{ "format": { "ADFL": { "label": "Flanking reads", "description": "Number of flanking reads consistent with the allele", "numberType": "NUMBER", "numberCount": 1, "type": "STRING" }, "ADIR": { "label": "In-repeat reads", "description": "Number of in-repeat reads consistent with the allele", "numberType": "NUMBER", "numberCount": 1, "type": "STRING" }, "RU_SPAN": { "label": "Spanning reads", "description": "Number of spanning reads consistent with the allele", "numberType": "PER_ALT", "type": "INTEGER" }, "LC": { "label": "Coverage", "description": "Locus coverage", "numberType": "NUMBER", "numberCount": 1, "type": "FLOAT" }, "REPCN": { "label": "Repeats", "description": "Number of repeat units spanned by the allele", "numberType": "NUMBER", "numberCount": 1, "type": "STRING" }, "VI": { "label": "Inheritance", "description": "An enumeration of possible inheritance modes based on the pedigree of the sample. Potential values: AD, AD_IP, AR, AR_C, XLR, XLD, YL, MT", "numberType": "OTHER", "separator": ",", "type": "CATEGORICAL", "categories": { "AD": { "label": "AD", "description": "Autosomal dominant" }, "AD_IP": { "label": "AD_IP", "description": "Autosomal dominant incomplete penetrance" }, "AR": { "label": "AR", "description": "Autosomal recessive" }, "AR_C": { "label": "AR_C", "description": "Autosomal recessive compound hetrozygote" }, "XLD": { "label": "XLD", "description": "X-linked dominant" }, "XLR": { "label": "XLR", "description": "X-linked recessive" }, "YL": { "label": "YL", "description": "Y-linked" }, "MT": { "label": "MT", "description": "Mitochondrial" } } }, "VIPC_S": { "label": "VIP sample classification", "numberType": "OTHER", "type": "CATEGORICAL", "separator": "," } }, "info": { "n_object0": { "nestedAttributes": { "separator": "|" }, "nestedFields": { "n_array1": { "label": "Array", "description": "Test array", "numberType": "OTHER", "separator": "&", "type": "INTEGER", "index": 2 }, "n_string1": { "label": "String", "description": "Test string", "numberType": "NUMBER", "numberCount": 1, "type": "STRING", "index": 0 } } }, "CSQ": { "nestedAttributes": { "prefix": "Consequence annotations from Ensembl VEP. Format: ", "separator": "|" }, "nestedFields": { "ALLELE_NUM": { "label": "Allele Nr.", "description": "Allele nr within the VCF file.", "numberType": "NUMBER", "numberCount": 1, "type": "INTEGER" }, "ALPHSCORE": { "label": "AlphScore", "description": "AlphScore pathogenicity score for missense variants", "numberType": "NUMBER", "numberCount": 1, "type": "FLOAT" }, "apogee_Score": { "label": "Apogee score", "description": "Apogee score for protein coding mtDNA variants", "numberType": "NUMBER", "numberCount": 1, "type": "FLOAT" }, "apogee_Uscore": { "label": "Apogee unbiased score", "description": "Apogee unbiased score for protein coding mtDNA variants", "numberType": "NUMBER", "numberCount": 1, "type": "FLOAT" }, "BIOTYPE": { "label": "Biotype", "description": "The Ensembl VEP Biotype.", "numberType": "NUMBER", "numberCount": 1, "type": "CATEGORICAL", "categories": { "IG_C_gene": { "label": "IG C gene" }, "protein_coding_CDS_not_defined": { "label": "protein coding CDS not defined" }, "Mt_tRNA": { "label": "Mt tRNA" }, "TR_V_pseudogene": { "label": "TR V pseudogene" }, "other": { "label": "other" }, "vault_RNA": { "label": "vault RNA" }, "scRNA": { "label": "scRNA" }, "transcribed_pseudogene": { "label": "transcribed pseudogene" }, "lncRNA": { "label": "lncRNA" }, "IG_pseudogene": { "label": "IG pseudogene" }, "transcribed_unprocessed_pseudogene": { "label": "transcribed unprocessed pseudogene" }, "IG_V_pseudogene": { "label": "IG V pseudogene" }, "transcribed_unitary_pseudogene": { "label": "transcribed unitary pseudogene" }, "pseudogene": { "label": "pseudogene" }, "RNase_P_RNA": { "label": "RNase P RNA" }, "rRNA": { "label": "rRNA" }, "TR_V_gene": { "label": "TR V gene" }, "rRNA_pseudogene": { "label": "rRNA pseudogene" }, "TR_J_gene": { "label": "TR J gene" }, "aligned_transcript": { "label": "aligned transcript" }, "RNase_MRP_RNA": { "label": "RNase MRP RNA" }, "TR_D_gene": { "label": "TR D gene" }, "unprocessed_pseudogene": { "label": "unprocessed pseudogene" }, "IG_J_pseudogene": { "label": "IG J pseudogene" }, "processed_transcript": { "label": "processed transcript" }, "telomerase_RNA": { "label": "telomerase RNA" }, "protein_coding_LoF": { "label": "protein coding LoF" }, "ncRNA": { "label": "ncRNA" }, "TR_J_pseudogene": { "label": "TR J pseudogene" }, "retained_intron": { "label": "retained intron" }, "nonsense_mediated_decay": { "label": "nonsense mediated decay" }, "snRNA": { "label": "snRNA" }, "transcribed_processed_pseudogene": { "label": "transcribed processed pseudogene" }, "TR_C_gene": { "label": "TR C gene" }, "processed_pseudogene": { "label": "processed pseudogene" }, "translated_processed_pseudogene": { "label": "translated processed pseudogene" }, "miRNA": { "label": "miRNA" }, "protein_coding": { "label": "protein coding" }, "antisense_RNA": { "label": "antisense RNA" }, "IG_D_gene": { "label": "IG D gene" }, "LRG_gene": { "label": "LRG gene" }, "Mt_rRNA": { "label": "Mt rRNA" }, "mRNA": { "label": "mRNA" }, "ribozyme": { "label": "ribozyme" }, "unitary_pseudogene": { "label": "unitary pseudogene" }, "IG_J_gene": { "label": "IG J gene" }, "IG_V_gene": { "label": "IG V gene" }, "artifact": { "label": "artifact" }, "cdna_update": { "label": "cdna update" }, "ncRNA_pseudogene": { "label": "ncRNA pseudogene" }, "IG_C_pseudogene": { "label": "IG C pseudogene" }, "TEC": { "label": "TEC" }, "non_stop_decay": { "label": "non stop decay" }, "sRNA": { "label": "sRNA" }, "ccds_gene": { "label": "ccds gene" }, "tRNA": { "label": "tRNA" }, "snoRNA": { "label": "snoRNA" }, "scaRNA": { "label": "scaRNA" }, "misc_RNA": { "label": "misc RNA" }, "Y_RNA": { "label": "Y RNA" }, "promoter": { "label": "promoter" }, "promoter_flanking_region": { "label": "promoter flanking region" }, "enhancer": { "label": "enhancer" }, "CTCF_binding_site": { "label": "CTCF binding site" }, "open_chromatin_region": { "label": "open chromatin region" }, "TF_binding_site": { "label": "transcription factor binding site" }, "non_transcribed_region": { "label": "non-transcribed region" } } }, "CAPICE_CL": { "label": "CAPICE", "description": "CAPICE classification", "numberType": "NUMBER", "numberCount": 1, "type": "CATEGORICAL", "categories": { "B": { "label": "B", "description": "Benign" }, "LB": { "label": "LB", "description": "Likely benign" }, "VUS": { "label": "VUS", "description": "Variant of uncertain significance" }, "LP": { "label": "LP", "description": "Likely pathogenic" }, "P": { "label": "P", "description": "Pathogenic" } } }, "CAPICE_SC": { "label": "CAPICE", "description": "CAPICE pathogenicity score", "numberType": "NUMBER", "numberCount": 1, "type": "FLOAT" }, "cDNA_position": { "label": "cDNA pos", "description": "Position within the cDNA.", "numberType": "NUMBER", "numberCount": 1, "type": "STRING" }, "CDS_position": { "label": "CDS pos", "description": "Position within the coding sequence.", "numberType": "NUMBER", "numberCount": 1, "type": "STRING" }, "CLIN_SIG": { "label": "ClinVar", "description": "ClinVar classification(s)", "numberType": "OTHER", "separator": "&", "type": "STRING" }, "clinVar": { "label": "ClinVar ID", "description": "ClinVar Variation ID", "numberType": "OTHER", "type": "INTEGER" }, "clinVar_CLNID": { "label": "ClinVar ID", "description": "ClinVar Variation ID", "numberType": "OTHER", "type": "INTEGER" }, "clinVar_CLNSIG": { "label": "ClinVar", "description": "Clinical significance for this single variant", "numberType": "OTHER", "separator": "/", "type": "CATEGORICAL", "categories": { "Benign": { "label": "B", "description": "Benign" }, "Likely_benign": { "label": "LB", "description": "Likely benign" }, "Uncertain_significance": { "label": "VUS", "description": "Variant of uncertain significance" }, "Likely_pathogenic": { "label": "LP", "description": "Likely pathogenic" }, "Pathogenic": { "label": "P", "description": "Pathogenic" }, "Conflicting_classifications_of_pathogenicity": { "label": "Conflict", "description": "Conflicting classifications of pathogenicity" }, "Other": { "label": "Other", "description": "Classifications that do not match the common categorical values." } } }, "clinVar_CLNSIGINCL": { "label": "ClinVar variant combination", "description": "Clinical significance for a haplotype or genotype that includes this variant", "numberType": "OTHER", "separator": "&", "type": "CATEGORICAL", "categories": { "Benign": { "label": "B", "description": "Benign" }, "Likely_benign": { "label": "LB", "description": "Likely benign" }, "Uncertain_significance": { "label": "VUS", "description": "Variant of uncertain significance" }, "Likely_pathogenic": { "label": "LP", "description": "Likely pathogenic" }, "Pathogenic": { "label": "P", "description": "Pathogenic" }, "Conflicting_classifications_of_pathogenicity": { "label": "Conflict", "description": "Conflicting classifications of pathogenicity" } } }, "clinVar_CLNREVSTAT": { "label": "ClinVar status", "description": "ClinVar review status", "numberType": "OTHER", "separator": "&", "type": "CATEGORICAL", "categories": { "practice_guideline": { "label": "Practice guideline", "description": "There is a submitted record with a classification from a practice guideline" }, "reviewed_by_expert_panel": { "label": "Reviewed by expert panel", "description": "There is a submitted record with a classification from an expert panel" }, "criteria_provided": { "label": "Criteria provided", "description": "Assertion criteria and evidence for the classification (or a public contact) were provided" }, "_multiple_submitters": { "label": "Multiple submitters", "description": "There are multiple submitted records with a classification" }, "_no_conflicts": { "label": "No conflicts", "description": "The classifications agree" }, "_single_submitter": { "label": "Single submitter", "description": "There is a single submitted record with a classification" }, "_conflicting_classifications": { "label": "Conflicting_classifications", "description": "There are conflicting classifications" }, "no_assertion_criteria_provided": { "label": "No assertion criteria provided", "description": "There are one or more submitted records with a classification but without assertion criteria and evidence for the classification (or a public contact)" }, "no_assertion_provided": { "label": "No assertion provided" }, "no_classification_for_the_single_variant": { "label": "No classification for the single variant" }, "no_classification_provided": { "label": "No classification provided" }, "no_classifications_from_unflagged_records": { "label": "No classifications from unflagged records" } } }, "Consequence": { "label": "Effect", "description": "Effect(s) described as Sequence Ontology term(s)", "numberType": "OTHER", "separator": "&", "type": "CATEGORICAL", "categories": { "transcript_ablation": { "label": "transcript ablation", "description": "A feature ablation whereby the deleted region includes a transcript feature" }, "splice_acceptor_variant": { "label": "splice acceptor variant", "description": "A splice variant that changes the 2 base region at the 3' end of an intron" }, "splice_donor_variant": { "label": "splice donor variant", "description": "A splice variant that changes the 2 base region at the 5' end of an intron" }, "stop_gained": { "label": "stop gained", "description": "A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript" }, "frameshift_variant": { "label": "frameshift variant", "description": "A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three" }, "stop_lost": { "label": "stop lost", "description": "A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript" }, "start_lost": { "label": "start lost", "description": "A codon variant that changes at least one base of the canonical start codon" }, "transcript_amplification": { "label": "transcript amplification", "description": "A feature amplification of a region containing a transcript" }, "feature_elongation": { "label": "feature elongation", "description": "A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence" }, "feature_truncation": { "label": "feature truncation", "description": "A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence" }, "inframe_insertion": { "label": "inframe insertion", "description": "An inframe non synonymous variant that inserts bases into in the coding sequence" }, "inframe_deletion": { "label": "inframe deletion", "description": "An inframe non synonymous variant that deletes bases from the coding sequence" }, "missense_variant": { "label": "missense variant", "description": "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved" }, "protein_altering_variant": { "label": "protein altering variant", "description": "A sequence_variant which is predicted to change the protein encoded in the coding sequence" }, "splice_donor_5th_base_variant": { "label": "splice donor 5th base variant", "description": "A sequence variant that causes a change at the 5th base pair after the start of the intron in the orientation of the transcript" }, "splice_region_variant": { "label": "splice region variant", "description": "A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron" }, "splice_donor_region_variant": { "label": "splice donor region variant", "description": "A sequence variant that falls in the region between the 3rd and 6th base after splice junction (5' end of intron)" }, "splice_polypyrimidine_tract_variant": { "label": "splice polypyrimidine tract variant", "description": "A sequence variant that falls in the polypyrimidine tract at 3' end of intron between 17 and 3 bases from the end (acceptor -3 to acceptor -17)" }, "incomplete_terminal_codon_variant": { "label": "incomplete terminal codon variant", "description": "A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed" }, "start_retained_variant": { "label": "start retained variant", "description": "A sequence variant where at least one base in the start codon is changed, but the start remains" }, "stop_retained_variant": { "label": "stop retained variant", "description": "A sequence variant where at least one base in the terminator codon is changed, but the terminator remains" }, "synonymous_variant": { "label": "synonymous variant", "description": "A sequence variant where there is no resulting change to the encoded amino acid" }, "coding_sequence_variant": { "label": "coding sequence variant", "description": "A sequence variant that changes the coding sequence" }, "mature_miRNA_variant": { "label": "mature miRNA variant", "description": "A transcript variant located with the sequence of the mature miRNA" }, "5_prime_UTR_variant": { "label": "5 prime UTR variant", "description": "A UTR variant of the 5' UTR" }, "3_prime_UTR_variant": { "label": "3 prime UTR variant", "description": "A UTR variant of the 3' UTR" }, "non_coding_transcript_exon_variant": { "label": "non coding transcript exon variant", "description": "A sequence variant that changes non-coding exon sequence in a non-coding transcript" }, "intron_variant": { "label": "intron variant", "description": "A transcript variant occurring within an intron" }, "NMD_transcript_variant": { "label": "NMD transcript variant", "description": "A variant in a transcript that is the target of NMD" }, "non_coding_transcript_variant": { "label": "non coding transcript variant", "description": "A transcript variant of a non coding RNA gene" }, "coding_transcript_variant": { "label": "coding transcript variant", "description": "A transcript variant of a protein coding gene" }, "upstream_gene_variant": { "label": "upstream gene variant", "description": "A sequence variant located 5' of a gene" }, "downstream_gene_variant": { "label": "downstream gene variant", "description": "A sequence variant located 3' of a gene" }, "TFBS_ablation": { "label": "TFBS ablation", "description": "A feature ablation whereby the deleted region includes a transcription factor binding site" }, "TFBS_amplification": { "label": "TFBS amplification", "description": "A feature amplification of a region containing a transcription factor binding site" }, "TF_binding_site_variant": { "label": "TF binding site variant", "description": "A sequence variant located within a transcription factor binding site" }, "regulatory_region_ablation": { "label": "regulatory region ablation", "description": "A feature ablation whereby the deleted region includes a regulatory region" }, "regulatory_region_amplification": { "label": "regulatory region amplification", "description": "A feature amplification of a region containing a regulatory region" }, "regulatory_region_variant": { "label": "regulatory region variant", "description": "A sequence variant located within a regulatory region" }, "intergenic_variant": { "label": "intergenic variant", "description": "A sequence variant located in the intergenic region, between genes" }, "sequence_variant": { "label": "sequence variant", "description": "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration" } } }, "Existing_variation": { "label": "Ex. var.", "description": "Existing variation.", "numberType": "OTHER", "separator": "&", "type": "STRING" }, "FATHMM_MKL_NC": { "label": "FATHMM-MKL-NC", "description": "Predict the Functional Consequences of Non-Coding Single Nucleotide Variants (SNVs)", "numberType": "NUMBER", "numberCount": 1, "type": "FLOAT" }, "GDB_PRO": { "label": "GDB_PRO", "description": "Highest GREEN-DB constraint score for overlapping promotor regions.", "numberType": "NUMBER", "numberCount": 1, "type": "FLOAT" }, "GDB_ENH": { "label": "GDB_ENH", "description": "Highest GREEN-DB constraint score for overlapping enhancer regions.", "numberType": "NUMBER", "numberCount": 1, "type": "FLOAT" }, "GDB_BIV": { "label": "GDB_BIV", "description": "Highest GREEN-DB constraint score for overlapping bivalent regions.", "numberType": "NUMBER", "numberCount": 1, "type": "FLOAT" }, "GDB_SIL": { "label": "GDB_SIL", "description": "Highest GREEN-DB constraint score for overlapping silencer regions.", "numberType": "NUMBER", "numberCount": 1, "type": "FLOAT" }, "GDB_INS": { "label": "GDB_INS", "description": "Highest GREEN-DB constraint score for overlapping insulater regions.", "numberType": "NUMBER", "numberCount": 1, "type": "FLOAT" }, "Feature_type": { "label": "Feature Type.", "description": "The VEP feature type", "numberType": "NUMBER", "numberCount": 1, "type": "CATEGORICAL", "categories": { "Transcript": { "label": "Transcript", "description": "Transcript" }, "RegulatoryFeature": { "label": "Regulatory", "description": "Regulatory feature" }, "MotifFeature": { "label": "Motif", "description": "Motif feature" } }, "required": true }, "FLAGS": { "label": "Flags", "description": "Flags", "numberType": "OTHER", "separator": "&", "type": "STRING" }, "GADO_PD": { "label": "GADO_PD", "description": "Gene-phenotypes association based on the GeneNetwork Assisted Diagnostic Optimization (GADO) gene prioritization Z-scores, see https://www.genenetwork.nl/gado and https://doi.org/10.1038/s41467-019-10649-4", "numberType": "NUMBER", "numberCount": 1, "type": "CATEGORICAL", "categories": { "HC": { "label": "High confidence", "description": "Gene phenotype relation predicted by GADO with high confidence; Z-Score greater than 5" }, "LC": { "label": "Low confidence", "description": "Gene phenotype relation predicted by GADO with low confidence; Z-Score greater than 3 but below 5" } } }, "GADO_SC": { "label": "GADO_SC", "description": "The combined prioritization GADO Z-score over the HPO of the proband(s) terms for this case.", "numberType": "NUMBER", "numberCount": 1, "type": "FLOAT" }, "gnomAD_AF": { "label": "gnomAD AF", "description": "gnomAD allele frequency", "numberType": "NUMBER", "numberCount": 1, "type": "FLOAT" }, "gnomAD_COV": { "label": "gnomAD COV", "description": "gnomAD coverage (percent of individuals in gnomAD source)", "numberType": "NUMBER", "numberCount": 1, "type": "FLOAT" }, "gnomAD_FAF95": { "label": "gnomAD FAF95", "description": "gnomAD filter allele frequency (95% confidence)", "numberType": "NUMBER", "numberCount": 1, "type": "FLOAT" }, "gnomAD_FAF99": { "label": "gnomAD FAF99", "description": "gnomAD filter allele frequency (99% confidence)", "numberType": "NUMBER", "numberCount": 1, "type": "FLOAT" }, "gnomAD_HN": { "label": "gnomAD HN", "description": "gnomAD number of homozygotes", "numberType": "NUMBER", "numberCount": 1, "type": "INTEGER" }, "gnomAD_SRC": { "label": "gnomAD SRC", "description": "gnomAD source", "numberType": "NUMBER", "numberCount": 1, "type": "CATEGORICAL", "categories": { "E": { "label": "Exomes" }, "G": { "label": "Genomes" }, "T": { "label": "Total", "description": "Total: exomes & genomes" } } }, "gnomAD_QC": { "label": "gnomAD QC", "description": "gnomAD quality control filters that failed", "numberType": "OTHER", "separator": "&", "type": "STRING" }, "HGNC_ID": { "label": "HGNC ID", "description": "The HGNC gene ID", "numberType": "NUMBER", "numberCount": 1, "type": "INTEGER" }, "HGVSc": { "label": "HGVS C", "description": "HGVS nomenclature: coding DNA reference sequence", "numberType": "NUMBER", "numberCount": 1, "type": "STRING" }, "HGVSp": { "label": "HGVS P", "description": "HGVS nomenclature: protein reference sequence", "numberType": "NUMBER", "numberCount": 1, "type": "STRING" }, "hmtvar_DiseaseScore": { "label": "HmtVar disease score", "description": "HmtVar disease score for mtDNA tRNA variants", "numberType": "NUMBER", "numberCount": 1, "type": "FLOAT" }, "HPO": { "label": "HPO", "description": "Human Phenotype Ontology (HPO) terms describing phenotypic abnormalities, see https://hpo.jax.org/ and https://doi.org/10.1093/nar/gkad1005", "numberType": "OTHER", "separator": "&", "type": "CATEGORICAL" }, "IMPACT": { "label": "Impact", "description": "The Impact as predicted by VEP", "numberType": "NUMBER", "numberCount": 1, "type": "CATEGORICAL", "categories": { "LOW": { "label": "Low" }, "MODERATE": { "label": "Moderate" }, "HIGH": { "label": "High" }, "MODIFIER": { "label": "Modifier" } }, "required": true }, "IncompletePenetrance": { "label": "Gene: Inc.Pen.", "description": "Is gene associated with incomplete penetrance?", "numberType": "NUMBER", "numberCount": 1, "type": "CATEGORICAL", "categories": { "1": { "label": "True", "description": "Gene is associated with incomplete penetrance" } }, "nullValue": { "label": "False" } }, "InheritanceModesGene": { "label": "Inh.Pat.", "description": "Inheritance pattern", "numberType": "OTHER", "separator": "&", "type": "CATEGORICAL", "categories": { "AD": { "label": "AD", "description": "Autosomal dominant" }, "AD_IP": { "label": "AD_IP", "description": "Autosomal dominant incomplete penetrance" }, "AR": { "label": "AR", "description": "Autosomal recessive" }, "AR_C": { "label": "AR_C", "description": "Autosomal recessive compound hetrozygote" }, "XL": { "label": "XL", "description": "X-linked" }, "XLD": { "label": "XLD", "description": "X-linked dominant" }, "XLR": { "label": "XLR", "description": "X-linked recessive" }, "YL": { "label": "YL", "description": "Y-linked" }, "MT": { "label": "MT", "description": "Mitochondrial" } } }, "mitoTip_Quartile": { "label": "MitoTIP Quartile", "description": "MitoTIP score quartile", "numberType": "NUMBER", "numberCount": 1, "type": "STRING" }, "mitoTip_Score": { "label": "MitoTip Score", "description": "MitoTIP score for mtDNA tRNA variants", "numberType": "NUMBER", "numberCount": 1, "type": "FLOAT" }, "ncER": { "label": "ncER", "description": "Non-coding essential regulation, from: 0(probably not essential for regulation) to 100 (probably essential for regulation).", "numberType": "NUMBER", "numberCount": 1, "type": "FLOAT" }, "PHENO": { "label": "Pheno", "description": "Phenotype match.", "numberType": "OTHER", "separator": "&", "type": "INTEGER" }, "PICK": { "label": "PICK", "description": "Boolean indicating if this is the VEP picked transcript.", "numberType": "NUMBER", "numberCount": 1, "type": "FLAG" }, "PolyPhen": { "label": "PolyPhen", "description": "PolyPhen score.", "numberType": "NUMBER", "numberCount": 1, "type": "FLOAT" }, "Protein_position": { "label": "Protein pos", "description": "Position within the protein.", "numberType": "NUMBER", "numberCount": 1, "type": "STRING" }, "PUBMED": { "label": "PubMed", "description": "PubMed citations", "numberType": "OTHER", "separator": "&", "type": "INTEGER" }, "ReMM": { "label": "ReMM", "description": "The Regulatory Mendelian Mutation (ReMM) score was created for relevance prediction of non-coding variations (SNVs and small InDels) in the human genome (hg19) in terms of Mendelian diseases.", "numberType": "NUMBER", "numberCount": 1, "type": "FLOAT" }, "SIFT": { "label": "SIFT", "description": "SIFT score.", "numberType": "NUMBER", "numberCount": 1, "type": "FLOAT" }, "SOMATIC": { "label": "Somatic", "description": "Somatic.", "numberType": "OTHER", "separator": "&", "type": "INTEGER" }, "SpliceAI_pred_DS_AG": { "label": "SpliceAI AG", "description": "SpliceAI Delta score (acceptor gain).", "numberType": "NUMBER", "numberCount": 1, "type": "FLOAT" }, "SpliceAI_pred_DS_AL": { "label": "SpliceAI AL", "description": "SpliceAI Delta score (acceptor loss).", "numberType": "NUMBER", "numberCount": 1, "type": "FLOAT" }, "SpliceAI_pred_DS_DG": { "label": "SpliceAI DG", "description": "SpliceAI Delta score (donor gain).", "numberType": "NUMBER", "numberCount": 1, "type": "FLOAT" }, "SpliceAI_pred_DS_DL": { "label": "SpliceAI DL", "description": "SpliceAI Delta score (donor loss).", "numberType": "NUMBER", "numberCount": 1, "type": "FLOAT" }, "STRAND": { "label": "Strand", "description": "The strand of the gene (0=- 1=+).", "numberType": "NUMBER", "numberCount": 1, "type": "INTEGER" }, "SYMBOL": { "label": "Gene", "description": "Gene symbol", "numberType": "NUMBER", "numberCount": 1, "type": "STRING" }, "SYMBOL_SOURCE": { "label": "Symbol Source", "description": "The source of the symbol.", "numberType": "NUMBER", "numberCount": 1, "type": "CATEGORICAL", "categories": { "EntrezGene": { "label": "EntrezGene", "description": "Symbol source Entrez Gene" } } }, "VIPP": { "label": "VIP path", "description": "VIP decision tree path", "numberType": "OTHER", "separator": "&", "type": "STRING", "required": true }, "VKGL_CL": { "label": "VKGL", "description": "Variant consensus classification from the Vereniging Klinisch Genetische Laboratoriumdiagnostiek (VKGL) datashare database, see https://vkgl.nl/nl/diagnostiek/vkgl-datashare-database", "numberType": "NUMBER", "numberCount": 1, "type": "CATEGORICAL", "categories": { "B": { "label": "B", "description": "Benign" }, "LB": { "label": "LB", "description": "Likely benign" }, "VUS": { "label": "VUS", "description": "Variant of uncertain significance" }, "LP": { "label": "LP", "description": "Likely pathogenic" }, "P": { "label": "P", "description": "Pathogenic" } } }, "VKGL_UMCG": { "label": "MVL", "description": "UMCG managed variant list classification", "numberType": "NUMBER", "numberCount": 1, "type": "CATEGORICAL", "categories": { "B": { "label": "B", "description": "Benign" }, "LB": { "label": "LB", "description": "Likely benign" }, "VUS": { "label": "VUS", "description": "Variant of uncertain significance" }, "LP": { "label": "LP", "description": "Likely pathogenic" }, "P": { "label": "P", "description": "Pathogenic" } } } } }, "STR_NORMAL_MAX": { "label": "STR normal max", "description": "Maximum number of repeats allowed to call as normal as defined in the Stranger catalogue", "numberType": "NUMBER", "numberCount": 1, "type": "INTEGER" }, "STR_PATHOLOGIC_MIN": { "label": "STR pathologic min", "description": "Mininum number of repeats required to call as pathologic as defined in the Stranger catalogue", "numberType": "NUMBER", "numberCount": 1, "type": "INTEGER" }, "STR_STATUS": { "label": "STR status", "description": "Repeat expansion status as decided by Stranger", "numberType": "PER_ALT", "separator": ",", "type": "CATEGORICAL", "categories": { "normal": { "label": "normal", "description": "Repeat count is smaller than or equal to the maximum number of repeats allowed to call as normal" }, "pre_mutation": { "label": "pre-mutation", "description": "Repeat count is greater than the maximum number of repeats allowed to call as normal and smaller than the minimum number of repeats required to call as pathologic" }, "full_mutation": { "label": "full-mutation", "description": "Repeat count is greater than or equal to the minimum number of repeats required to call as pathologic" } } }, "SVTYPE": { "label": "SV type", "description": "Type of structural variant", "numberType": "NUMBER", "numberCount": 1, "type": "STRING" }, "RU_CI": { "label": "Repeat CI", "description": "Confidence interval for the number of repeat units spanned by the allele", "numberType": "PER_ALT", "type": "STRING" }, "VIPC_S": { "label": "VIP sample classification", "numberType": "OTHER", "type": "CATEGORICAL", "separator": "," } } }