dbNSFP
The GTB format dbNSFP database retains only the functional prediction scores ((including rank scores, totaling 86 fields) and conservation scores (including rank scores, totaling 19 fields) from dbNSFP4.4a. The Field descriptions are sourced from the dbNSFP4.4.a README file.
| #Field | Description | Type |
|---|---|---|
| SIFT_score | SIFT score (SIFTori). Scores range from 0 to 1. The smaller the score the more likely the SNP has damaging effect. | Float |
| 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. | Float |
| SIFT4G_score | SIFT 4G score (SIFT4G). Scores range from 0 to 1. The smaller the score the more likely the SNP has damaging effect. | Float |
| 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. | Float |
| PROVEAN_score | PROVEAN score (PROVEANori). The smaller the score the more likely the SNP has damaging effect. Range: [-14, 14]. | Float |
| 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. | Float |
| Polyphen2_HDIV_score | Polyphen2 score based on HumDiv, i.e. hdiv_prob. Range: [0, 1]. | Float |
| 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. | Float |
| Polyphen2_HVAR_score | Polyphen2 score based on HumVar, i.e. hvar_prob. Range: [0, 1]. | Float |
| 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. | Float |
| LRT_score | The original LRT two-sided p-value (LRTori). Range: [0, 1]. | Float |
| LRT_converted_rankscore | LRTori scores were first converted as LRTnew=1-LRTori0.5 if Omega<1, or LRTnew=LRTori0.5 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. | Float |
| LRT_Omega | estimated nonsynonymous-to-synonymous-rate ratio (Omega, reported by LRT) | Float |
| MutationTaster_score | MutationTaster p-value (MTori). Range: [0, 1]. | Float |
| 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. The rankscore is the ratio of the rank of the score over the total number of MTnew scores in dbNSFP. | Float |
| MutationAssessor_score | MutationAssessor functional impact combined score (MAori). Range: [-5.17, 6.49]. | Float |
| 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. | Float |
| FATHMM_score | FATHMM default score (weighted for human inherited-disease mutations with Disease Ontology) (FATHMMori). The smaller the score the more likely the SNP has damaging effect.Range: [-16.13, 10.64]. | Float |
| 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. | Float |
| fathmm-MKL_coding_score | fathmm-MKL p-values. Range: [0, 1]. | Float |
| 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. | Float |
| fathmm-XF_coding_score | fathmm-XF p-values. Range: [0, 1]. | Float |
| 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. | Float |
| CADD_raw | CADD raw score for functional prediction of a SNP. The larger the score the more likely the SNP has damaging effect. Range:[-6.458163, 18.301497]. | Float |
| 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. | Float |
| CADD_phred | CADD phred-like score. This is phred-like rank score based on whole genome CADD raw scores. The larger the score the more likely the SNP has damaging effect. | Float |
| VEST4_score | VEST 4.0 score. The larger the score the more likely the mutation may cause functional change. Range: [0, 1]. | Float |
| 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. | Float |
| MetaSVM_score | 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. Range: [-2, 3]. | Float |
| 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. | Float |
| MetaLR_score | 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. Range: [0, 1]. | Float |
| 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. | Float |
| MetaRNN_score | 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. Range: [0, 1]. | Float |
| 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. | Float |
| M-CAP_score | M-CAP is hybrid ensemble score. The larger the score the more likely the SNP has damaging effect. Range: [0, 1]. | Float |
| 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. | Float |
| REVEL_score | REVEL is an ensemble score based on 13 individual scores for predicting the pathogenicity of missense variants. The larger the score the more likely the SNP has damaging effect. Range: [0, 1]. | Float |
| 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. | Float |
| MutPred_score | General MutPred score. The larger the score the more likely the SNP has damaging effect. Range: [0, 1]. | Float |
| 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. | Float |
| MVP_score | A pathogenicity prediction score for missense variants using deep learning approach. The larger the score, the more likely the variant is pathogenic. Range: [0, 1]. | Float |
| 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. | Float |
| gMVP_score | A pathogenicity prediction score for missense variants using a graph attention neural network model. The larger the score, the more likely the variant is pathogenic. Range: [0, 1]. | Float |
| 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. | Float |
| MPC_score | A deleteriousness prediction score for missense variants based on regional missense constraint. The larger the score, the more likely the variant is pathogenic. Range: [0, 5]. | Float |
| 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. | Float |
| PrimateAI_score | A pathogenicity prediction score for missense variants based on common variants of non-human primate species using a deep neural network. The larger the score, the more likely the variant is pathogenic. Range: [0, 1]. | Float |
| 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. | Float |
| 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". The larger the score, the more likely the variant is deleterious. Range: [0, 1]. | Float |
| 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. | Float |
| BayesDel_addAF_score | A deleteriousness preidction meta-score for SNVs and indels with inclusion of MaxAF. The higher the score, the more likely the variant is pathogenic. Range: [-1.11707, 0.750927]. | Float |
| 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. | Float |
| BayesDel_noAF_score | A deleteriousness preidction meta-score for SNVs and indels without inclusion of MaxAF. The higher the score, the more likely the variant is pathogenic. Range: [-1.31914, 0.840878]. | Float |
| 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. | Float |
| ClinPred_score | A deleteriousness preidction meta-score for nonsynonymous SNVs. The higher the score, the more likely the variant is pathogenic. Range: [0, 1]. | Float |
| 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. | Float |
| LIST-S2_score | A deleteriousness preidction score for nonsynonymous SNVs. The higher the score, the more likely the variant is pathogenic. Range: [0, 1]. | Float |
| 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. | Float |
| VARITY_R_score | VARITY_R scores are pathogenicity prediction scores for rare human missense variants. The larger the score, the more likely the variant is pathogenic. Range: [0, 1]. | Float |
| 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. | Float |
| VARITY_ER_score | VARITY_ER scores are pathogenicity prediction scores for extreme rare human missense variants. The larger the score, the more likely the variant is pathogenic. Range: [0, 1]. | Float |
| 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. | Float |
| VARITY_R_LOO_score | Same as VARITY_R except the prediction on the variants used for training was made using Leave-One-Variant out. | Float |
| 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. | Float |
| VARITY_ER_LOO_score | Same as VARITY_ER except the prediction on the variants used for training was made using Leave-One-Variant out. | Float |
| 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. | Float |
| DANN_score | DANN is a functional prediction score retrained based on the training data of CADD using deep neural network. A larger number indicate a higher probability to be damaging. Range: [0, 1]. | Float |
| 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. | Float |
| 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. | Float |
| 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. | Float |
| Eigen-phred_coding | Eigen score in phred scale. | Float |
| 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. | Float |
| 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. | Float |
| Eigen-PC-phred_coding | Eigen PC score in phred scale. | Float |
| GenoCanyon_score | A functional prediction score based on conservation and biochemical annotations using an unsupervised statistical learning. | Float |
| 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. | Float |
| 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. 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). Range: [0, 1]. | Float |
| 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. | Float |
| GM12878_fitCons_score | GM12878 fitCons scores are based on cell type GM12878. | Float |
| 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. | Float |
| H1-hESC_fitCons_score | H1-hESC fitCons scores are based on cell type H1-hESC. | Float |
| 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. | Float |
| HUVEC_fitCons_score | HUVEC fitCons scores are based on cell type HUVEC. | Float |
| 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. | Float |
| LINSIGHT | The LINSIGHT score measures the probability of negative selection on noncoding sites. | Float |
| 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. | Float |
| GERP++_NR | GERP++ neutral rate. | Float |
| GERP++_RS | GERP++ RS score, the larger the score, the more conserved the site. Range: [-12.3, 6.17]. | Float |
| 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. | Float |
| 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. Range: [-20.0, 10.003]. | Float |
| 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. | Float |
| 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. Range: [-20, 11.936]. | Float |
| 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. | Float |
| phyloP17way_primate | a conservation score based on 17way alignment primate set, the higher the more conservative. Range: [-13.362, 0.756]. | Float |
| phyloP17way_primate_rankscore | the rank of the phyloP17way_primate score among all phyloP17way_primate scores in dbNSFP. | Float |
| 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. Range: [0, 1]. | Float |
| 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. | Float |
| 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. Range: [0, 1]. | Float |
| 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. | Float |
| phastCons17way_primate | a conservation score based on 17way alignment primate set. The larger the score, the more conserved the site. Range: [0, 1]. | Float |
| phastCons17way_primate_rankscore | the rank of the phastCons17way_primate score among all phastCons17way_primate scores in dbNSFP. | Float |
| SiPhy_29way_logOdds | SiPhy score based on 29 mammals genomes. The larger the score, the more conserved the site. Range: [0, 37.9718]. | Float |
| 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. | Float |
| bStatistic | Background selection (B) value 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. Range: [0, 1000]. | Float |
| 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. | Float |