (Significance Of Rare VAriants). Please see doi: 10.1101/103218 for details. 536 SORVA_LOF_MAF0.005_HomOrCompoundHet: the fraction of individuals in the 1000 Genomes Project data (N=2504) who are either Compound Heterozygote or Homozygote of LOF SNVs whose MAF<0.005. This fraction is from a method for ranking genes based on mutational burden called SORVA (Significance Of Rare VAriants). Please see doi: 10.1101/103218 for details. 537 SORVA_LOF_MAF0.001_HetOrHom: the fraction of individuals in the 1000 Genomes Project data (N=2504) who are either Heterozygote or Homozygote of LOF SNVs whose MAF<0.001. This fraction is from a method for ranking genes based on mutational burden called SORVA (Significance Of Rare VAriants). Please see doi: 10.1101/103218 for details. 538 SORVA_LOF_MAF0.001_HomOrCompoundHet: the fraction of individuals in the 1000 Genomes Project data (N=2504) who are either Compound Heterozygote or Homozygote of LOF SNVs whose MAF<0.001. This fraction is from a method for ranking genes based on mutational burden called SORVA (Significance Of Rare VAriants). Please see doi: 10.1101/103218 for details. 539 SORVA_LOForMissense_MAF0.005_HetOrHom: the fraction of individuals in the 1000 Genomes Project data (N=2504) who are either Heterozygote or Homozygote of LOF or missense SNVs whose MAF<0.005. This fraction is from a method for ranking genes based on mutational burden called SORVA (Significance Of Rare VAriants). Please see doi: 10.1101/103218 for details. 540 SORVA_LOForMissense_MAF0.005_HomOrCompoundHet: the fraction of individuals in the 1000 Genomes Project data (N=2504) who are either Compound Heterozygote or Homozygote of LOF or missense SNVs whose MAF<0.005. This fraction is from a method for ranking genes based on mutational burden called SORVA (Significance Of Rare VAriants). Please see doi: 10.1101/103218 for details. 541 SORVA_LOForMissense_MAF0.001_HetOrHom: the fraction of individuals in the 1000 Genomes Project data (N=2504) who are either Heterozygote or Homozygote of LOF or missense SNVs whose MAF<0.001. This fraction is from a method for ranking genes based on mutational burden called SORVA (Significance Of Rare VAriants). Please see doi: 10.1101/103218 for details. 542 SORVA_LOForMissense_MAF0.001_HomOrCompoundHet: the fraction of individuals in the 1000 Genomes Project data (N=2504) who are either Compound Heterozygote or Homozygote of LOF or missense SNVs whose MAF<0.001. This fraction is from a method for ranking genes based on mutational burden called SORVA (Significance Of Rare VAriants). Please see doi: 10.1101/103218 for details. 543 Essential_gene: Essential ("E") or Non-essential phenotype-changing ("N") based on Mouse Genome Informatics database. from doi:10.1371/journal.pgen.1003484 544 Essential_gene_CRISPR: Essential ("E") or Non-essential phenotype-changing ("N") based on large scale CRISPR experiments. from doi: 10.1126/science.aac7041 545 Essential_gene_CRISPR2: Essential ("E"), context-Specific essential ("S"), or Non-essential phenotype-changing ("N") based on large scale CRISPR experiments. from http://dx.doi.org/10.1016/j.cell.2015.11.015 546 Essential_gene_gene-trap: Essential ("E"), HAP1-Specific essential ("H"), KBM7-Specific essential ("K"), or Non-essential phenotype-changing ("N"), based on large scale mutagenesis experiments. from doi: 10.1126/science.aac7557 547 Gene_indispensability_score: A probability prediction of the gene being essential. From doi:10.1371/journal.pcbi.1002886 548 Gene_indispensability_pred: Essential ("E") or loss-of-function tolerant ("N") based on Gene_indispensability_score. 549 MGI_mouse_gene: Homolog mouse gene name from MGI 550 MGI_mouse_phenotype: Phenotype description for the homolog mouse gene from MGI 551 ZFIN_zebrafish_gene: Homolog zebrafish gene name from ZFIN 552 ZFIN_zebrafish_structure: Affected structure of the homolog zebrafish gene from ZFIN 553 ZFIN_zebrafish_phenotype_quality: Phenotype description for the homolog zebrafish gene from ZFIN 554 ZFIN_zebrafish_phenotype_tag: Phenotype tag for the homolog zebrafish gene from ZFIN Columns of dbscSNV1.1: chr: chromosome number pos: physical position on the chromosome as to hg19 (1-based coordinate) ref: reference nucleotide allele (as on the + strand) alt: alternative nucleotide allele (as on the + strand) hg38_chr: chromosome number as to hg38 hg38_pos: physical position on the chromosome as to hg38 (1-based coordinate) RefSeq?: whether the SNV is a scSNV according to RefSeq Ensembl?: whether the SNV is a scSNV according to Ensembl RefSeq_region: functional region the SNV located according to RefSeq RefSeq_gene: gene name according to RefSeq RefSeq_functional_consequence: functional consequence of the SNV according to RefSeq RefSeq_id_c.change_p.change: SNV in format of c.change and p.change according to RefSeq Ensembl_region: functional region the SNV located according to Ensembl Ensembl_gene: gene id according to Ensembl Ensembl_functional_consequence: functional consequence of the SNV according to Ensembl Ensembl_id_c.change_p.change: SNV in format of c.change and p.change according to Ensembl ada_score: ensemble prediction score based on ada-boost. Ranges 0 to 1. The larger the score the higher probability the scSNV will affect splicing. The suggested cutoff for a binary prediction (affecting splicing vs. not affecting splicing) is 0.6. rf_score: ensemble prediction score based on random forests. Ranges 0 to 1. The larger the score the higher probability the scSNV will affect splicing. The suggested cutoff for a binary prediction (affecting splicing vs. not affecting splicing) is 0.6. Note 1: Missing data is designated as '.'. Note 2: Multiple annotations are separated by ';' Please cite: 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. Liu X, Wu C, Li C and Boerwinkle E. 2016. dbNSFP v3.0: A One-Stop Database of Functional Predictions and Annotations for Human Non-synonymous and Splice Site SNVs. Human Mutation. 37(3):235-241. Contact: Xiaoming Liu, Ph.D. Associate Professor, USF Genomics, College of Public Health, University of South Florida Email: xmliu.uth{at}gmail.com Changelog: February 23, 2011: dbNSFP and search_dbNSFP v0.9 released. April 4, 2011: A bug related to the prediction scores of MutationTaster is fixed. dbNSFP v1.0 released. A change to the chromosome search order of the search_dbNSFP. A readme file added. search_dbNSFP v1.0 released. May 30, 2011: dbNSFP and search_dbNSFP v1.1 released. Version 1.1 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. May 31, 2011: dbNSFP_light and search_dbNSFP_light v1.0 released. dbNSFP_light v1.0 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. 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. The unziped database is 6Gb. October 24, 2011: dbNSFP_light v1.1 and search_dbNSFP_light v1.1 released. dbNSFP v1.2 and search_dbNSFP v1.2 released. The new versions added GERP++ neutral rates and RS scores. October 25, 2011: dbNSFP v1.3 released. It added Uniprot ID, accession number and amino acid position based on Polyphen-2 annotation. Users now can search amino acid change directly referring to a Uniprot ID or accession number. November 3, 2011: dbNSFP_light v1.2 released. It added Uniprot ID, accession number and amino acid position based on Polyphen-2 annotation. Users now can search amino acid change directly referring to a Uniprot ID or accession number. November 10, 2011: A bug fixed in the companion search program for dbNSFP v1.3, which causes invalid search using AA mutations with Uniprot ID or accession number. December 16, 2011: dbNSFP_light v1.3 released. It updated SIFT scores (August, 2011 version) and Polyphen-2 scores (May, 2011 version). Uniprot ID, accession number and amino acid position based on the Polyphen-2 annotations have been updated too. April 11, 2012: dbNSFP2.0b1_variant released. This is beta test version of the variant sub-database of dbNSFP v2.0, which is rebuilt based on Gencode release 9 / Ensembl version 64. June 2, 2012: dbNSFP v2.0b2 released. It includes both the dbNSFP_variant and dbNSFP_gene sub-databases. Slight changes have been made to the Ensembl gene and transcript ids of dbNSFP_variant in order to be compatible to other database sources. July 2, 2012: dbNSFP v2.0b3 released. An additional 2.2 million splicing site SNPs have been added to dbNSFP_variant. In the table those SNPs have missing (".") in aaref, aaalt and "-1" in aapos. There's no change to the format of search input file. August 28, 2012: The companion java search program search_dbNSFP20b3 is updated. Added features include supporting vcf file as input file and options for output contents (columns). October 27, 2012: dbNSFP v2.0b4 is released. A new functional prediction score MutationAssessor is added (I thank Mr. Yevgeniy Antipin for his recommendation). Allele frequencies from ESP 5400 data set are replaced by ESP 6500 data set. February 25, 2013: dbNSFP v2.0 is released. A new functional prediction score FATHMM is added. March 22, 2013: A bug which caused a lot of missing FATHMM scores has been fixed. May 31, 2013: The source code of the companion Java search program is now available under the RECEX SHARED SOURCE LICENSE. October 3, 2013: dbNSFP v2.1 is released. MutationTaster and FATHMM scores have been updated. Converted scores of SIFT, LRT, MutationTaster, MutationAssessor and FATHMM have been added. Columns of SIFT and FATHMM predictions have been added. The gene database has also been updated. Database IDs are updated. GO Slim terms, pathway and protein interaction information from the ConsensusPathDB, and list of essential and non-essential genes (based on phenotypes of mouse homologs) have been added. January 23, 2014: dbNSFP v2.2 is released. SIFT and FATHMM now have multiple scores corresponding to different Ensembl ENSP ids and amino acid positions (aapos_SIFT and aapos_FATHMM). Accordingly, our companion search program now supports SNP searches based on Ensembl ENSP ids and amino acid positions. A bug is fixed for a small proportion of MutationTaster scores. January 26, 2014: dbNSFP v2.3 is released. Two ensemble scores (RadialSVM and LR) and their predictions have been added. February 12, 2014: A bug was fixed in dbNSFP v2.2 and v2.3, which caused missing delimiters in columns aapos_SIFT, SIFT_score_converted and SIFT_pred. (I thank Mr. Yevgeniy Antipin for his reminder). March 5, 2014: dbNSFP v2.4 is released. A whole genome functional prediction score called CADD was added, along with five more conservation scores (phyloP46way_primate, phyloP100way_vertebrate, phastCons46way_primate, phastCons46way_placental, phastCons100way_vertebarate). To facilitate comparison between scores, we added rank scores for most functional prediction scores and conservation scores, and replacing the "converted" scores in the previous versions. June 1, 2014: dbNSFP v2.5 is released. A new functional score VEST 3.0 has been added. We thank Dr. Karchin for kindly providing the score. A bug that causes the MutationTaster score error since v2.1 for variants with a prediction of "Polymorphism_automatic" has been fixed. We thank John McGuigan and James Ireland for reporting this bug. As MutationTaster can also predict splicing change and other functional effects, in case a variant has multiple predictions based on their different model, we took the most damaging score and prediction for dbNSFP. July 26, 2014: dbNSFP v2.6 is released. rs numbers from dbSNP 141 have been added to the variant database files. Mouse and zebra fish homolog genes and phenotypes have been added to the gene database file (I thank Alex Li for his suggestion and helps). Trait_association(GWAS) was also updated. An attached database called dbscSNV is available for download. It includes all potential human SNVs within splicing consensus regions (−3 to +8 at the 5’ splice site and −12 to +2 at the 3’ splice site), i.e. scSNVs, related functional annotations and two ensemble prediction scores for predicting their potential of altering splicing. A manuscript describing those scores have been submitted. search_dbNSFP26 now supports searching dbNSFP along with dbscSNV using option "-s". September 12, 2014: dbNSFP v2.7 is released. Chromosomes and positions of human reference hg38 have been added. search_ dbNSFP27.class now supports query dbNSFP using the positions based on hg38 with the "-v hg38" option. clinvar (freeze 20140902) annotations have been added. Allele frequencies from 2303 exomes of African Americans and 3203 exomes of European Americans from the Atherosclerosis Risk in Communities Study (ARIC) cohort study have been added. As the columns for gene interactions in dbNSFP_gene table contain very long strings, especially for gene UBC, which may cause problems when viewing the results in Excel, now we only report the number of interacting genes in those columns. Full information is retained in the dbNSFP_gene.complete table. November 21, 2014: dbNSFP v2.8 is released. COSMIC (Catalogue Of Somatic Mutations In Cancer) annotation have been added. Pathway information from BioCarta and KEGG (old version) has been added to the dbNSFP2.8_gene. A bug causing inconsistency between MutationTaster scores and MutationTaster_pred, which affects v2.5 to v2.7, has been fixed. I thank Adam Novak for reporting this bug. February 3, 2015: dbNSFP v2.9 is released. SIFT score has been updated to ensembl66 version. PROVEAN score (Protein Variation Effect Analyzer) v1.1 has been added. I thank Yongwook Choi from jcvi for providing the SIFT and PROVEAN scores. CADD score has been updated to 1.3 version. Please note the following copyright statement for CADD: "CADD scores (http://cadd.gs.washington.edu/) are Copyright 2013 University of Washington and Hudson-Alpha Institute for Biotechnology (all rights reserved) but are freely available for all academic, non-commercial applications. For commercial licensing information contact Jennifer McCullar (mccullaj@uw.edu)." Allele frequency v0.3 of ~60,706 unrelated individuals from The Exome Aggregation Consortium (ExAC) has been added. ExAC data are released under a Fort Lauderdale Agreement. Please refer to http://exac.broadinstitute.org/terms for terms of use. I also want to thank Dr. CS (Jonathan) Liu from Softgenetics for providing hosting space. April 6, 2015: dbNSFP v3.0b1 is released. The core set of nsSNVs and ssSNVs has been rebuilt based on Gencode 22/ Ensembl 79 with human reference sequence hg38. Putative genes have been included. Genes with incomplete 5' have been excluded (I thank Chris Gillies for reporting the issues for genes with incomplete 5' end.) Genes on mitochondrial DNA have been included. Allele frequencies from the UK10K cohorts and genotypes of two Neanderthals have been added. Some resources have been updated, including the MutationTaster (I thank Dr. Dominik Seelow for kindly providing the scores), allele frequencies from the 1000 Genomes Project populations, ancestral alleles, dbSNP, ClinVar and InterPro. The presentation of the prediction scores has been improved by adding columns for the corresponding transcript/protein ids. PhyloP and PhastCons conservation scores based on hg19 have been replaced by the scores based on hg38. Some resources have been dropped due to various reasons, including SLR test statistic, UniSNP ids, allele frequencies from the ARIC cohorts and allele counts in COSMIC. dbNSFP_gene has also been completely rebuilt using the up-to-date resources. Residual Variation Intolerance Scores (RVIS) have been added. GO Slim terms have been replaced by full GO terms. Two branches of dbNSFP are now provided: dbNSFP3.0b1a suitable for academic use, which includes all the resources, and dbNSFP3.0b1c suitable for commercial use, which does not include VEST3 and CADD. April 12, 2015: dbNSFP v3.0b2 is released. This update fixed the issues due to inconsistent mitochondrial reference sequences used by different resources. I thank Dr. Lishuang Shen at MEEI for helping solving the issues. For mitochondrial SNV, the pos (i.e. hg38) refers to the rCRS (GenBank: NC_012920) and hg19_pos refers to a YRI sequence (GenBank: AF347015). The ancestral allele of mitochondrial SNV now comes from the Reconstructed Sapiens Reference Sequence (RSRS, doi:10.1016/j.ajhg.2012.03.002). The affected content include ancestral alleles, Neanderthal/Denisova genotypes and MutationTaster columns of the chrM file. The rankscores of MutationTaster has also been updated to reflect the update of its chrM scores. dbscSNV has been updated to v1.1 and added hg38 positions liftovered from its hg19 positions. Using search_dbNSFP30b2a or search_dbNSFP30b2c you can search dbscSNV1.1 along with dbNSFP v3.0b2 with either hg19 coordinates or hg38 coordinates. August 3, 2015: dbNSFP v3.0 is released. Three new functional prediction scores (DANN, fathmm-MKL and fitCons) and two conservation scores (phyloP20way_mammalian and phastCons20way_mammalian) have been added to dbNSFP v3.0a. All five scores except DANN are also included in bNSFP v3.0c. For commercial application of DANN, please contact Daniel Quang (dxquang@uci.edu). CADD scores have been updated to v1.3. I thank Dr. Xueqiu Jian and Kirill Prusov for suggestions on README files. dbNSFP v3.0 will be integrated into our new whole genome annotation pipeline WGSA version 0.6. Please join our Email group for news and updates from dbNSFP. Columns updated: CADD_raw (dbNSFP v3.0a only), CADD_raw_rankscore (dbNSFP v3.0a only), CADD_phred (dbNSFP v3.0a only). New columns: DANN_score (dbNSFP v3.0a only), DANN_rankscore (dbNSFP v3.0a only), fathmm-MKL_coding_score, fathmm-MKL_coding_rankscore, fathmm-MKL_coding_pred, fathmm-MKL_coding_group, integrated_fitCons_score, integrated_fitCons_rankscore, integrated_confidence_value, GM12878_fitCons_score, GM12878_fitCons_rankscore, GM12878_confidence_value, H1-hESC_fitCons_score, H1-hESC_fitCons_rankscore, H1-hESC_confidence_value, HUVEC_fitCons_score, HUVEC_fitCons_rankscore, HUVEC_confidence_value. November 24, 2015: dbNSFP v3.1 is released. Significant eQTLs from GTEx V6 has been added. dbSNP rs has been updated to build 144. Gene expression information (rpkm of RNAseq) of 53 tissues from GTEx V6 has been added to dbNSFP_gene. Three gene intolerance scores (RVIS based on ExAC r0.3, GDI and LoFtool) has been added to dbNSFP_gene. March 20, 2016: dbNSFP v3.2 is released. Eigen score, Eigen PC score (doi: 10.1038/ng.3477) and GenoCanyon score (doi:10.1038/srep10576) have been added. Allele frequencies of two commonly used subsets of ExAC data (nonTCGA and nonpsych) have been added. Mutation Assessor scores have been updated to release 3. PhyloP7way_vertebrate and PhastCons7way_vertebrate conservation scores have been updated to PhyloP100way_vertebrate and PhastCons100way_vertebrate, respectively. rankscores have been updated accordingly. Ancestral alleles have been updated based on Ensembl 84. dbSNP has been updated to build 146. Clinvar has been updated to 20160302. InterPro has been updated to v56. Gene name cross-links, IntAct, Uniprot, GWAS catalog, BioGRID, GO, ConsensusPathDB, mouse genes and zebra fish genes information for the dbNSFP_gene table have been updated. November 30, 2016: dbNSFP v3.3 and v2.9.2 are released. M-CAP score (DOI: 10.1038/ng.3703) has been added. We thank Dr. Gill Bejerano for providing the score. Eigen and Eigen PC scores have been updated to v1.1. dbSNP has been updated to v147. clinvar has been updated to 20161101. March 12, 2017: dbNSFP v3.4 and v2.9.3 are released. REVEL score ( doi: 10.1016/j.ajhg.2016.08.016) and MutPred score (doi: 10.1093/bioinformatics/btp528) have been added. SORVA gene ranking scores (doi: 10.1101/103218) have been added to gene annotation. August 6, 2017: dbNSFP v3.5 is released. Allele frequencies from the exomes and genomes of the Genome Aggregation Database (gnomAD) have been added. Interpro, dbSNP, clinvar, ancestral alleles, Altai Neanderthal genotypes, Denisova genotypes and GTEx eQTLs have been updated. dbNSFP_gene has been rebuilt with updated annotations. Other changes to dbNSFP_gene include: Interactions columns now show the gene list instead of the total number; GTEx gene expression annotations have been removed; LoF FDR p-value from RVIS has been added; Genome-wide haploinsufficiency score (GHIS) has been added; LoF and CNV intolerance/tolerance scores based on ExAC data have been added. December 8, 2018: dbNSFP v4.0b1 is released for beta testing. The core set of nsSNVs and ssSNVs has been rebuilt based on Gencode 29/ Ensembl 94 with human reference sequence hg38. Eight deleteriousness prediction scores (ALoFT, DEOGEN2, FATHMM-XF, MPC, MVP, PrimateAI, LINSIGHT, SIFT4G) have been added. Three conservation scores (phyloP17way_primate, phastCons17way_primate, bStatistic) have been added. Allele frequencies from the gnomAD consortium, eQTLs from the Geuvadis project, and genotypes of a Vindija33.19 Neanderthal have been added. Some resources have been updated, including VEST (We thank Dr. Karchin), CADD, M-CAP, ancestral alleles, dbSNP, ClinVar, GTEx and InterPro. The presentation of the prediction scores has been further improved by adding the correspondence to transcript/protein ids in a systematic way. APPRIS, GENCODE_basic, TSL and VEP_canonical have been added to facilitate the choice of appropriate transcripts. dbNSFP_gene has also been completely rebuilt using the up-to-date resources. HIPred, gene constraint scores from the gnomAD data, essential genes predictions based on CRISPR, gene-trap and gene networks have been added. Two branches of dbNSFP are provided: dbNSFP4.0b1a suitable for academic use, which includes all the resources, and dbNSFP4.0b1c suitable for commercial use, which does not include Polyphen2, VEST, REVEL, CADD, LINSIGHT, and GenoCanyon. Please contact Dr. Xiaoming Liu (xmliu.uth{at}gmail.com) for commercial usage of dbNSFP. December 30, 2018: A bug causing id mapping issue from Uniprot to Ensembl, which further causing increased missing rates of Polyphen2, MutationAssessor and DEOGEN2, has been found and fixed (We thank Dr. Daniele Raimondi). February 20, 2019: sprot_varsplic was included in the mapping from Uniprot to Ensembl. Fixed column title inconsistency between the README file and data file. (We thank Kevin Xin and Julius Jacobsen for pointing out the inconsistency.) dbMTS was added as an attached database. search_dbNSFP added support for searching dbMTS with option '-m'. May 3, 2019: dbNSFP v4.0 is released. HGVS c. and p. presentations from ANNOVAR, SnpEff and VEP have been added. search_dbNSFP now supports search based on HGVS c. and p. presentations. Please refer to search_dbNSFP40a.readme.pdf or search_dbNSFP40c.readme.pdf for details. MedGen ID, OMIM ID and Orphanet ID from clinvar have been added. December 5, 2019: A minor bug is fixed in dbNSFP v4.0. In the previous release the content of the following columns were compressed, i.e. if annotations for all transcripts are identical, only one annotation was presented: genename, cds_strand, refcodon, codonpos, codon_degeneracy, FATHMM_score, FATHMM_pred, Interpro_domain. In this release those columns are decompressed, i.e. have the same number of annotations as the number of transcripts. A Java-based graphic user interface (GUI) search program (search_dbNSFP40a.jar or search_dbNSFP40c.jar) has been added. Users can double-click the jar file to launch the GUI (it supports commandline also, please check the search_dbNSFP readme pdf for details). May 15, 2020: A minor bug is fixed in dbNSFP v4.0. In the previous release, the column Primate_AI_pred was not 100% correct. We thank Alex Kouris for reporting this issue. June 16, 2020: dbNSFP v4.1 is released. BayesDel (https://doi.org/10.1002/humu.23158), ClinPred (https://doi.org/10.1016/j.ajhg.2018.08.005) and LIST-S2 (https://doi.org/10.1093/nar/gkaa288) scores have been added. CADD has been updated to v1.6, CADD score based on hg19 model has been added. Clinvar, GTEx and gnomAD genomes have been updated. HPO terms have been added to the dbNSFP_gene. search_dbNSFP programs now support searching SpliceAI as an attached database. Jan 27, 2021: The command-line only version of the search programs for v4.1a and v4.1c were added. Feb 10, 2021: A bug fixed. In the previous release, the gnomAD_pLI, gnomAD_pRec and gnomAD_pNull scores in dbNSFP4.1_gene.gz and dbNSFP4.1_gene.complete.gz have a problem that the scores are not always corresponding to the canonical transcripts of the genes. We thank Dr. Raphaël Helaers for reporting this bug. March 12, 2021: A bug fixed. In the previous release, some ALoFT scores/information are missing in dbNSFP. We thank Dr. Shuwei Li for reporting this bug. April 6, 2021: dbNSFP v4.2 is released. MetaRNN scores have been added. Allele frequencies of gnomAD exome have been updated to r2.1.1. Allele Frequencies of gnomAD genome have been updated to v3.1. dbSNP has been updated to 154. clinvar has been updated to 20210131. February 18, 2022: dbNSFP v4.3 is released. REVEL scores have been updated with transcript ids, i.e., the scores are now transcript-specific. Genotypes of Chagyrskaya neandertals have been added. dbSNP has been updated to b155. clinvar has been updated to 20220122. May 6, 2023: dbNSFP v4.4 is released. gMVP and VARITY scores have been added. Allele frequencies of ALFA (Allele Frequency Aggregator) have been added. dbSNP has been updated to b156. clinvar has been updated to 20230430. phyloP30way_mammalian has been replaced by phyloP470way_mammalian. phastCons30way_mammalian has been replaced by phastCons470way_mammalian. A bug in MutPred scores (not all SNVs causing the same AA change have scores) has been fixed. November 2, 2023: dbNSFP v4.5 is released. ClinVar has been updated to 20231028. ESM1b, EVE and AlphaMissense scores have been added. AlphaMissense scores are for non-commercial research use only: "AlphaMissense Database Copyright (2023) DeepMind Technologies Limited. All predictions are provided for non-commercial research use only under CC BY-NC-SA license." This distribution of the derived AlphaMissense_score, AlphaMissense_rankscore, and AlphaMissense_pred in dbNSFP are also under CC BY-NC-SA license and only included in the "a" branch of dbNSFP. A copy of CC BY-NC-SA license can be found at https://creativecommons.org/licenses/by-nc-sa/4.0/. February 18, 2024: dbNSFP v4.6 is released. ClinVar has been updated to 20240215. GTEx V8 splicing QTLs (sQTLs) have been added. eQTLs from eQTLGen phase I have been added. There was a bug in v4.5 causing a large proportion of ESM1b scores to be misaligned. It has been fixed. We thank Dr. In-Hee Lee for reporting this bug. March 3, 2024: dbNSFP v4.7 is released. CADD has been updated to v1.7. Allele frequencies of gnomAD exomes and genomes have been updated to v4.0.0. One bug in v4.6 causing eQTLGen eQTLs of some tissues missing has been fixed. March 13, 2024: AlphaMissense scores are now licensed under the Creative Commons Attribution 4.0 International License (CC-BY), thereby been added to dbNSFP v4.7 "c" branch. June 13, 2024: dbNSFP v4.8 is released. MutFormer and PHACTboost scores have been added. GERP conservation score calculated based on 91 mammals has been added. August 8, 2024: dbNSFP v4.9 is released. MutScore has been added. ClinVar has been updated.