.. _dbNSFP_variants: dbNSFP_variants =============== * **Versions:** 4.0 * **Reference genome builds:** GRCh37, GRCh38 * **Type:** :class:`hail.Table` Schema (4.0, GRCh37) ~~~~~~~~~~~~~~~~~~~~ .. code-block:: text ---------------------------------------- Global fields: None ---------------------------------------- Row fields: 'pos(1-based)': int32 'ref': str 'alt': str 'aaref': str 'aaalt': str 'rs_dbSNP151': str 'hg19_chr': str 'hg19_pos(1-based)': int32 'hg18_chr': str 'hg18_pos(1-based)': int32 'aapos': str 'genename': str 'Ensembl_geneid': str 'Ensembl_transcriptid': str 'Ensembl_proteinid': str 'Uniprot_acc': str 'Uniprot_entry': str 'HGVSc_ANNOVAR': str 'HGVSp_ANNOVAR': str 'HGVSc_snpEff': str 'HGVSp_snpEff': str 'HGVSc_VEP': str 'HGVSp_VEP': str 'APPRIS': str 'GENCODE_basic': str 'TSL': str 'VEP_canonical': str 'cds_strand': str 'refcodon': str 'codonpos': str 'codon_degeneracy': str 'Ancestral_allele': str 'AltaiNeandertal': str 'Denisova': str 'VindijiaNeandertal': str 'SIFT_score': str 'SIFT_converted_rankscore': float64 'SIFT_pred': str 'SIFT4G_score': str 'SIFT4G_converted_rankscore': float64 'SIFT4G_pred': str 'Polyphen2_HDIV_score': str 'Polyphen2_HDIV_rankscore': float64 'Polyphen2_HDIV_pred': str 'Polyphen2_HVAR_score': str 'Polyphen2_HVAR_rankscore': float64 'Polyphen2_HVAR_pred': str 'LRT_score': float64 'LRT_converted_rankscore': float64 'LRT_pred': str 'LRT_Omega': float64 'MutationTaster_score': str 'MutationTaster_converted_rankscore': float64 'MutationTaster_pred': str 'MutationTaster_model': str 'MutationTaster_AAE': str 'MutationAssessor_score': str 'MutationAssessor_rankscore': float64 'MutationAssessor_pred': str 'FATHMM_score': str 'FATHMM_converted_rankscore': float64 'FATHMM_pred': str 'PROVEAN_score': str 'PROVEAN_converted_rankscore': float64 'PROVEAN_pred': str 'VEST4_score': str 'VEST4_rankscore': float64 'MetaSVM_score': float64 'MetaSVM_rankscore': float64 'MetaSVM_pred': str 'MetaLR_score': float64 'MetaLR_rankscore': float64 'MetaLR_pred': str 'Reliability_index': int32 'M-CAP_score': float64 'M-CAP_rankscore': float64 'M-CAP_pred': str 'REVEL_score': float64 'REVEL_rankscore': float64 'MutPred_score': str 'MutPred_rankscore': float64 'MutPred_protID': str 'MutPred_AAchange': str 'MutPred_Top5features': str 'MVP_score': str 'MVP_rankscore': float64 'MPC_score': str 'MPC_rankscore': float64 'PrimateAI_score': float64 'PrimateAI_rankscore': float64 'PrimateAI_pred': str 'DEOGEN2_score': str 'DEOGEN2_rankscore': float64 'DEOGEN2_pred': str 'Aloft_Fraction_transcripts_affected': str 'Aloft_prob_Tolerant': str 'Aloft_prob_Recessive': str 'Aloft_prob_Dominant': str 'Aloft_pred': str 'Aloft_Confidence': str 'CADD_raw': float64 'CADD_raw_rankscore': float64 'CADD_phred': float64 'DANN_score': float64 'DANN_rankscore': float64 'fathmm-MKL_coding_score': float64 'fathmm-MKL_coding_rankscore': float64 'fathmm-MKL_coding_pred': str 'fathmm-MKL_coding_group': str 'fathmm-XF_coding_score': float64 'fathmm-XF_coding_rankscore': float64 'fathmm-XF_coding_pred': str 'Eigen-raw_coding': float64 'Eigen-raw_coding_rankscore': float64 'Eigen-pred_coding': float64 'Eigen-PC-raw_coding': float64 'Eigen-PC-raw_coding_rankscore': float64 'Eigen-PC-phred_coding': float64 'GenoCanyon_score': float64 'GenoCanyon_rankscore': float64 'integrated_fitCons_score': float64 'integrated_fitCons_rankscore': float64 'integrated_confidence_value': int32 'GM12878_fitCons_score': float64 'GM12878_fitCons_rankscore': float64 'GM12878_confidence_value': int32 'H1-hESC_fitCons_score': float64 'H1-hESC_fitCons_rankscore': float64 'H1-hESC_confidence_value': int32 'HUVEC_fitCons_score': float64 'HUVEC_fitCons_rankscore': float64 'HUVEC_confidence_value': int32 'LINSIGHT': float64 'LINSIGHT_rankscore': float64 'GERP++_NR': float64 'GERP++_RS': float64 'GERP++_RS_rankscore': float64 'phyloP100way_vertebrate': float64 'phyloP100way_vertebrate_rankscore': float64 'phyloP30way_mammalian': float64 'phyloP30way_mammalian_rankscore': float64 'phyloP17way_primate': float64 'phyloP17way_primate_rankscore': float64 'phastCons100way_vertebrate': float64 'phastCons100way_vertebrate_rankscore': float64 'phastCons30way_mammalian': float64 'phastCons30way_mammalian_rankscore': float64 'phastCons17way_primate': float64 'phastCons17way_primate_rankscore': float64 'SiPhy_29way_pi': str 'SiPhy_29way_logOdds': float64 'SiPhy_29way_logOdds_rankscore': float64 'bStatistic': int32 'bStatistic_rankscore': float64 '1000Gp3_AC': int32 '1000Gp3_AF': float64 '1000Gp3_AFR_AC': int32 '1000Gp3_AFR_AF': float64 '1000Gp3_EUR_AC': int32 '1000Gp3_EUR_AF': float64 '1000Gp3_AMR_AC': int32 '1000Gp3_AMR_AF': float64 '1000Gp3_EAS_AC': int32 '1000Gp3_EAS_AF': float64 '1000Gp3_SAS_AC': int32 '1000Gp3_SAS_AF': float64 'TWINSUK_AC': int32 'TWINSUK_AF': float64 'ALSPAC_AC': int32 'ALSPAC_AF': float64 'UK10K_AC': int32 'UK10K_AF': float64 'ESP6500_AA_AC': int32 'ESP6500_AA_AF': float64 'ESP6500_EA_AC': int32 'ESP6500_EA_AF': float64 'ExAC_AC': int32 'ExAC_AF': float64 'ExAC_Adj_AC': int32 'ExAC_Adj_AF': float64 'ExAC_AFR_AC': int32 'ExAC_AFR_AF': float64 'ExAC_AMR_AC': int32 'ExAC_AMR_AF': float64 'ExAC_EAS_AC': int32 'ExAC_EAS_AF': float64 'ExAC_FIN_AC': int32 'ExAC_FIN_AF': float64 'ExAC_NFE_AC': int32 'ExAC_NFE_AF': float64 'ExAC_SAS_AC': int32 'ExAC_SAS_AF': float64 'ExAC_nonTCGA_AC': int32 'ExAC_nonTCGA_AF': float64 'ExAC_nonTCGA_Adj_AC': int32 'ExAC_nonTCGA_Adj_AF': float64 'ExAC_nonTCGA_AFR_AC': int32 'ExAC_nonTCGA_AFR_AF': float64 'ExAC_nonTCGA_AMR_AC': int32 'ExAC_nonTCGA_AMR_AF': float64 'ExAC_nonTCGA_EAS_AC': int32 'ExAC_nonTCGA_EAS_AF': float64 'ExAC_nonTCGA_FIN_AC': int32 'ExAC_nonTCGA_FIN_AF': float64 'ExAC_nonTCGA_NFE_AC': int32 'ExAC_nonTCGA_NFE_AF': float64 'ExAC_nonTCGA_SAS_AC': int32 'ExAC_nonTCGA_SAS_AF': float64 'ExAC_nonpsych_AC': int32 'ExAC_nonpsych_AF': float64 'ExAC_nonpsych_Adj_AC': int32 'ExAC_nonpsych_Adj_AF': float64 'ExAC_nonpsych_AFR_AC': int32 'ExAC_nonpsych_AFR_AF': float64 'ExAC_nonpsych_AMR_AC': int32 'ExAC_nonpsych_AMR_AF': float64 'ExAC_nonpsych_EAS_AC': int32 'ExAC_nonpsych_EAS_AF': float64 'ExAC_nonpsych_FIN_AC': int32 'ExAC_nonpsych_FIN_AF': float64 'ExAC_nonpsych_NFE_AC': int32 'ExAC_nonpsych_NFE_AF': float64 'ExAC_nonpsych_SAS_AC': int32 'ExAC_nonpsych_SAS_AF': float64 'gnomAD_exomes_flag': str 'gnomAD_exomes_AC': int32 'gnomAD_exomes_AN': int32 'gnomAD_exomes_AF': float64 'gnomAD_exomes_nhomalt': int32 'gnomAD_exomes_AFR_AC': int32 'gnomAD_exomes_AFR_AN': int32 'gnomAD_exomes_AFR_AF': float64 'gnomAD_exomes_AFR_nhomalt': int32 'gnomAD_exomes_AMR_AC': int32 'gnomAD_exomes_AMR_AN': int32 'gnomAD_exomes_AMR_AF': float64 'gnomAD_exomes_AMR_nhomalt': int32 'gnomAD_exomes_ASJ_AC': int32 'gnomAD_exomes_ASJ_AN': int32 'gnomAD_exomes_ASJ_AF': float64 'gnomAD_exomes_ASJ_nhomalt': int32 'gnomAD_exomes_EAS_AC': int32 'gnomAD_exomes_EAS_AN': int32 'gnomAD_exomes_EAS_AF': float64 'gnomAD_exomes_EAS_nhomalt': int32 'gnomAD_exomes_FIN_AC': int32 'gnomAD_exomes_FIN_AN': int32 'gnomAD_exomes_FIN_AF': float64 'gnomAD_exomes_FIN_nhomalt': int32 'gnomAD_exomes_NFE_AC': int32 'gnomAD_exomes_NFE_AN': int32 'gnomAD_exomes_NFE_AF': float64 'gnomAD_exomes_NFE_nhomalt': int32 'gnomAD_exomes_SAS_AC': int32 'gnomAD_exomes_SAS_AN': int32 'gnomAD_exomes_SAS_AF': float64 'gnomAD_exomes_SAS_nhomalt': int32 'gnomAD_exomes_POPMAX_AC': int32 'gnomAD_exomes_POPMAX_AN': int32 'gnomAD_exomes_POPMAX_AF': float64 'gnomAD_exomes_POPMAX_nhomalt': int32 'gnomAD_exomes_controls_AC': int32 'gnomAD_exomes_controls_AN': int32 'gnomAD_exomes_controls_AF': float64 'gnomAD_exomes_controls_nhomalt': int32 'gnomAD_exomes_controls_AFR_AC': int32 'gnomAD_exomes_controls_AFR_AN': int32 'gnomAD_exomes_controls_AFR_AF': float64 'gnomAD_exomes_controls_AFR_nhomalt': int32 'gnomAD_exomes_controls_AMR_AC': int32 'gnomAD_exomes_controls_AMR_AN': int32 'gnomAD_exomes_controls_AMR_AF': float64 'gnomAD_exomes_controls_AMR_nhomalt': int32 'gnomAD_exomes_controls_ASJ_AC': int32 'gnomAD_exomes_controls_ASJ_AN': int32 'gnomAD_exomes_controls_ASJ_AF': float64 'gnomAD_exomes_controls_ASJ_nhomalt': int32 'gnomAD_exomes_controls_EAS_AC': int32 'gnomAD_exomes_controls_EAS_AN': int32 'gnomAD_exomes_controls_EAS_AF': float64 'gnomAD_exomes_controls_EAS_nhomalt': int32 'gnomAD_exomes_controls_FIN_AC': int32 'gnomAD_exomes_controls_FIN_AN': int32 'gnomAD_exomes_controls_FIN_AF': float64 'gnomAD_exomes_controls_FIN_nhomalt': int32 'gnomAD_exomes_controls_NFE_AC': int32 'gnomAD_exomes_controls_NFE_AN': int32 'gnomAD_exomes_controls_NFE_AF': float64 'gnomAD_exomes_controls_NFE_nhomalt': int32 'gnomAD_exomes_controls_SAS_AC': int32 'gnomAD_exomes_controls_SAS_AN': int32 'gnomAD_exomes_controls_SAS_AF': float64 'gnomAD_exomes_controls_SAS_nhomalt': int32 'gnomAD_exomes_controls_POPMAX_AC': int32 'gnomAD_exomes_controls_POPMAX_AN': int32 'gnomAD_exomes_controls_POPMAX_AF': float64 'gnomAD_exomes_controls_POPMAX_nhomalt': int32 'gnomAD_genomes_flag': str 'gnomAD_genomes_AC': int32 'gnomAD_genomes_AN': int32 'gnomAD_genomes_AF': float64 'gnomAD_genomes_nhomalt': int32 'gnomAD_genomes_AFR_AC': int32 'gnomAD_genomes_AFR_AN': int32 'gnomAD_genomes_AFR_AF': float64 'gnomAD_genomes_AFR_nhomalt': int32 'gnomAD_genomes_AMR_AC': int32 'gnomAD_genomes_AMR_AN': int32 'gnomAD_genomes_AMR_AF': float64 'gnomAD_genomes_AMR_nhomalt': int32 'gnomAD_genomes_ASJ_AC': int32 'gnomAD_genomes_ASJ_AN': int32 'gnomAD_genomes_ASJ_AF': float64 'gnomAD_genomes_ASJ_nhomalt': int32 'gnomAD_genomes_EAS_AC': int32 'gnomAD_genomes_EAS_AN': int32 'gnomAD_genomes_EAS_AF': float64 'gnomAD_genomes_EAS_nhomalt': int32 'gnomAD_genomes_FIN_AC': int32 'gnomAD_genomes_FIN_AN': int32 'gnomAD_genomes_FIN_AF': float64 'gnomAD_genomes_FIN_nhomalt': int32 'gnomAD_genomes_NFE_AC': int32 'gnomAD_genomes_NFE_AN': int32 'gnomAD_genomes_NFE_AF': float64 'gnomAD_genomes_NFE_nhomalt': int32 'gnomAD_genomes_POPMAX_AC': int32 'gnomAD_genomes_POPMAX_AN': int32 'gnomAD_genomes_POPMAX_AF': float64 'gnomAD_genomes_POPMAX_nhomalt': int32 'gnomAD_genomes_controls_AC': int32 'gnomAD_genomes_controls_AN': int32 'gnomAD_genomes_controls_AF': float64 'gnomAD_genomes_controls_nhomalt': int32 'gnomAD_genomes_controls_AFR_AC': int32 'gnomAD_genomes_controls_AFR_AN': int32 'gnomAD_genomes_controls_AFR_AF': float64 'gnomAD_genomes_controls_AFR_nhomalt': int32 'gnomAD_genomes_controls_AMR_AC': int32 'gnomAD_genomes_controls_AMR_AN': int32 'gnomAD_genomes_controls_AMR_AF': float64 'gnomAD_genomes_controls_AMR_nhomalt': int32 'gnomAD_genomes_controls_ASJ_AC': int32 'gnomAD_genomes_controls_ASJ_AN': int32 'gnomAD_genomes_controls_ASJ_AF': float64 'gnomAD_genomes_controls_ASJ_nhomalt': int32 'gnomAD_genomes_controls_EAS_AC': int32 'gnomAD_genomes_controls_EAS_AN': int32 'gnomAD_genomes_controls_EAS_AF': float64 'gnomAD_genomes_controls_EAS_nhomalt': int32 'gnomAD_genomes_controls_FIN_AC': int32 'gnomAD_genomes_controls_FIN_AN': int32 'gnomAD_genomes_controls_FIN_AF': float64 'gnomAD_genomes_controls_FIN_nhomalt': int32 'gnomAD_genomes_controls_NFE_AC': int32 'gnomAD_genomes_controls_NFE_AN': int32 'gnomAD_genomes_controls_NFE_AF': float64 'gnomAD_genomes_controls_NFE_nhomalt': int32 'gnomAD_genomes_controls_POPMAX_AC': int32 'gnomAD_genomes_controls_POPMAX_AN': int32 'gnomAD_genomes_controls_POPMAX_AF': float64 'gnomAD_genomes_controls_POPMAX_nhomalt': int32 'clinvar_id': int32 'clinvar_clnsig': str 'clinvar_trait': str 'clinvar_review': str 'clinvar_hgvs': str 'clinvar_var_source': str 'clinvar_MedGen_id': str 'clinvar_OMIM_id': str 'clinvar_Orphanet_id': str 'Interpro_domain': str 'GTEx_V7_gene': str 'GTEx_V7_tissue': str 'Geuvadis_eQTL_target_gene': str 'locus': locus 'alleles': array 'chr': str ---------------------------------------- Key: ['locus', 'alleles'] ----------------------------------------