{ "geneReports": { "CPIC": { "ABCG2": { "alleleDefinitionVersion": null, "alleleDefinitionSource": "UNKNOWN", "phenotypeVersion": "2024-08-27-21-12", "phenotypeSource": "CPIC", "geneSymbol": "ABCG2", "chr": null, "phased": false, "effectivelyPhased": false, "callSource": "OUTSIDE", "uncalledHaplotypes": [], "messages": [ { "rule_name": "pcat-outside-call", "version": "1", "matches": { "gene": null, "hapsCalled": [], "hapsMissing": [], "variantsMissing": [], "variant": null, "dips": [], "drugs": [] }, "exception_type": "", "message": "This comes from an outside data source which does not supply position-level detail. For specific disclaimers and limitations, see the original genotyping source." }, { "rule_name": "prefer-sample-data", "version": null, "matches": null, "exception_type": "note", "message": "PharmCAT would have called rs2231142 reference (G)/rs2231142 reference (G) based on the VCF but it has been ignored in favor of the outside call. 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If you want to use the PharmCAT call for this gene then remove the gene from the outside call data." } ], "relatedDrugs": [], "sourceDiplotypes": [ { "allele1": { "gene": "CYP4F2", "name": "*4", "function": null, "reference": false, "activityValue": null }, "allele2": { "gene": "CYP4F2", "name": "*5", "function": null, "reference": false, "activityValue": null }, "gene": "CYP4F2", "phenotypes": [], "outsidePhenotype": false, "outsidePhenotypeMismatch": null, "activityScore": null, "outsideActivityScore": false, "outsideActivityScoreMismatch": null, "variant": null, "lookupKey": [], "label": "*4/*5", "inferred": false, "combination": false, "phenotypeDataSource": "CPIC", "diplotypeKey": {} } ], "matcherComponentHaplotypes": [], "matcherHomozygousComponentHaplotypes": [], "recommendationDiplotypes": [ { "allele1": { "gene": "CYP4F2", "name": "*4", "function": null, "reference": false, "activityValue": null }, "allele2": { "gene": "CYP4F2", "name": "*5", "function": null, "reference": false, "activityValue": null }, "gene": "CYP4F2", "phenotypes": [], "outsidePhenotype": false, "outsidePhenotypeMismatch": null, "activityScore": null, "outsideActivityScore": false, "outsideActivityScoreMismatch": null, "variant": null, "lookupKey": [], "label": "*4/*5", "inferred": false, "combination": false, "phenotypeDataSource": "CPIC", "diplotypeKey": {} } ], "variants": [], "variantsOfInterest": [], "hasUndocumentedVariations": false, "treatUndocumentedVariationsAsReference": false }, "DPYD": { "alleleDefinitionVersion": null, "alleleDefinitionSource": "UNKNOWN", "phenotypeVersion": "2024-08-27-21-12", "phenotypeSource": "CPIC", "geneSymbol": "DPYD", "chr": null, "phased": false, "effectivelyPhased": false, "callSource": "OUTSIDE", "uncalledHaplotypes": [], "messages": [ { "rule_name": "pcat-outside-call", "version": "1", "matches": { "gene": null, "hapsCalled": [], "hapsMissing": [], "variantsMissing": [], "variant": null, "dips": [], "drugs": [] }, "exception_type": "", "message": "This comes from an outside data source which does not supply position-level detail. For specific disclaimers and limitations, see the original genotyping source." }, { "rule_name": "prefer-sample-data", "version": null, "matches": null, "exception_type": "note", "message": "PharmCAT would have called Reference/Reference based on the VCF but it has been ignored in favor of the outside call. If you want to use the PharmCAT call for this gene then remove the gene from the outside call data." } ], "relatedDrugs": [], "sourceDiplotypes": [ { "allele1": { "gene": "DPYD", "name": "Reference", "function": "Normal function", "reference": true, "activityValue": "1.0" }, "allele2": { "gene": "DPYD", "name": "Reference", "function": "Normal function", "reference": true, "activityValue": "1.0" }, "gene": "DPYD", "phenotypes": [ "Normal Metabolizer" ], "outsidePhenotype": false, "outsidePhenotypeMismatch": null, "activityScore": "2.0", "outsideActivityScore": false, "outsideActivityScoreMismatch": null, "variant": null, "lookupKey": [ "2.0" ], "label": "Reference/Reference", "inferred": false, "combination": false, "phenotypeDataSource": "CPIC", "diplotypeKey": {} } ], "matcherComponentHaplotypes": [], "matcherHomozygousComponentHaplotypes": [], "recommendationDiplotypes": [ { "allele1": { "gene": "DPYD", "name": "Reference", "function": "Normal function", "reference": true, "activityValue": "1.0" }, "allele2": { "gene": "DPYD", "name": "Reference", "function": "Normal function", "reference": true, "activityValue": "1.0" }, "gene": "DPYD", "phenotypes": [ "Normal Metabolizer" ], "outsidePhenotype": false, "outsidePhenotypeMismatch": null, "activityScore": "2.0", "outsideActivityScore": false, "outsideActivityScoreMismatch": null, "variant": null, "lookupKey": [ "2.0" ], "label": "Reference/Reference", "inferred": false, "combination": false, "phenotypeDataSource": "CPIC", "diplotypeKey": { "Reference": 2.0 } } ], "variants": [], "variantsOfInterest": [], "hasUndocumentedVariations": false, "treatUndocumentedVariationsAsReference": false }, "G6PD": { "alleleDefinitionVersion": null, "alleleDefinitionSource": "UNKNOWN", "phenotypeVersion": "2024-08-27-21-12", "phenotypeSource": "CPIC", "geneSymbol": "G6PD", "chr": null, "phased": false, "effectivelyPhased": false, "callSource": "OUTSIDE", "uncalledHaplotypes": [], "messages": [ { "rule_name": "pcat-outside-call", "version": "1", "matches": { "gene": null, "hapsCalled": [], "hapsMissing": [], "variantsMissing": [], "variant": null, "dips": [], "drugs": [] }, "exception_type": "", "message": "This comes from an outside data source which does not supply position-level detail. For specific disclaimers and limitations, see the original genotyping source." }, { "rule_name": "prefer-sample-data", "version": null, "matches": null, "exception_type": "note", "message": "PharmCAT would have called B (reference)/B (reference) based on the VCF but it has been ignored in favor of the outside call. If you want to use the PharmCAT call for this gene then remove the gene from the outside call data." } ], "relatedDrugs": [], "sourceDiplotypes": [ { "allele1": { "gene": "G6PD", "name": "B (reference)", "function": "IV/Normal", "reference": true, "activityValue": "n/a" }, "allele2": { "gene": "G6PD", "name": "B (reference)", "function": "IV/Normal", "reference": true, "activityValue": "n/a" }, "gene": "G6PD", "phenotypes": [ "Normal" ], "outsidePhenotype": false, "outsidePhenotypeMismatch": null, "activityScore": null, "outsideActivityScore": false, "outsideActivityScoreMismatch": null, "variant": null, "lookupKey": [ "Normal" ], "label": "B (reference)/B (reference)", "inferred": false, "combination": false, "phenotypeDataSource": "CPIC", "diplotypeKey": {} } ], "matcherComponentHaplotypes": [], "matcherHomozygousComponentHaplotypes": [], "recommendationDiplotypes": [ { "allele1": { "gene": "G6PD", "name": "B (reference)", "function": "IV/Normal", "reference": true, "activityValue": "n/a" }, "allele2": { "gene": "G6PD", "name": "B (reference)", "function": "IV/Normal", "reference": true, "activityValue": "n/a" }, "gene": "G6PD", "phenotypes": [ "Normal" ], "outsidePhenotype": false, "outsidePhenotypeMismatch": null, "activityScore": null, "outsideActivityScore": false, "outsideActivityScoreMismatch": null, "variant": null, "lookupKey": [ "Normal" ], "label": "B (reference)/B (reference)", "inferred": false, "combination": false, "phenotypeDataSource": "CPIC", "diplotypeKey": {} } ], "variants": [], "variantsOfInterest": [], "hasUndocumentedVariations": false, "treatUndocumentedVariationsAsReference": false }, "HLA-A": { "alleleDefinitionVersion": null, "alleleDefinitionSource": "UNKNOWN", "phenotypeVersion": null, "phenotypeSource": "CPIC", "geneSymbol": "HLA-A", "chr": null, "phased": false, "effectivelyPhased": false, "callSource": "OUTSIDE", "uncalledHaplotypes": [], "messages": [ { "rule_name": "pcat-outside-call", "version": "1", "matches": { "gene": null, "hapsCalled": [], "hapsMissing": [], "variantsMissing": [], "variant": null, "dips": [], "drugs": [] }, "exception_type": "", "message": "This comes from an outside data source which does not supply position-level detail. For specific disclaimers and limitations, see the original genotyping source." } ], "relatedDrugs": [], "sourceDiplotypes": [ { "allele1": { "gene": "HLA-A", "name": "*01:01", "function": null, "reference": false, "activityValue": null }, "allele2": { "gene": "HLA-A", "name": "*26:01", "function": null, "reference": false, "activityValue": null }, "gene": "HLA-A", "phenotypes": [ "*31:01 negative" ], "outsidePhenotype": false, "outsidePhenotypeMismatch": null, "activityScore": null, "outsideActivityScore": false, "outsideActivityScoreMismatch": null, "variant": null, "lookupKey": [ "*31:01 negative" ], "label": "*01:01/*26:01", "inferred": false, "combination": false, "phenotypeDataSource": "CPIC", "diplotypeKey": {} } ], "matcherComponentHaplotypes": [], "matcherHomozygousComponentHaplotypes": [], "recommendationDiplotypes": [ { "allele1": { "gene": "HLA-A", "name": "*01:01", "function": null, "reference": false, "activityValue": null }, "allele2": { "gene": "HLA-A", "name": "*26:01", "function": null, "reference": false, "activityValue": null }, "gene": "HLA-A", "phenotypes": [ "*31:01 negative" ], "outsidePhenotype": false, "outsidePhenotypeMismatch": null, "activityScore": null, "outsideActivityScore": false, "outsideActivityScoreMismatch": null, "variant": null, "lookupKey": [ "*31:01 negative" ], "label": "*01:01/*26:01", "inferred": false, "combination": false, "phenotypeDataSource": "CPIC", "diplotypeKey": {} } ], "variants": [], "variantsOfInterest": [], "hasUndocumentedVariations": false, "treatUndocumentedVariationsAsReference": false }, "HLA-B": { "alleleDefinitionVersion": null, "alleleDefinitionSource": "UNKNOWN", "phenotypeVersion": null, "phenotypeSource": "CPIC", "geneSymbol": "HLA-B", "chr": null, "phased": false, "effectivelyPhased": false, "callSource": "OUTSIDE", "uncalledHaplotypes": [], "messages": [ { "rule_name": "pcat-outside-call", "version": "1", "matches": { "gene": null, "hapsCalled": [], "hapsMissing": [], "variantsMissing": [], "variant": null, "dips": [], "drugs": [] }, "exception_type": "", "message": "This comes from an outside data source which does not supply position-level detail. For specific disclaimers and limitations, see the original genotyping source." } ], "relatedDrugs": [], "sourceDiplotypes": [ { "allele1": { "gene": "HLA-B", "name": "*38:01", "function": null, "reference": false, "activityValue": null }, "allele2": { "gene": "HLA-B", "name": "*35:08", "function": null, "reference": false, "activityValue": null }, "gene": "HLA-B", "phenotypes": [ "*15:02 negative", "*57:01 negative", "*58:01 negative" ], "outsidePhenotype": false, "outsidePhenotypeMismatch": null, "activityScore": null, "outsideActivityScore": false, "outsideActivityScoreMismatch": null, "variant": null, "lookupKey": [ "*15:02 negative", "*57:01 negative", "*58:01 negative" ], "label": "*35:08/*38:01", "inferred": false, "combination": false, "phenotypeDataSource": "CPIC", "diplotypeKey": {} } ], "matcherComponentHaplotypes": [], "matcherHomozygousComponentHaplotypes": [], "recommendationDiplotypes": [ { "allele1": { "gene": "HLA-B", "name": "*38:01", "function": null, "reference": false, "activityValue": null }, "allele2": { "gene": "HLA-B", "name": "*35:08", "function": null, "reference": false, "activityValue": null }, "gene": "HLA-B", "phenotypes": [ "*15:02 negative", "*57:01 negative", "*58:01 negative" ], "outsidePhenotype": false, "outsidePhenotypeMismatch": null, "activityScore": null, "outsideActivityScore": false, "outsideActivityScoreMismatch": null, "variant": null, "lookupKey": [ "*15:02 negative", "*57:01 negative", "*58:01 negative" ], "label": "*35:08/*38:01", "inferred": false, "combination": false, "phenotypeDataSource": "CPIC", "diplotypeKey": {} } ], "variants": [], "variantsOfInterest": [], "hasUndocumentedVariations": false, "treatUndocumentedVariationsAsReference": false }, "IFNL3": { "alleleDefinitionVersion": null, "alleleDefinitionSource": "UNKNOWN", "phenotypeVersion": "2024-08-27-21-12", "phenotypeSource": "CPIC", "geneSymbol": "IFNL3", "chr": null, "phased": false, "effectivelyPhased": false, "callSource": "OUTSIDE", "uncalledHaplotypes": [], "messages": [ { "rule_name": "pcat-outside-call", "version": "1", "matches": { "gene": null, "hapsCalled": [], "hapsMissing": [], "variantsMissing": [], "variant": null, "dips": [], "drugs": [] }, "exception_type": "", "message": "This comes from an outside data source which does not supply position-level detail. For specific disclaimers and limitations, see the original genotyping source." }, { "rule_name": "prefer-sample-data", "version": null, "matches": null, "exception_type": "note", "message": "PharmCAT would have called rs12979860 reference (C)/rs12979860 reference (C) based on the VCF but it has been ignored in favor of the outside call. If you want to use the PharmCAT call for this gene then remove the gene from the outside call data." } ], "relatedDrugs": [], "sourceDiplotypes": [ { "allele1": { "gene": "IFNL3", "name": "rs12979860 reference (C)", "function": "Favorable response allele", "reference": true, "activityValue": "n/a" }, "allele2": { "gene": "IFNL3", "name": "rs12979860 reference (C)", "function": "Favorable response allele", "reference": true, "activityValue": "n/a" }, "gene": "IFNL3", "phenotypes": [ "n/a" ], "outsidePhenotype": false, "outsidePhenotypeMismatch": null, "activityScore": null, "outsideActivityScore": false, "outsideActivityScoreMismatch": null, "variant": null, "lookupKey": [ "n/a" ], "label": "rs12979860 reference (C)/rs12979860 reference (C)", "inferred": false, "combination": false, "phenotypeDataSource": "CPIC", "diplotypeKey": {} } ], "matcherComponentHaplotypes": [], "matcherHomozygousComponentHaplotypes": [], "recommendationDiplotypes": [ { "allele1": { "gene": "IFNL3", "name": "rs12979860 reference (C)", "function": "Favorable response allele", "reference": true, "activityValue": "n/a" }, "allele2": { "gene": "IFNL3", "name": "rs12979860 reference (C)", "function": "Favorable response allele", "reference": true, "activityValue": "n/a" }, "gene": "IFNL3", "phenotypes": [ "n/a" ], "outsidePhenotype": false, "outsidePhenotypeMismatch": null, "activityScore": null, "outsideActivityScore": false, "outsideActivityScoreMismatch": null, "variant": null, "lookupKey": [ "n/a" ], "label": "rs12979860 reference (C)/rs12979860 reference (C)", "inferred": false, "combination": false, "phenotypeDataSource": "CPIC", "diplotypeKey": {} } ], "variants": [], "variantsOfInterest": [], "hasUndocumentedVariations": false, "treatUndocumentedVariationsAsReference": false }, "MT-RNR1": { "alleleDefinitionVersion": null, "alleleDefinitionSource": "UNKNOWN", "phenotypeVersion": "2024-08-27-21-12", "phenotypeSource": "CPIC", "geneSymbol": "MT-RNR1", "chr": null, "phased": false, "effectivelyPhased": false, "callSource": "OUTSIDE", "uncalledHaplotypes": [], "messages": [ { "rule_name": "pcat-outside-call", "version": "1", "matches": { "gene": null, "hapsCalled": [], "hapsMissing": [], "variantsMissing": [], "variant": null, "dips": [], "drugs": [] }, "exception_type": "", "message": "This comes from an outside data source which does not supply position-level detail. For specific disclaimers and limitations, see the original genotyping source." } ], "relatedDrugs": [], "sourceDiplotypes": [ { "allele1": { "gene": "MT-RNR1", "name": "Reference", "function": "Normal risk of aminoglycoside-induced hearing loss", "reference": true, "activityValue": "n/a" }, "allele2": null, "gene": "MT-RNR1", "phenotypes": [ "normal risk of aminoglycoside-induced hearing loss" ], "outsidePhenotype": false, "outsidePhenotypeMismatch": null, "activityScore": null, "outsideActivityScore": false, "outsideActivityScoreMismatch": null, "variant": null, "lookupKey": [ "normal risk of aminoglycoside-induced hearing loss" ], "label": "Reference", "inferred": false, "combination": false, "phenotypeDataSource": "CPIC", "diplotypeKey": {} } ], "matcherComponentHaplotypes": [], "matcherHomozygousComponentHaplotypes": [], "recommendationDiplotypes": [ { "allele1": { "gene": "MT-RNR1", "name": "Reference", "function": "Normal risk of aminoglycoside-induced hearing loss", "reference": true, "activityValue": "n/a" }, "allele2": null, "gene": "MT-RNR1", "phenotypes": [ "normal risk of aminoglycoside-induced hearing loss" ], "outsidePhenotype": false, "outsidePhenotypeMismatch": null, "activityScore": null, "outsideActivityScore": false, "outsideActivityScoreMismatch": null, "variant": null, "lookupKey": [ "normal risk of aminoglycoside-induced hearing loss" ], "label": "Reference", "inferred": false, "combination": false, "phenotypeDataSource": "CPIC", "diplotypeKey": {} } ], "variants": [], "variantsOfInterest": [], "hasUndocumentedVariations": false, "treatUndocumentedVariationsAsReference": false }, "NUDT15": { "alleleDefinitionVersion": null, "alleleDefinitionSource": "UNKNOWN", "phenotypeVersion": "2024-08-27-21-12", "phenotypeSource": "CPIC", "geneSymbol": "NUDT15", "chr": null, "phased": false, "effectivelyPhased": false, "callSource": "OUTSIDE", "uncalledHaplotypes": [], "messages": [ { "rule_name": "pcat-outside-call", "version": "1", "matches": { "gene": null, "hapsCalled": [], "hapsMissing": [], "variantsMissing": [], "variant": null, "dips": [], "drugs": [] }, "exception_type": "", "message": "This comes from an outside data source which does not supply position-level detail. For specific disclaimers and limitations, see the original genotyping source." }, { "rule_name": "prefer-sample-data", "version": null, "matches": null, "exception_type": "note", "message": "PharmCAT would have called *1/*1 based on the VCF but it has been ignored in favor of the outside call. If you want to use the PharmCAT call for this gene then remove the gene from the outside call data." } ], "relatedDrugs": [], "sourceDiplotypes": [ { "allele1": { "gene": "NUDT15", "name": "*1", "function": "Normal function", "reference": true, "activityValue": "n/a" }, "allele2": { "gene": "NUDT15", "name": "*1", "function": "Normal function", "reference": true, "activityValue": "n/a" }, "gene": "NUDT15", "phenotypes": [ "Normal Metabolizer" ], "outsidePhenotype": false, "outsidePhenotypeMismatch": null, "activityScore": null, "outsideActivityScore": false, "outsideActivityScoreMismatch": null, "variant": null, "lookupKey": [ "Normal Metabolizer" ], "label": "*1/*1", "inferred": false, "combination": false, "phenotypeDataSource": "CPIC", "diplotypeKey": {} } ], "matcherComponentHaplotypes": [], "matcherHomozygousComponentHaplotypes": [], "recommendationDiplotypes": [ { "allele1": { "gene": "NUDT15", "name": "*1", "function": "Normal function", "reference": true, "activityValue": "n/a" }, "allele2": { "gene": "NUDT15", "name": "*1", "function": "Normal function", "reference": true, "activityValue": "n/a" }, "gene": "NUDT15", "phenotypes": [ "Normal Metabolizer" ], "outsidePhenotype": false, "outsidePhenotypeMismatch": null, "activityScore": null, "outsideActivityScore": false, "outsideActivityScoreMismatch": null, "variant": null, "lookupKey": [ "Normal Metabolizer" ], "label": "*1/*1", "inferred": false, "combination": false, "phenotypeDataSource": "CPIC", "diplotypeKey": {} } ], "variants": [], "variantsOfInterest": [], "hasUndocumentedVariations": false, "treatUndocumentedVariationsAsReference": false }, "RYR1": { "alleleDefinitionVersion": null, "alleleDefinitionSource": "UNKNOWN", "phenotypeVersion": "2024-08-27-21-12", "phenotypeSource": "CPIC", "geneSymbol": "RYR1", "chr": null, "phased": false, "effectivelyPhased": false, "callSource": "OUTSIDE", "uncalledHaplotypes": [], "messages": [ { "rule_name": "pcat-outside-call", "version": "1", "matches": { "gene": null, "hapsCalled": [], "hapsMissing": [], "variantsMissing": [], "variant": null, "dips": [], "drugs": [] }, "exception_type": "", "message": "This comes from an outside data source which does not supply position-level detail. For specific disclaimers and limitations, see the original genotyping source." }, { "rule_name": "prefer-sample-data", "version": null, "matches": null, "exception_type": "note", "message": "PharmCAT would have called Reference/Reference based on the VCF but it has been ignored in favor of the outside call. If you want to use the PharmCAT call for this gene then remove the gene from the outside call data." } ], "relatedDrugs": [], "sourceDiplotypes": [ { "allele1": { "gene": "RYR1", "name": "Reference", "function": "Normal function", "reference": true, "activityValue": "n/a" }, "allele2": { "gene": "RYR1", "name": "Reference", "function": "Normal function", "reference": true, "activityValue": "n/a" }, "gene": "RYR1", "phenotypes": [ "Uncertain Susceptibility" ], "outsidePhenotype": false, "outsidePhenotypeMismatch": null, "activityScore": null, "outsideActivityScore": false, "outsideActivityScoreMismatch": null, "variant": null, "lookupKey": [ "Uncertain Susceptibility" ], "label": "Reference/Reference", "inferred": false, "combination": false, "phenotypeDataSource": "CPIC", "diplotypeKey": {} } ], "matcherComponentHaplotypes": [], "matcherHomozygousComponentHaplotypes": [], "recommendationDiplotypes": [ { "allele1": { "gene": "RYR1", "name": "Reference", "function": "Normal function", "reference": true, "activityValue": "n/a" }, "allele2": { "gene": "RYR1", "name": "Reference", "function": "Normal function", "reference": true, "activityValue": "n/a" }, "gene": "RYR1", "phenotypes": [ "Uncertain Susceptibility" ], "outsidePhenotype": false, "outsidePhenotypeMismatch": null, "activityScore": null, "outsideActivityScore": false, "outsideActivityScoreMismatch": null, "variant": null, "lookupKey": [ "Uncertain Susceptibility" ], "label": "Reference/Reference", "inferred": false, "combination": false, "phenotypeDataSource": "CPIC", "diplotypeKey": { "Reference": 2.0 } } ], "variants": [], "variantsOfInterest": [], "hasUndocumentedVariations": false, "treatUndocumentedVariationsAsReference": false }, "SLCO1B1": { "alleleDefinitionVersion": null, "alleleDefinitionSource": "UNKNOWN", "phenotypeVersion": "2024-08-27-21-12", "phenotypeSource": "CPIC", "geneSymbol": "SLCO1B1", "chr": null, "phased": false, "effectivelyPhased": false, "callSource": "OUTSIDE", "uncalledHaplotypes": [], "messages": [ { "rule_name": "pcat-outside-call", "version": "1", "matches": { "gene": null, "hapsCalled": [], "hapsMissing": [], "variantsMissing": [], "variant": null, "dips": [], "drugs": [] }, "exception_type": "", "message": "This comes from an outside data source which does not supply position-level detail. For specific disclaimers and limitations, see the original genotyping source." }, { "rule_name": "prefer-sample-data", "version": null, "matches": null, "exception_type": "note", "message": "PharmCAT would have called *1/*1 based on the VCF but it has been ignored in favor of the outside call. If you want to use the PharmCAT call for this gene then remove the gene from the outside call data." } ], "relatedDrugs": [], "sourceDiplotypes": [ { "allele1": { "gene": "SLCO1B1", "name": "*1", "function": "Normal function", "reference": true, "activityValue": "n/a" }, "allele2": { "gene": "SLCO1B1", "name": "*1", "function": "Normal function", "reference": true, "activityValue": "n/a" }, "gene": "SLCO1B1", "phenotypes": [ "Normal Function" ], "outsidePhenotype": false, "outsidePhenotypeMismatch": null, "activityScore": null, "outsideActivityScore": false, "outsideActivityScoreMismatch": null, "variant": null, "lookupKey": [ "Normal Function" ], "label": "*1/*1", "inferred": false, "combination": false, "phenotypeDataSource": "CPIC", "diplotypeKey": {} } ], "matcherComponentHaplotypes": [], "matcherHomozygousComponentHaplotypes": [], "recommendationDiplotypes": [ { "allele1": { "gene": "SLCO1B1", "name": "*1", "function": "Normal function", "reference": true, "activityValue": "n/a" }, "allele2": { "gene": "SLCO1B1", "name": "*1", "function": "Normal function", "reference": true, "activityValue": "n/a" }, "gene": "SLCO1B1", "phenotypes": [ "Normal Function" ], "outsidePhenotype": false, "outsidePhenotypeMismatch": null, "activityScore": null, "outsideActivityScore": false, "outsideActivityScoreMismatch": null, "variant": null, "lookupKey": [ "Normal Function" ], "label": "*1/*1", "inferred": false, "combination": false, "phenotypeDataSource": "CPIC", "diplotypeKey": {} } ], "variants": [], "variantsOfInterest": [], "hasUndocumentedVariations": false, "treatUndocumentedVariationsAsReference": false }, "TPMT": { "alleleDefinitionVersion": null, "alleleDefinitionSource": "UNKNOWN", "phenotypeVersion": "2024-08-27-21-12", "phenotypeSource": "CPIC", "geneSymbol": "TPMT", "chr": null, "phased": false, "effectivelyPhased": false, "callSource": "OUTSIDE", "uncalledHaplotypes": [], "messages": [ { "rule_name": "pcat-outside-call", "version": "1", "matches": { "gene": null, "hapsCalled": [], "hapsMissing": [], "variantsMissing": [], "variant": null, "dips": [], "drugs": [] }, "exception_type": "", "message": "This comes from an outside data source which does not supply position-level detail. For specific disclaimers and limitations, see the original genotyping source." }, { "rule_name": "prefer-sample-data", "version": null, "matches": null, "exception_type": "note", "message": "PharmCAT would have called *1/*1 based on the VCF but it has been ignored in favor of the outside call. If you want to use the PharmCAT call for this gene then remove the gene from the outside call data." } ], "relatedDrugs": [], "sourceDiplotypes": [ { "allele1": { "gene": "TPMT", "name": "*1", "function": "Normal function", "reference": true, "activityValue": "n/a" }, "allele2": { "gene": "TPMT", "name": "*1", "function": "Normal function", "reference": true, "activityValue": "n/a" }, "gene": "TPMT", "phenotypes": [ "Normal Metabolizer" ], "outsidePhenotype": false, "outsidePhenotypeMismatch": null, "activityScore": null, "outsideActivityScore": false, "outsideActivityScoreMismatch": null, "variant": null, "lookupKey": [ "Normal Metabolizer" ], "label": "*1/*1", "inferred": false, "combination": false, "phenotypeDataSource": "CPIC", "diplotypeKey": {} } ], "matcherComponentHaplotypes": [], "matcherHomozygousComponentHaplotypes": [], "recommendationDiplotypes": [ { "allele1": { "gene": "TPMT", "name": "*1", "function": "Normal function", "reference": true, "activityValue": "n/a" }, "allele2": { "gene": "TPMT", "name": "*1", "function": "Normal function", "reference": true, "activityValue": "n/a" }, "gene": "TPMT", "phenotypes": [ "Normal Metabolizer" ], "outsidePhenotype": false, "outsidePhenotypeMismatch": null, "activityScore": null, "outsideActivityScore": false, "outsideActivityScoreMismatch": null, "variant": null, "lookupKey": [ "Normal Metabolizer" ], "label": "*1/*1", "inferred": false, "combination": false, "phenotypeDataSource": "CPIC", "diplotypeKey": {} } ], "variants": [], "variantsOfInterest": [], "hasUndocumentedVariations": false, "treatUndocumentedVariationsAsReference": false }, "UGT1A1": { "alleleDefinitionVersion": null, "alleleDefinitionSource": "UNKNOWN", "phenotypeVersion": "2024-08-27-21-12", "phenotypeSource": "CPIC", "geneSymbol": "UGT1A1", "chr": null, "phased": false, "effectivelyPhased": false, "callSource": "OUTSIDE", "uncalledHaplotypes": [], "messages": [ { "rule_name": "pcat-outside-call", "version": "1", "matches": { "gene": null, "hapsCalled": [], "hapsMissing": [], "variantsMissing": [], "variant": null, "dips": [], "drugs": [] }, "exception_type": "", "message": "This comes from an outside data source which does not supply position-level detail. For specific disclaimers and limitations, see the original genotyping source." }, { "rule_name": "prefer-sample-data", "version": null, "matches": null, "exception_type": "note", "message": "PharmCAT would have called *1/*1 based on the VCF but it has been ignored in favor of the outside call. If you want to use the PharmCAT call for this gene then remove the gene from the outside call data." } ], "relatedDrugs": [], "sourceDiplotypes": [ { "allele1": { "gene": "UGT1A1", "name": "*1", "function": "Normal function", "reference": true, "activityValue": "n/a" }, "allele2": { "gene": "UGT1A1", "name": "*1", "function": "Normal function", "reference": true, "activityValue": "n/a" }, "gene": "UGT1A1", "phenotypes": [ "Normal Metabolizer" ], "outsidePhenotype": false, "outsidePhenotypeMismatch": null, "activityScore": null, "outsideActivityScore": false, "outsideActivityScoreMismatch": null, "variant": null, "lookupKey": [ "Normal Metabolizer" ], "label": "*1/*1", "inferred": false, "combination": false, "phenotypeDataSource": "CPIC", "diplotypeKey": {} } ], "matcherComponentHaplotypes": [], "matcherHomozygousComponentHaplotypes": [], "recommendationDiplotypes": [ { "allele1": { "gene": "UGT1A1", "name": "*1", "function": "Normal function", "reference": true, "activityValue": "n/a" }, "allele2": { "gene": "UGT1A1", "name": "*1", "function": "Normal function", "reference": true, "activityValue": "n/a" }, "gene": "UGT1A1", "phenotypes": [ "Normal Metabolizer" ], "outsidePhenotype": false, "outsidePhenotypeMismatch": null, "activityScore": null, "outsideActivityScore": false, "outsideActivityScoreMismatch": null, "variant": null, "lookupKey": [ "Normal Metabolizer" ], "label": "*1/*1", "inferred": false, "combination": false, "phenotypeDataSource": "CPIC", "diplotypeKey": {} } ], "variants": [], "variantsOfInterest": [], "hasUndocumentedVariations": false, "treatUndocumentedVariationsAsReference": false }, "VKORC1": { "alleleDefinitionVersion": null, "alleleDefinitionSource": "UNKNOWN", "phenotypeVersion": null, "phenotypeSource": "CPIC", "geneSymbol": "VKORC1", "chr": null, "phased": false, "effectivelyPhased": false, "callSource": "OUTSIDE", "uncalledHaplotypes": [], "messages": [ { "rule_name": "pcat-outside-call", "version": "1", "matches": { "gene": null, "hapsCalled": [], "hapsMissing": [], "variantsMissing": [], "variant": null, "dips": [], "drugs": [] }, "exception_type": "", "message": "This comes from an outside data source which does not supply position-level detail. For specific disclaimers and limitations, see the original genotyping source." }, { "rule_name": "prefer-sample-data", "version": null, "matches": null, "exception_type": "note", "message": "PharmCAT would have called rs9923231 variant (T)/rs9923231 variant (T) based on the VCF but it has been ignored in favor of the outside call. If you want to use the PharmCAT call for this gene then remove the gene from the outside call data." } ], "relatedDrugs": [], "sourceDiplotypes": [ { "allele1": { "gene": "VKORC1", "name": "rs9923231 variant (T)", "function": null, "reference": false, "activityValue": null }, "allele2": { "gene": "VKORC1", "name": "rs9923231 variant (T)", "function": null, "reference": false, "activityValue": null }, "gene": "VKORC1", "phenotypes": [], "outsidePhenotype": false, "outsidePhenotypeMismatch": null, "activityScore": null, "outsideActivityScore": false, "outsideActivityScoreMismatch": null, "variant": null, "lookupKey": [], "label": "rs9923231 variant (T)/rs9923231 variant (T)", "inferred": false, "combination": false, "phenotypeDataSource": "CPIC", "diplotypeKey": {} } ], "matcherComponentHaplotypes": [], "matcherHomozygousComponentHaplotypes": [], "recommendationDiplotypes": [ { "allele1": { "gene": "VKORC1", "name": "rs9923231 variant (T)", "function": null, "reference": false, "activityValue": null }, "allele2": { "gene": "VKORC1", "name": "rs9923231 variant (T)", "function": null, "reference": false, "activityValue": null }, "gene": "VKORC1", "phenotypes": [], "outsidePhenotype": false, "outsidePhenotypeMismatch": null, "activityScore": null, "outsideActivityScore": false, "outsideActivityScoreMismatch": null, "variant": null, "lookupKey": [], "label": "rs9923231 variant (T)/rs9923231 variant (T)", "inferred": false, "combination": false, "phenotypeDataSource": "CPIC", "diplotypeKey": {} } ], "variants": [], "variantsOfInterest": [], "hasUndocumentedVariations": false, "treatUndocumentedVariationsAsReference": false } }, "DPWG": { "ABCG2": { "alleleDefinitionVersion": null, "alleleDefinitionSource": "UNKNOWN", "phenotypeVersion": "2024-08-27-21-12", "phenotypeSource": "DPWG", "geneSymbol": "ABCG2", "chr": null, "phased": false, "effectivelyPhased": false, "callSource": "OUTSIDE", "uncalledHaplotypes": [], "messages": [ { "rule_name": "pcat-outside-call", "version": "1", "matches": { "gene": null, "hapsCalled": [], "hapsMissing": [], "variantsMissing": [], "variant": null, "dips": [], "drugs": [] }, "exception_type": "", "message": "This comes from an outside data source which does not supply position-level detail. For specific disclaimers and limitations, see the original genotyping source." }, { "rule_name": "prefer-sample-data", "version": null, "matches": null, "exception_type": "note", "message": "PharmCAT would have called rs2231142 reference (G)/rs2231142 reference (G) based on the VCF but it has been ignored in favor of the outside call. If you want to use the PharmCAT call for this gene then remove the gene from the outside call data." } ], "relatedDrugs": [], "sourceDiplotypes": [ { "allele1": { "gene": "ABCG2", "name": "rs2231142 reference (G)", "function": "Normal function", "reference": true, "activityValue": "n/a" }, "allele2": { "gene": "ABCG2", "name": "rs2231142 reference (G)", "function": "Normal function", "reference": true, "activityValue": "n/a" }, "gene": "ABCG2", "phenotypes": [ "Normal Function" ], "outsidePhenotype": false, "outsidePhenotypeMismatch": null, "activityScore": null, "outsideActivityScore": false, "outsideActivityScoreMismatch": null, "variant": null, "lookupKey": [ "Normal Function" ], "label": "rs2231142 reference (G)/rs2231142 reference (G)", "inferred": false, "combination": false, "phenotypeDataSource": "DPWG", "diplotypeKey": {} } ], "matcherComponentHaplotypes": [], "matcherHomozygousComponentHaplotypes": [], "recommendationDiplotypes": [ { "allele1": { "gene": "ABCG2", "name": "rs2231142 reference (G)", "function": "Normal function", "reference": true, "activityValue": "n/a" }, "allele2": { "gene": "ABCG2", "name": "rs2231142 reference (G)", "function": "Normal function", "reference": true, "activityValue": "n/a" }, "gene": "ABCG2", "phenotypes": [ "Normal Function" ], "outsidePhenotype": false, "outsidePhenotypeMismatch": null, "activityScore": null, "outsideActivityScore": false, "outsideActivityScoreMismatch": null, "variant": null, "lookupKey": [ "Normal Function" ], "label": "rs2231142 reference (G)/rs2231142 reference (G)", "inferred": false, "combination": false, "phenotypeDataSource": "DPWG", "diplotypeKey": {} } ], "variants": [], "variantsOfInterest": [], "hasUndocumentedVariations": false, "treatUndocumentedVariationsAsReference": false }, "CACNA1S": { "alleleDefinitionVersion": null, "alleleDefinitionSource": "UNKNOWN", "phenotypeVersion": null, "phenotypeSource": "DPWG", "geneSymbol": "CACNA1S", "chr": null, "phased": false, "effectivelyPhased": false, "callSource": "OUTSIDE", "uncalledHaplotypes": [], "messages": [ { "rule_name": "pcat-outside-call", "version": "1", "matches": { "gene": null, "hapsCalled": [], "hapsMissing": [], "variantsMissing": [], "variant": null, "dips": [], "drugs": [] }, "exception_type": "", "message": "This comes from an outside data source which does not supply position-level detail. For specific disclaimers and limitations, see the original genotyping source." } ], "relatedDrugs": [], "sourceDiplotypes": [ { "allele1": { "gene": "CACNA1S", "name": "Reference", "function": null, "reference": true, "activityValue": null }, "allele2": { "gene": "CACNA1S", "name": "Reference", "function": null, "reference": true, "activityValue": null }, "gene": "CACNA1S", "phenotypes": [], "outsidePhenotype": false, "outsidePhenotypeMismatch": null, "activityScore": null, "outsideActivityScore": false, "outsideActivityScoreMismatch": null, "variant": null, "lookupKey": [], "label": "Reference/Reference", "inferred": false, "combination": false, "phenotypeDataSource": "DPWG", "diplotypeKey": {} } ], "matcherComponentHaplotypes": [], "matcherHomozygousComponentHaplotypes": [], "recommendationDiplotypes": [ { "allele1": { "gene": "CACNA1S", "name": "Reference", "function": null, "reference": true, "activityValue": null }, "allele2": { "gene": "CACNA1S", "name": "Reference", "function": null, "reference": true, "activityValue": null }, "gene": "CACNA1S", "phenotypes": [], "outsidePhenotype": false, "outsidePhenotypeMismatch": null, "activityScore": null, "outsideActivityScore": false, "outsideActivityScoreMismatch": null, "variant": null, "lookupKey": [], "label": "Reference/Reference", "inferred": false, "combination": false, "phenotypeDataSource": "DPWG", "diplotypeKey": {} } ], "variants": [], "variantsOfInterest": [], "hasUndocumentedVariations": false, "treatUndocumentedVariationsAsReference": false }, "CFTR": { "alleleDefinitionVersion": null, "alleleDefinitionSource": "UNKNOWN", "phenotypeVersion": null, "phenotypeSource": "DPWG", "geneSymbol": "CFTR", "chr": null, "phased": false, "effectivelyPhased": false, "callSource": "OUTSIDE", "uncalledHaplotypes": [], "messages": [ { "rule_name": "pcat-outside-call", "version": "1", "matches": { "gene": null, "hapsCalled": [], "hapsMissing": [], "variantsMissing": [], "variant": null, "dips": [], "drugs": [] }, "exception_type": "", "message": "This comes from an outside data source which does not supply position-level detail. For specific disclaimers and limitations, see the original genotyping source." } ], "relatedDrugs": [], "sourceDiplotypes": [ { "allele1": { "gene": "CFTR", "name": "ivacaftor non-responsive CFTR sequence", "function": null, "reference": true, "activityValue": null }, "allele2": { "gene": "CFTR", "name": "ivacaftor non-responsive CFTR sequence", "function": null, "reference": true, "activityValue": null }, "gene": "CFTR", "phenotypes": [], "outsidePhenotype": false, "outsidePhenotypeMismatch": null, "activityScore": null, "outsideActivityScore": false, "outsideActivityScoreMismatch": null, "variant": null, "lookupKey": [], "label": "Reference/Reference", "inferred": false, "combination": false, "phenotypeDataSource": "DPWG", "diplotypeKey": {} } ], "matcherComponentHaplotypes": [], "matcherHomozygousComponentHaplotypes": [], "recommendationDiplotypes": [ { "allele1": { "gene": "CFTR", "name": "ivacaftor non-responsive CFTR sequence", "function": null, "reference": true, "activityValue": null }, "allele2": { "gene": "CFTR", "name": "ivacaftor non-responsive CFTR sequence", "function": null, "reference": true, "activityValue": null }, "gene": "CFTR", "phenotypes": [], "outsidePhenotype": false, "outsidePhenotypeMismatch": null, "activityScore": null, "outsideActivityScore": false, "outsideActivityScoreMismatch": null, "variant": null, "lookupKey": [], "label": "Reference/Reference", "inferred": false, "combination": false, "phenotypeDataSource": "DPWG", "diplotypeKey": {} } ], "variants": [], "variantsOfInterest": [], "hasUndocumentedVariations": false, "treatUndocumentedVariationsAsReference": false }, "CYP2B6": { "alleleDefinitionVersion": null, "alleleDefinitionSource": "UNKNOWN", "phenotypeVersion": "2024-08-27-21-12", "phenotypeSource": "DPWG", "geneSymbol": "CYP2B6", "chr": null, "phased": false, "effectivelyPhased": false, "callSource": "OUTSIDE", "uncalledHaplotypes": [], "messages": [ { "rule_name": "pcat-outside-call", "version": "1", "matches": { "gene": null, "hapsCalled": [], "hapsMissing": [], "variantsMissing": [], "variant": null, "dips": [], "drugs": [] }, "exception_type": "", "message": "This comes from an outside data source which does not supply position-level detail. For specific disclaimers and limitations, see the original genotyping source." }, { "rule_name": "prefer-sample-data", "version": null, "matches": null, "exception_type": "note", "message": "PharmCAT would have called *2/*5 based on the VCF but it has been ignored in favor of the outside call. If you want to use the PharmCAT call for this gene then remove the gene from the outside call data." } ], "relatedDrugs": [], "sourceDiplotypes": [ { "allele1": { "gene": "CYP2B6", "name": "*5", "function": "Normal function", "reference": false, "activityValue": "n/a" }, "allele2": { "gene": "CYP2B6", "name": "*2", "function": "Unassigned function", "reference": false, "activityValue": "n/a" }, "gene": "CYP2B6", "phenotypes": [ "n/a" ], "outsidePhenotype": false, "outsidePhenotypeMismatch": null, "activityScore": null, "outsideActivityScore": false, "outsideActivityScoreMismatch": null, "variant": null, "lookupKey": [ "n/a" ], "label": "*2/*5", "inferred": false, "combination": false, "phenotypeDataSource": "DPWG", "diplotypeKey": {} } ], "matcherComponentHaplotypes": [], "matcherHomozygousComponentHaplotypes": [], "recommendationDiplotypes": [ { "allele1": { "gene": "CYP2B6", "name": "*5", "function": "Normal function", "reference": false, "activityValue": "n/a" }, "allele2": { "gene": "CYP2B6", "name": "*2", "function": "Unassigned function", "reference": false, "activityValue": "n/a" }, "gene": "CYP2B6", "phenotypes": [ "n/a" ], "outsidePhenotype": false, "outsidePhenotypeMismatch": null, "activityScore": null, "outsideActivityScore": false, "outsideActivityScoreMismatch": null, "variant": null, "lookupKey": [ "n/a" ], "label": "*2/*5", "inferred": false, "combination": false, "phenotypeDataSource": "DPWG", "diplotypeKey": {} } ], "variants": [], "variantsOfInterest": [], "hasUndocumentedVariations": false, "treatUndocumentedVariationsAsReference": false }, "CYP2C19": { "alleleDefinitionVersion": null, "alleleDefinitionSource": "UNKNOWN", "phenotypeVersion": "2024-08-27-21-12", "phenotypeSource": "DPWG", "geneSymbol": "CYP2C19", "chr": null, "phased": false, "effectivelyPhased": false, "callSource": "OUTSIDE", "uncalledHaplotypes": [], "messages": [ { "rule_name": "pcat-outside-call", "version": "1", "matches": { "gene": null, "hapsCalled": [], "hapsMissing": [], "variantsMissing": [], "variant": null, "dips": [], "drugs": [] }, "exception_type": "", "message": "This comes from an outside data source which does not supply position-level detail. For specific disclaimers and limitations, see the original genotyping source." }, { "rule_name": "prefer-sample-data", "version": null, "matches": null, "exception_type": "note", "message": "PharmCAT would have called *1/*1 based on the VCF but it has been ignored in favor of the outside call. If you want to use the PharmCAT call for this gene then remove the gene from the outside call data." } ], "relatedDrugs": [], "sourceDiplotypes": [ { "allele1": { "gene": "CYP2C19", "name": "*1", "function": "Normal function", "reference": false, "activityValue": "n/a" }, "allele2": { "gene": "CYP2C19", "name": "*1", "function": "Normal function", "reference": false, "activityValue": "n/a" }, "gene": "CYP2C19", "phenotypes": [ "Normal Metabolizer" ], "outsidePhenotype": false, "outsidePhenotypeMismatch": null, "activityScore": null, "outsideActivityScore": false, "outsideActivityScoreMismatch": null, "variant": null, "lookupKey": [ "Normal Metabolizer" ], "label": "*1/*1", "inferred": false, "combination": false, "phenotypeDataSource": "DPWG", "diplotypeKey": {} } ], "matcherComponentHaplotypes": [], "matcherHomozygousComponentHaplotypes": [], "recommendationDiplotypes": [ { "allele1": { "gene": "CYP2C19", "name": "*1", "function": "Normal function", "reference": false, "activityValue": "n/a" }, "allele2": { "gene": "CYP2C19", "name": "*1", "function": "Normal function", "reference": false, "activityValue": "n/a" }, "gene": "CYP2C19", "phenotypes": [ "Normal Metabolizer" ], "outsidePhenotype": false, "outsidePhenotypeMismatch": null, "activityScore": null, "outsideActivityScore": false, "outsideActivityScoreMismatch": null, "variant": null, "lookupKey": [ "Normal Metabolizer" ], "label": "*1/*1", "inferred": false, "combination": false, "phenotypeDataSource": "DPWG", "diplotypeKey": {} } ], "variants": [], "variantsOfInterest": [], "hasUndocumentedVariations": false, "treatUndocumentedVariationsAsReference": false }, "CYP2C9": { "alleleDefinitionVersion": null, "alleleDefinitionSource": "UNKNOWN", "phenotypeVersion": "2024-08-27-21-12", "phenotypeSource": "DPWG", "geneSymbol": "CYP2C9", "chr": null, "phased": false, "effectivelyPhased": false, "callSource": "OUTSIDE", "uncalledHaplotypes": [], "messages": [ { "rule_name": "pcat-outside-call", "version": "1", "matches": { "gene": null, "hapsCalled": [], "hapsMissing": [], "variantsMissing": [], "variant": null, "dips": [], "drugs": [] }, "exception_type": "", "message": "This comes from an outside data source which does not supply position-level detail. For specific disclaimers and limitations, see the original genotyping source." }, { "rule_name": "prefer-sample-data", "version": null, "matches": null, "exception_type": "note", "message": "PharmCAT would have called *1/*1 based on the VCF but it has been ignored in favor of the outside call. 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For specific disclaimers and limitations, see the original genotyping source." }, { "rule_name": "prefer-sample-data", "version": null, "matches": null, "exception_type": "note", "message": "PharmCAT would have called *1/*1 based on the VCF but it has been ignored in favor of the outside call. 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