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fieldConfig.txt
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ToolName DataSource SourceField ID Number Type Label Description Category URL DataURL Hidden AllowableValues IsIndexed InDefaultColumns
Funcotator ACMG_recommendation Disease_Name ACMG_Disease UNBOUNDED String ACMG Disease This lists any diseases listed in ACMG associated with genes overlapping this variant Genes and Gene Predictions https://www.ncbi.nlm.nih.gov/clinvar/docs/acmg/ https://www.ncbi.nlm.nih.gov/clinvar/docs/acmg/acmg59_test_cleaned.txt true
Funcotator ACMGLMMLof LOF_Mechanism ACMGLMM_LOF UNBOUNDED String LMM LOF Mechanism The mechanism of inheritance from custom list of genes found with (or without) LoF mechanisms in earlier studies from the Laboratory for Molecular Medicine (LMM). This datasource provides information whether a given gene was found in that list and whether there were any LoF variants found by the LMM. Genes and Gene Predictions https://gnomad.broadinstitute.org/news/2020-10-loss-of-function-curations-in-gnomad/ funcotator bundle true
Funcotator ACMGLMMLof Mode_of_Inheritance ACMGLMM_MOI UNBOUNDED String LMM Mode of Inheritance Loss of function mechanism from custom list of genes found with (or without) LoF mechanisms in earlier studies from the Laboratory for Molecular Medicine (LMM). This datasource provides information whether a given gene was found in that list and whether there were any LoF variants found by the LMM. Genes and Gene Predictions https://gnomad.broadinstitute.org/news/2020-10-loss-of-function-curations-in-gnomad/ funcotator bundle true
Funcotator ACMGLMMLof Notes ACMGLMM_GN UNBOUNDED String LMM Genes Notes LOF Custom list of genes found with (or without) LoF mechanisms in earlier studies from the Laboratory for Molecular Medicine (LMM). This datasource provides information whether a given gene was found in that list and whether there were any LoF variants found by the LMM. The ACMG59 recommendation list for clinical intervention. See https://www.ncbi.nlm.nih.gov/clinvar/docs/acmg/ for more information. Genes and Gene Predictions https://gnomad.broadinstitute.org/news/2020-10-loss-of-function-curations-in-gnomad/ funcotator bundle true
Funcotator CADD CADD_PH CADD_Score A Float CADD Score "CADD phred scaled score, which is a prediction of the deleteriousness of this variant" Genes and Gene Predictions https://cadd.gs.washington.edu/ true true
Funcotator CGC Cancer_Syndrome CGC_Synd UNBOUNDED String CGC Syndrome Cancer Syndrome associated with genes overlapping this variant Genes and Gene Predictions https://cancer.sanger.ac.uk/census ftp://[email protected]/bundle/oncotator/ true
Funcotator CGC GeneID CGC_GeneID UNBOUNDED String CGC Gene ID GeneID The Cancer Gene Census (CGC) is an ongoing effort to catalogue those genes which contain mutations that have been causally implicated in cancer and explain how dysfunction of these genes drives cancer. This lists any overlapping genes implicated in cancer. Genes and Gene Predictions https://cancer.sanger.ac.uk/census ftp://[email protected]/bundle/oncotator/ true
Funcotator CGC Mutation_Type CGC_Mut_Type UNBOUNDED String CGC Mutation Type Mutation Type Genes and Gene Predictions https://cancer.sanger.ac.uk/census ftp://[email protected]/bundle/oncotator/ true
Funcotator CGC Tissue_Type CGC_Tissue UNBOUNDED String CGC Tissue Types Tissue Type Genes and Gene Predictions https://cancer.sanger.ac.uk/census ftp://[email protected]/bundle/oncotator/
Funcotator CGC Tumour_Types_(Germline_Mutations) CGC_Germline UNBOUNDED String CGC Tumour Types (Germline) Tumour types associated with mutations in an overlapping gene (germline mutations) Genes and Gene Predictions https://cancer.sanger.ac.uk/census ftp://[email protected]/bundle/oncotator/
Funcotator CGC Tumour_Types__(Somatic_Mutations) CGC_Somatic UNBOUNDED String CGC Tumour Types (Somatic) Tumour types associated with mutations in an overlapping gene (somatic mutations) Genes and Gene Predictions https://cancer.sanger.ac.uk/census ftp://[email protected]/bundle/oncotator/
Funcotator Capice CAPICE CAPICE A Float CAPICE Score Contains precomputed effect scores for InDels in genome build 37 Genes and Gene Predictions https://github.com/molgenis/capice https://download.molgeniscloud.org/downloads/vip/resources/GRCh37/ true
Funcotator Clinpred ClinPredScore ClinPredScore A Float ClinPred Score Pre-computed ClinPred scores for all possible human missense variants in the exome Genes and Gene Predictions https://pubmed.ncbi.nlm.nih.gov/30220433/ https://cvmfs-hubs.vhost38.genap.ca/~alirezai/ClinPred true
Funcotator dbSNP CAF AFby1000KG A String AF by 1000 Genomes "An ordered, comma delimited list of allele frequencies based on 1000Genomes, starting with the reference allele followed by alternate alleles as ordered in the ALT column. Where a 1000Genomes alternate allele is not in the dbSNPs alternate allele set, the allele is added to the ALT column. The minor allele is the second largest value in the list, and was previuosly reported in VCF as the GMAF. This is the GMAF reported on the RefSNP and EntrezSNP pages and VariationReporter" Variation and Repeats https://www.ncbi.nlm.nih.gov/projects/SNP/snp_summary.cgi ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b151_GRCh37p13/VCF/All_20180423.vcf.gz true
Funcotator dbSNP COMMON CommonSNP A String Is Common Human SNP RS is a common SNP. A common SNP is one that has at least one 1000Genomes population with a minor allele of frequency = 1% and for which 2 or more founders contribute to that minor allele frequency. Variation and Repeats https://www.ncbi.nlm.nih.gov/projects/SNP/snp_summary.cgi ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b151_GRCh37p13/VCF/All_20180423.vcf.gz true
Funcotator dbSNP dbSNPBuildID dbSNPBuildID A String dbSNP Build ID First dbSNP Build for RS Variation and Repeats https://www.ncbi.nlm.nih.gov/projects/SNP/snp_summary.cgi ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b151_GRCh37p13/VCF/All_20180423.vcf.gz
Funcotator dbSNP RS RS A String dbSNP ID dbSNP ID (i.e. rs number) Variation and Repeats https://www.ncbi.nlm.nih.gov/projects/SNP/snp_summary.cgi ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b151_GRCh37p13/VCF/All_20180423.vcf.gz
Funcotator ERB ERB_TYPE ERB_TYPE UNBOUNDED String Ensemble Regulatory Build Type Ensembl Regulatory Build classification Genes and Gene Predictions http://useast.ensembl.org/info/genome/funcgen/index.html http://ftp.ensembl.org/pub/current_regulation/homo_sapiens/homo_sapiens.GRCh38.Regulatory_Build.regulatory_features.20221007.gff.gz true
Funcotator Familial_Cancer_Genes Syndrome Fam_Synd UNBOUNDED String Familial Cancer Genes " A mapping of Familial Cancer Genes. This mapping goes from Gene Name to Syndrome, with Synonyms for the Syndrome itself and the Reference from which the association was created. Any implicated gene overlapping this variant is annotated." Genes and Gene Predictions http://www.broadinstitute.org/oncotator/ ftp://[email protected]/bundle/oncotator/
Funcotator FANTOM_ENHANCER ENHANCERID FANTOM_ENHNCRID UNBOUNDED String FANTOM ENHANCER ID "FANTOM5 used Cap Analysis of Gene Expression (CAGE) to map the sets of transcripts, transcription factors, promoters and enhancers active in the majority of mammalian primary cell types. This is the ID of overlapping enhancer elements" Genes and Gene Predictions https://www.internationalgenome.org/data-portal/sample funcotator bundle true
Funcotator FANTOM_ENHANCER SCORE FANTOM_SCORE UNBOUNDED String FANTOM Enhancer Score "FANTOM5 used Cap Analysis of Gene Expression (CAGE) to map the sets of transcripts, transcription factors, promoters and enhancers active in the majority of mammalian primary cell types. This is a score associated with overlapping enhancer elements" Genes and Gene Predictions https://www.internationalgenome.org/data-portal/sample https://fantom.gsc.riken.jp/5/datafiles/latest/extra/Enhancers/human_permissive_enhancers_phase_1_and_2.bed.gz true
Funcotator FANTOM_ENHANCER STRAND FANTOM_STRND UNBOUNDED String FATHOM Enhancer STRAND This is the strand of the overlapping enhancer Genes and Gene Predictions https://www.internationalgenome.org/data-portal/sample true
Funcotator FANTOM5_TFBS SCORE FANTOM_TFBS_SCORE UNBOUNDED Float FANTOM TFBS SCORE "The transcription factor binding score, computed by FANTOM" Genes and Gene Predictions https://fantom.gsc.riken.jp/5/ https://fantom.gsc.riken.jp/5/datafiles/phase1.3/extra/Motifs/TFBS/sites.txt.bz2 true
Funcotator FANTOM5_TFBS STRAND FANTOM_TFBS_STRAND UNBOUNDED String FANTOM TFBS Factor Strand "The strand on which the overlapping TFBS is predicted, computed by FANTOM" Genes and Gene Predictions https://fantom.gsc.riken.jp/5/ https://fantom.gsc.riken.jp/5/datafiles/phase1.3/extra/Motifs/TFBS/sites.txt.bz2 true
Funcotator FANTOM5_TFBS TF FANTOM_TF UNBOUNDED String FANTOM Transcription Factor "Transcription factor binding predicted to overlap this variant, computed by FANTOM" Genes and Gene Predictions https://fantom.gsc.riken.jp/5/ https://fantom.gsc.riken.jp/5/datafiles/phase1.3/extra/Motifs/TFBS/sites.txt.bz2 true
Funcotator FATHMM_MKL F_C F_C A Float FATHMM Score "This is the fathmm-MKL coding score, which is a prediction of the functional consequence of the variant. Predictions are given as p-values in the range [0, 1]: values above 0.5 are predicted to be deleterious, while those below 0.5 are predicted to be neutral or benign. P-values close to the extremes (0 or 1) are the highest-confidence predictions that yield the highest accuracy" Comparative Genomics http://fathmm.biocompute.org.uk/ http://fathmm.biocompute.org.uk/database/fathmm-MKL_Current.tab.gz true
Funcotator FATHMM_MKL F_CG F_CG A String FATHMM Functional Group "These are the functional groups defined by the fathmm-MKL coding score, indicating the categories of functional consequence. See the fanthamm paper for their meanings" Comparative Genomics http://fathmm.biocompute.org.uk/ http://fathmm.biocompute.org.uk/database/fathmm-MKL_Current.tab.gz true
Funcotator FATHMM_MKL F_NC F_NC A Float FATHMM Non-Coding Score "This is the fathmm-MKL noncoding score, which is a prediction of the functional consequence of the variant. Predictions are given as p-values in the range [0, 1]: values above 0.5 are predicted to be deleterious, while those below 0.5 are predicted to be neutral or benign. P-values close to the extremes (0 or 1) are the highest-confidence predictions that yield the highest accuracy" Comparative Genomics http://fathmm.biocompute.org.uk/ http://fathmm.biocompute.org.uk/database/fathmm-MKL_Current.tab.gz true
Funcotator FATHMM_MKL F_NCG F_NCG A String FATHMM Non-Coding Group "These are the functional groups defined by the fathmm-MKL non-coding score, indicating the categories of functional consequence. See the fanthamm paper for their meanings" Comparative Genomics http://fathmm.biocompute.org.uk/ http://fathmm.biocompute.org.uk/database/fathmm-MKL_Current.tab.gz false
Funcotator funseq2 FS2 FS2 UNBOUNDED Float Funseq2 Non-coding Score Funseq2 is designed to prioritize regulatory variants form cancer genome sequencing. This score is intended to predict the effect of non-coding variants. Genes and Gene Predictions http://funseq2.gersteinlab.org/ http://org.gersteinlab.funseq.s3-website-us-east-1.amazonaws.com/funseq2/hg19_wg_score.tsv.gz true
Funcotator gnomAD AF AF_gnomAD A Float gnomAD Allele frequency "Allele frequency from The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available for the wider scientific community." Comparative Genomics https://gnomad.broadinstitute.org/news/2020-10-gnomad-v3-1-new-content-methods-annotations-and-data-availability/ gs://gnomad-public/release/2.1/vcf/genomes/gnomad.genomes.r2.1.sites.vcf.bgz true
Funcotator gnomAD AF_afr gnomAD_AF_afr A Float gnomAD Allele frequency of African Individuals "AF_afr african allele frequency from The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available for the wider scientific community." Comparative Genomics https://gnomad.broadinstitute.org/news/2020-10-gnomad-v3-1-new-content-methods-annotations-and-data-availability/ gs://gnomad-public/release/2.1/vcf/genomes/gnomad.genomes.r2.1.sites.vcf.bgz
Funcotator gnomAD AF_amr gnomAD_AF_amr A Float gnomAD Allele frequency of American Individuals "AF_amr is the american allele frequency The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available for the wider scientific community." Comparative Genomics https://gnomad.broadinstitute.org/news/2020-10-gnomad-v3-1-new-content-methods-annotations-and-data-availability/ gs://gnomad-public/release/2.1/vcf/genomes/gnomad.genomes.r2.1.sites.vcf.bgz
Funcotator gnomAD AF_asj gnomAD_AF_AsJ A Float gnomAD Allele frequency of Ashkenazi Jewish Individuals "AF_asjAshkenazi Jewish allele frequency The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available for the wider scientific community." Comparative Genomics https://gnomad.broadinstitute.org/news/2020-10-gnomad-v3-1-new-content-methods-annotations-and-data-availability/ gs://gnomad-public/release/2.1/vcf/genomes/gnomad.genomes.r2.1.sites.vcf.bgz
Funcotator gnomAD AF_nfe gnomAD_AF_nfe A Float gnomAD Allele frequency of Non-Finnish European Individuals AF_nfe non finnish european allele frequency Allele frequency from The Genome Aggregation Database (gnomAD) Comparative Genomics https://gnomad.broadinstitute.org/news/2020-10-gnomad-v3-1-new-content-methods-annotations-and-data-availability/ gs://gnomad-public/release/2.1/vcf/genomes/gnomad.genomes.r2.1.sites.vcf.bgz
Funcotator LMMKnown LMM_FLAGGED LMM_FLAGGED A String LMM DNA Repair "Variants flagged as possibly having pathogenic effects found by the Laboratory for Molecular Medicine (LMM). A table of genes implicated in the repair of DNA. This is an update of the table cited in Wood RD, Mitchell M, & Lindahl T Mutation Research, 2005, in Science, 2001, in the reference book DNA Repair and Mutagenesis, 2nd edition, 2006, and in Nature Reviews Cancer, 2011." Genes and Gene Predictions https://personalizedmedicine.partners.org/laboratory-for-molecular-medicine/ gs://gnomad-public/release/2.1/vcf/genomes/gnomad.genomes.r2.1.sites.vcf.bgz
Funcotator Omim GENESYMBOL OMIM_GENESYMBOL UNBOUNDED String OMIM Gene The Ensembl gene symbol for overlapping OMIM genes Genes and Gene Predictions https://omim.org/ https://omim.org/static/omim/data/genemap2.txt true
Funcotator Omim MIMNUMBER MIMNUMBER UNBOUNDED String OMIM ID The OMIM ID number for gene/phenotypes overlapping this variant Genes and Gene Predictions https://omim.org/ https://omim.org/static/omim/data/genemap2.txt true
Funcotator Omim PHENOTYPES OMIM_PHENO UNBOUNDED String OMIM Disorder/Phenotype(s) OMIM phenotypes associated with an overlapping gene Genes and Gene Predictions https://omim.org/ https://omim.org/static/omim/data/genemap2.txt true
Funcotator Oreganno Values OR_V UNBOUNDED String Oreganno Known Regulatory Elements This lists known regulatory elements overlapping this variant Variation and Repeats https://www.bcgsc.ca/resources/software/oreganno http://www.oreganno.org/dump/ORegAnno_Combined_2016.01.19.tsv true
Funcotator phylop_placental PHYLOP_PLACENTAL PHYLOP_PLCNTL UNBOUNDED Float Phylop Conservation Score in Placental Mammals "Phylop conservation scores PhyloP basewise conservation score derived from Multiz alignment of 46 vertebrate species. This series includes two SGA files, one for all vertebrates and one for placental mammals only." Comparative Genomics https://ccg.epfl.ch/mga/hg19/phylop/phylop.html https://ccg.epfl.ch/mga/hg19/phylop/phylop_placental.sga.gz true
Funcotator phylop_vert PHYLOP_VERT PHYLOP_VRT UNBOUNDED Float Phylop Conservation Score in Vertebrates "Phylop conservation scores PhyloP basewise conservation score derived from Multiz alignment of 46 vertebrate species. This series includes two SGA files, one for all vertebrates and one for vertabrates." Comparative Genomics https://ccg.epfl.ch/mga/hg19/phylop/phylop.html https://ccg.epfl.ch/mga/hg19/phylop/phylop_placental.sga.gz true
Funcotator Simple_Uniprot GO_Biological_Process GO_BP UNBOUNDED String GO Biological Process The GO biological process of overlapping genes Genes and Gene Predictions http://geneontology.org/ ftp://[email protected]/bundle/oncotator/
Funcotator Simple_Uniprot GO_Cellular_Component GO_CC UNBOUNDED String GO Cellular Component The GO cellular component of overlapping genes Genes and Gene Predictions http://geneontology.org/ ftp://[email protected]/bundle/oncotator/
Funcotator Simple_Uniprot GO_Molecular_Function GO_MF UNBOUNDED String GO Molecular Function The GO molecular function of overlapping genes Genes and Gene Predictions http://geneontology.org/ ftp://[email protected]/bundle/oncotator/
Funcotator Siphy BranchLength SP_BL A String Siphy Base Selection Detects bases under selection. Reports the branch length of the 29 mammals with omega lods elements and fdr of .01 to compute branch lengths Genes and Gene Predictions http://portals.broadinstitute.org/genome_bio/siphy/index.html www.broadinstitute.org/ftp/pub/assemblies/mammals/29mammals/hg19/hg19_29way_omega_lods_elements_12mers.chr_specific.fdr_0.1_with_scores.txt.gz
Funcotator Siphy LODSCORE SP_LODSCORE A Float Siphy LOD SCORE Detects bases under selection. This is the theoretical chis-sequared p-value of the obtained log-odds ratio. Genes and Gene Predictions http://portals.broadinstitute.org/genome_bio/siphy/index.html www.broadinstitute.org/ftp/pub/assemblies/mammals/29mammals/hg19/hg19_29way_omega_lods_elements_12mers.chr_specific.fdr_0.1_with_scores.txt.gz
Funcotator dbNSFP VEP_canonical VEP_canonical A String VEP canonical HGVSc_VEP: HGVS coding variant presentation from VEP Functional Predictions
Funcotator dbNSFP Aloft_Confidence Aloft_Confidence A String 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." Functional Predictions http://aloft.gersteinlab.org/
Funcotator dbNSFP Aloft_Fraction_transcripts_affected Aloft_Fraction_transcripts_affected A String 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." Functional Predictions http://aloft.gersteinlab.org/
Funcotator dbNSFP Aloft_pred Aloft_pred A String Aloft pred "final classification predicted by ALoFT; values can be Tolerant, Recessive or Dominant multiple values separated by ;, corresponding to Ensembl_proteinid." Functional Predictions http://aloft.gersteinlab.org/
Funcotator dbNSFP Aloft_prob_Dominant Aloft_prob_Dominant A String Aloft prob Dominant "Probability of the SNP being classified as dominant disease-causing by ALoFT multiple values separated by ;, corresponding to Ensembl_proteinid." Functional Predictions http://aloft.gersteinlab.org/
Funcotator dbNSFP Aloft_prob_Recessive Aloft_prob_Recessive A String Aloft prob Recessive "Probability of the SNP being classified as recessive disease-causing by ALoFT multiple values separated by ;, corresponding to Ensembl_proteinid." Functional Predictions http://aloft.gersteinlab.org/
Funcotator dbNSFP Aloft_prob_Tolerant Aloft_prob_Tolerant A String Aloft prob Tolerant "Probability of the SNP being classified as benign by ALoFT multiple values separated by ;, corresponding to Ensembl_proteinid." Functional Predictions http://aloft.gersteinlab.org/
Funcotator dbNSFP BayesDel_addAF_pred BayesDel_addAF_pred A String 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." Functional Predictions http://fengbj-laboratory.org/BayesDel/BayesDel.html true
Funcotator dbNSFP BayesDel_addAF_rankscore BayesDel_addAF_RS A 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. Functional Predictions http://fengbj-laboratory.org/BayesDel/BayesDel.html true
Funcotator dbNSFP BayesDel_addAF_score BayesDel_addAF_S A Float BayesDel addAF score "A deleteriousness preidction meta-score for SNVs and indels with inclusion of MaxAF. See https 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." Functional Predictions http://fengbj-laboratory.org/BayesDel/BayesDel.html true
Funcotator dbNSFP BayesDel_noAF_pred BayesDel_noAF_pred A String 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." Functional Predictions http://fengbj-laboratory.org/BayesDel/BayesDel.html true
Funcotator dbNSFP BayesDel_noAF_rankscore BayesDel_noAF_RS A 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. Functional Predictions http://fengbj-laboratory.org/BayesDel/BayesDel.html true
Funcotator dbNSFP BayesDel_noAF_score BayesDel_noAF_S A Float BayesDel noAF score "A deleteriousness preidction meta-score for SNVs and indels without inclusion of MaxAF. See https The higher the score, the more likely the variant is pathogenic. The author suggested cutoff between deleterious (D) and tolerated (T) is -0.0570105." Functional Predictions http://fengbj-laboratory.org/BayesDel/BayesDel.html true
Funcotator dbNSFP DANN_rankscore DANN_RS A 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. Functional Predictions https://cbcl.ics.uci.edu/public_data/DANN/
Funcotator dbNSFP DANN_score DANN_S A Float 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. Functional Predictions https://cbcl.ics.uci.edu/public_data/DANN/
Funcotator dbNSFP DEOGEN2_pred DEOGEN2_pred A String 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." Functional Predictions https://deogen2.mutaframe.com/
Funcotator dbNSFP DEOGEN2_rankscore DEOGEN2_RS A 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. Functional Predictions https://deogen2.mutaframe.com/
Funcotator dbNSFP DEOGEN2_score DEOGEN2_S A 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. 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." Functional Predictions https://deogen2.mutaframe.com/
Funcotator dbNSFP Eigen-PC-phred_coding Eigen_PC_phred_coding A Float Eigen-PC-phred coding Eigen PC score in phred scale. Functional Predictions http://www.columbia.edu/~ii2135/eigen.html
Funcotator dbNSFP Eigen-PC-raw_coding Eigen_PC_raw_coding A Float Eigen-PC-raw coding Eigen PC score for genome-wide SNVs. A functional prediction score based on Functional Predictions http://www.columbia.edu/~ii2135/eigen.html
Funcotator dbNSFP Eigen-PC-raw_coding_rankscore Eigen_PC_raw_coding_RS A 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. Functional Predictions http://www.columbia.edu/~ii2135/eigen.html
Funcotator dbNSFP Eigen-phred_coding Eigen_phred_coding A Float Eigen-phred coding Eigen score in phred scale. Functional Predictions http://www.columbia.edu/~ii2135/eigen.html
Funcotator dbNSFP Eigen-raw_coding Eigen_raw_coding A 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" Functional Predictions http://www.columbia.edu/~ii2135/eigen.html
Funcotator dbNSFP Eigen-raw_coding_rankscore Eigen_raw_coding_RS A 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. Functional Predictions http://www.columbia.edu/~ii2135/eigen.html
Funcotator dbNSFP FATHMM_converted_rankscore FATHMM_converted_RS A 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. If there are multiple scores, only the most damaging (largest) rankscore is presented. The scores range from 0 to 1." Functional Predictions http://fathmm.biocompute.org.uk true
Funcotator dbNSFP FATHMM_pred FATHMM_pred A String 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." Functional Predictions http://fathmm.biocompute.org.uk true
Funcotator dbNSFP FATHMM_score FATHMM_S A Float 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." Functional Predictions http://fathmm.biocompute.org.uk true
Funcotator dbNSFP fathmm-MKL_coding_group fathmm_MKL_coding_group A String 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. Functional Predictions http://fathmm.biocompute.org.uk/fathmmMKL.htm true
Funcotator dbNSFP fathmm-MKL_coding_pred fathmm_MKL_coding_pred A String 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).129 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. Functional Predictions http://fathmm.biocompute.org.uk/fathmmMKL.htm true
Funcotator dbNSFP fathmm-MKL_coding_rankscore fathmm_MKL_coding_RS A 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. Functional Predictions http://fathmm.biocompute.org.uk/fathmmMKL.htm true
Funcotator dbNSFP fathmm-MKL_coding_score fathmm_MKL_coding_S A Float 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." Functional Predictions http://fathmm.biocompute.org.uk/fathmmMKL.htm true
Funcotator dbNSFP fathmm-XF_coding_pred fathmm_XF_coding_pred A String 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)." Functional Predictions http://fathmm.biocompute.org.uk/fathmm-xf/ true
Funcotator dbNSFP fathmm-XF_coding_rankscore fathmm_XF_coding_RS A 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. Functional Predictions http://fathmm.biocompute.org.uk/fathmm-xf/ true
Funcotator dbNSFP fathmm-XF_coding_score fathmm_XF_coding_S A Float 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." Functional Predictions http://fathmm.biocompute.org.uk/fathmm-xf/ true
Funcotator dbNSFP GenoCanyon_rankscore GenoCanyon_RS A 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. Functional Predictions http://genocanyon.med.yale.edu/index.html true
Funcotator dbNSFP GenoCanyon_score GenoCanyon_S A Float GenoCanyon score A functional prediction score based on conservation and biochemical annotations using an unsupervised statistical learning. (doi Functional Predictions http://genocanyon.med.yale.edu/index.html true
Funcotator dbNSFP GERP++_NR GERP_NR A String GERP++ NR GERP++ neutral rate Functional Predictions http://mendel.stanford.edu/SidowLab/downloads/gerp/ false
Funcotator dbNSFP GERP++_RS GERP_RS A Float GERP++ RS "GERP++ RS score, the larger the score, the more conserved the site. Scores range from -12.3 to 6.17." Functional Predictions http://mendel.stanford.edu/SidowLab/downloads/gerp/ true
Funcotator dbNSFP GERP++_RS_rankscore GERP_RS_RS A 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. Functional Predictions http://mendel.stanford.edu/SidowLab/downloads/gerp/ true
Funcotator dbNSFP GM12878_confidence_value GM12878_confidence_value A Float 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). Functional Predictions http://compgen.bscb.cornell.edu/fitCons/ true
Funcotator dbNSFP GM12878_fitCons_rankscore GM12878_fitCons_RS A 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. Functional Predictions http://compgen.bscb.cornell.edu/fitCons/ true
Funcotator dbNSFP GM12878_fitCons_score GM12878_fitCons_S A Float 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" Functional Predictions http://compgen.bscb.cornell.edu/fitCons/ true
Funcotator dbNSFP H1-hESC_confidence_value H1_hESC_confidence_value A Float 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). Functional Predictions http://compgen.bscb.cornell.edu/fitCons/
Funcotator dbNSFP H1-hESC_fitCons_rankscore H1_hESC_fitCons_RS A 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. Functional Predictions http://compgen.bscb.cornell.edu/fitCons/
Funcotator dbNSFP H1-hESC_fitCons_score H1_hESC_fitCons_S A Float 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" Functional Predictions http://compgen.bscb.cornell.edu/fitCons/
Funcotator dbNSFP HUVEC_confidence_value HUVEC_confidence_value A Float 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). Functional Predictions http://compgen.bscb.cornell.edu/fitCons/
Funcotator dbNSFP HUVEC_fitCons_rankscore HUVEC_fitCons_RS A 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. Functional Predictions http://compgen.bscb.cornell.edu/fitCons/
Funcotator dbNSFP HUVEC_fitCons_score HUVEC_fitCons_S A Float 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" Functional Predictions http://compgen.bscb.cornell.edu/fitCons/
Funcotator dbNSFP integrated_confidence_value integrated_confidence_value A Float 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). Functional Predictions http://compgen.bscb.cornell.edu/fitCons/
Funcotator dbNSFP integrated_fitCons_rankscore integrated_fitCons_RS A 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. Functional Predictions http://compgen.bscb.cornell.edu/fitCons/
Funcotator dbNSFP integrated_fitCons_score integrated_fitCons_S A 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. 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 doi10.1038/ng.3196." Functional Predictions http://compgen.bscb.cornell.edu/fitCons/
Funcotator dbNSFP LINSIGHT LINSIGHT A Float LINSIGHT The LINSIGHT score measures the probability of negative selection on noncoding sites Details refer to doi Functional Predictions http://compgen.cshl.edu/~yihuang/LINSIGHT/
Funcotator dbNSFP LINSIGHT_rankscore LINSIGHT_RS A 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. Functional Predictions http://compgen.cshl.edu/~yihuang/LINSIGHT/
Funcotator dbNSFP LIST-S2_pred LIST_S2_pred A String 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." Functional Predictions https://precomputed.list-s2.msl.ubc.ca/
Funcotator dbNSFP LIST-S2_rankscore LIST_S2_RS A 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. Functional Predictions https://precomputed.list-s2.msl.ubc.ca/
Funcotator dbNSFP LIST-S2_score LIST_S2_S A Float LIST-S2 score "A deleteriousness preidction score for nonsynonymous SNVs. See https 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." Functional Predictions https://precomputed.list-s2.msl.ubc.ca/
Funcotator dbNSFP LRT_converted_rankscore LRT_converted_RS A Float LRT converted rankscore "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." Functional Predictions http://www.genetics.wustl.edu/jflab/lrt_query.html
Funcotator dbNSFP LRT_Omega LRT_Omega A Float LRT Omega "estimated nonsynonymous-to-synonymous-rate ratio (Omega, reported by LRT)" Functional Predictions http://www.genetics.wustl.edu/jflab/lrt_query.html
Funcotator dbNSFP LRT_pred LRT_pred A String LRT pred "LRT prediction, D(eleterious), N(eutral) or U(nknown), which is not solely determined by the score." Functional Predictions http://www.genetics.wustl.edu/jflab/lrt_query.html
Funcotator dbNSFP LRT_score LRT_S A Float LRT score "The original LRT two-sided p-value (LRTori), ranges from 0 to 1." Functional Predictions http://www.genetics.wustl.edu/jflab/lrt_query.html
Funcotator dbNSFP M-CAP_pred M_CAP_pred A String 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." Functional Predictions http://bejerano.stanford.edu/MCAP/
Funcotator dbNSFP M-CAP_rankscore M_CAP_RS A 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. Functional Predictions http://bejerano.stanford.edu/MCAP/
Funcotator dbNSFP M-CAP_score M_CAP_S A Float M-CAP score M-CAP is hybrid ensemble score (details in DOI from 0 to 1. The larger the score the more likely the SNP has damaging effect. Functional Predictions http://bejerano.stanford.edu/MCAP/
Funcotator dbNSFP MetaLR_pred MetaLR_pred A String 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." Functional Predictions doi: 10.1093/hmg/ddu733
Funcotator dbNSFP MetaLR_rankscore MetaLR_RS A 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. The scores range from 0 to 1. Functional Predictions doi: 10.1093/hmg/ddu733
Funcotator dbNSFP MetaLR_score MetaLR_S A Float 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." Functional Predictions doi: 10.1093/hmg/ddu733
Funcotator dbNSFP MetaSVM_pred MetaSVM_pred A String 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." Functional Predictions doi: 10.1093/hmg/ddu733
Funcotator dbNSFP MetaSVM_rankscore MetaSVM_RS A 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. The scores range from 0 to 1. Functional Predictions doi: 10.1093/hmg/ddu733
Funcotator dbNSFP MetaSVM_score MetaSVM_S A Float 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." Functional Predictions doi: 10.1093/hmg/ddu733
Funcotator dbNSFP MPC_rankscore MPC_RS A 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. Functional Predictions ftp://ftp.broadinstitute.org/pub/ExAC_release/release1/regional_missense_constraint/
Funcotator dbNSFP MPC_score MPC_S A Float 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 Multiple entries are separated by ;, corresponding to Ensembl_transcriptid." Functional Predictions ftp://ftp.broadinstitute.org/pub/ExAC_release/release1/regional_missense_constraint/
Funcotator dbNSFP MutationAssessor_pred MutationAssessor_pred A String 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." Functional Predictions http://mutationassessor.org/
Funcotator dbNSFP MutationAssessor_rankscore MutationAssessor_RS A 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. The scores range from 0 to 1. Functional Predictions http://mutationassessor.org/
Funcotator dbNSFP MutationAssessor_score MutationAssessor_S A Float MutationAssessor score MutationAssessor functional impact combined score (MAori). The score ranges from -5.17 to 6.49 in dbNSFP. Functional Predictions http://mutationassessor.org/
Funcotator dbNSFP MutationTaster_AAE MutationTaster_AAE A Float MutationTaster AAE MutationTaster predicted amino acid change. Functional Predictions http://www.mutationtaster.org/
Funcotator dbNSFP MutationTaster_converted_rankscore MutationTaster_converted_RS A 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. 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." Functional Predictions http://www.mutationtaster.org/
Funcotator dbNSFP MutationTaster_model MutationTaster_model A Float MutationTaster model MutationTaster prediction models. Functional Predictions http://www.mutationtaster.org/
Funcotator dbNSFP MutationTaster_pred MutationTaster_pred A String 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." Functional Predictions http://www.mutationtaster.org/
Funcotator dbNSFP MutationTaster_score MutationTaster_S A Float 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" Functional Predictions http://www.mutationtaster.org/
Funcotator dbNSFP MutPred_AAchange MutPred_AAchange A Float MutPred AAchange Amino acid change used for MutPred_score calculation. Functional Predictions http://mutpred.mutdb.org/
Funcotator dbNSFP MutPred_protID MutPred_protID A Float MutPred protID UniProt accession or Ensembl transcript ID used for MutPred_score calculation. Functional Predictions http://mutpred.mutdb.org/
Funcotator dbNSFP MutPred_rankscore MutPred_RS A 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.87 MutPred_protID88 MutPred_AAchange89 MutPred_Top5features 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. Functional Predictions http://mutpred.mutdb.org/
Funcotator dbNSFP MutPred_score MutPred_S A Float MutPred score General MutPred score. Scores range from 0 to 1. The larger the score the more likely the SNP has damaging effect. Functional Predictions http://mutpred.mutdb.org/
Funcotator dbNSFP MutPred_Top5features MutPred_Top5features A Float 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. Functional Predictions http://mutpred.mutdb.org/
Funcotator dbNSFP MVP_rankscore MVP_RS A 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. 92 MPC_score constraint. The range of MPC score is 0 to 5. The larger the score, the more likely the variant is pathogenic. Details see doi Multiple entries are separated by ;, corresponding to Ensembl_transcriptid." Functional Predictions https://github.com/ShenLab/missense
Funcotator dbNSFP MVP_score MVP_S A Float 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 Multiple entries are separated by ;, corresponding to Ensembl_transcriptid." Functional Predictions https://github.com/ShenLab/missense
Funcotator dbNSFP phastCons100way_vertebrate phastCons100way_vertebrate A 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. Scores range from 0 to 1." Comparative Genomics http://hgdownload.soe.ucsc.edu/goldenPath/hg38/phastCons100way/ true
Funcotator dbNSFP phastCons100way_vertebrate_rankscore phastCons100way_vertebrate_RS A 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. Comparative Genomics http://hgdownload.soe.ucsc.edu/goldenPath/hg38/phastCons100way/ true
Funcotator dbNSFP phastCons17way_primate phastCons17way_primate A Float 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." Comparative Genomics http://hgdownload.soe.ucsc.edu/goldenPath/hg38/phastCons17way/ true
Funcotator dbNSFP phastCons17way_primate_rankscore phastCons17way_primate_RS A Float phastCons17way primate rankscore the rank of the phastCons17way_primate score among all phastCons17way_primate scores in dbNSFP. Comparative Genomics http://hgdownload.soe.ucsc.edu/goldenPath/hg38/phastCons17way/ true
Funcotator dbNSFP phastCons470way_mammalian phastCons470way_mammalian A Float phastCons470way mammalian "phastCons conservation score based on the multiple alignmentsof 470 mammalian genomes (including human). The larger the score, the more conserved the site. Scores range from 0 to 1." Comparative Genomics https://hgdownload.cse.ucsc.edu/goldenpath/hg38/phastCons470way/ true
Funcotator dbNSFP phastCons470way_mammalian_rankscore phastCons470way_mammalian_RS A 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. Comparative Genomics https://hgdownload.cse.ucsc.edu/goldenpath/hg38/phastCons470way/ true
Funcotator dbNSFP phyloP100way_vertebrate phyloP100way_vertebrate A 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. Scores range from -20.0 to 10.003 in dbNSFP." Comparative Genomics http://hgdownload.soe.ucsc.edu/goldenPath/hg38/phyloP100way/ true
Funcotator dbNSFP phyloP100way_vertebrate_rankscore phyloP100way_vertebrate_RS A 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. Comparative Genomics http://hgdownload.soe.ucsc.edu/goldenPath/hg38/phyloP100way/ true
Funcotator dbNSFP phyloP17way_primate phyloP17way_primate A Float 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." Comparative Genomics http://hgdownload.soe.ucsc.edu/goldenPath/hg38/phyloP17way/ true
Funcotator dbNSFP phyloP17way_primate_rankscore phyloP17way_primate_RS A Float phyloP17way primate rankscore the rank of the phyloP17way_primate score among all phyloP17way_primate scores in dbNSFP. Comparative Genomics http://hgdownload.soe.ucsc.edu/goldenPath/hg38/phyloP17way/ true
Funcotator dbNSFP phyloP470way_mammalian phyloP470way_mammalian A Float phyloP 470-way mammalian rankscore "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." Comparative Genomics https://hgdownload.soe.ucsc.edu/goldenPath/hg38/phyloP470way/ true
Funcotator dbNSFP phyloP470way_mammalian_rankscore phyloP470way_mammalian_RS A Float phyloP 470-way 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 Comparative Genomics https://hgdownload.soe.ucsc.edu/goldenPath/hg38/phyloP470way/ true
Funcotator dbNSFP Polyphen2_HDIV_pred Polyphen2_HDIV_pred A String 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." Functional Predictions http://genetics.bwh.harvard.edu/pph2/ true true
Funcotator dbNSFP Polyphen2_HDIV_rankscore Polyphen2_HDIV_RS A 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. If there are multiple scores, only the most damaging (largest) rankscore is presented. The scores range from 0.03061 to 0.91137." Functional Predictions http://genetics.bwh.harvard.edu/pph2/ true
Funcotator dbNSFP Polyphen2_HDIV_score Polyphen2_HDIV_S A Float 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." Functional Predictions http://genetics.bwh.harvard.edu/pph2/ true
Funcotator dbNSFP Polyphen2_HVAR_pred Polyphen2_HVAR_pred A String Polyphen2 HVAR pred "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." Functional Predictions http://genetics.bwh.harvard.edu/pph2/ true
Funcotator dbNSFP Polyphen2_HVAR_rankscore Polyphen2_HVAR_RS A 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. If there are multiple scores, only the most damaging (largest) rankscore is presented. The scores range from 0.01493 to 0.97581." Functional Predictions http://genetics.bwh.harvard.edu/pph2/ true
Funcotator dbNSFP Polyphen2_HVAR_score Polyphen2_HVAR_S A Float 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" Functional Predictions http://genetics.bwh.harvard.edu/pph2/ true
Funcotator dbNSFP PrimateAI_pred PrimateAI_pred A String 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." Functional Predictions https://github.com/Illumina/PrimateAI true
Funcotator dbNSFP PrimateAI_rankscore PrimateAI_RS A 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. Functional Predictions https://github.com/Illumina/PrimateAI true
Funcotator dbNSFP PrimateAI_score PrimateAI_S A 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 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" Functional Predictions https://github.com/Illumina/PrimateAI true
Funcotator dbNSFP PROVEAN_converted_rankscore PROVEAN_converted_RS A 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. If there are multiple scores, only the most damaging (largest) rankscore is presented. The scores range from 0 to 1." Functional Predictions
Funcotator dbNSFP PROVEAN_pred PROVEAN_pred A String 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." Functional Predictions
Funcotator dbNSFP PROVEAN_score PROVEAN_S A Float 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." Functional Predictions
Funcotator dbNSFP Reliability_index Reliability_index A Float 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." Functional Predictions
Funcotator dbNSFP REVEL_rankscore REVEL_RS A 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. Functional Predictions https://sites.google.com/site/revelgenomics/
Funcotator dbNSFP REVEL_score REVEL_S A Float 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 ([email protected]) Multiple entries are separated by ;, corresponding to Ensembl_transcriptid." Functional Predictions https://sites.google.com/site/revelgenomics/
Funcotator dbNSFP SIFT_converted_rankscore SIFT_converted_RS A 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. If there are multiple scores, only the most damaging (largest) rankscore is presented.The rankscores range from 0.00964 to 0.91255." Functional Predictions http://provean.jcvi.org/index.php true
Funcotator dbNSFP SIFT_pred SIFT_pred A String 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 ; Functional Predictions http://provean.jcvi.org/index.php true
Funcotator dbNSFP SIFT_score SIFT_S A Float SIFT score "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." Functional Predictions https://usf.app.box.com/s/6yi6huheisol3bhmld8bitcon1oi53pm true
Funcotator dbNSFP SIFT4G_converted_rankscore SIFT4G_converted_RS A 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. If there are multiple scores, only the most damaging (largest) rankscore is presented." Functional Predictions http://sift.bii.a-star.edu.sg/sift4g/public//Homo_sapiens/ true
Funcotator dbNSFP SIFT4G_pred SIFT4G_pred A String 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 commas, corresponding to Ensembl_transcriptid" Functional Predictions http://sift.bii.a-star.edu.sg/sift4g/public//Homo_sapiens/ true
Funcotator dbNSFP SIFT4G_score SIFT4G_S A Float SIFT4G score "SIFT 4G score (SIFT4G). Scores range from 0 to 1. The smaller the score themore likely the SNP has damaging effect. Multiple scores separated by comma, corresponding to Ensembl_transcriptid" Functional Predictions http://sift.bii.a-star.edu.sg/sift4g/public//Homo_sapiens/ true
Funcotator dbNSFP VEST4_rankscore VEST4_RS A 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. 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 the Johns Hopkins Technology Transfer office." Functional Predictions http://karchinlab.org/apps/appVest.html true
Funcotator dbNSFP VEST4_score VEST4_S A Float 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 the Johns Hopkins Technology Transfer office." Functional Predictions http://karchinlab.org/apps/appVest.html true