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December 6, 2016 18:29
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possible more-SEPIO-like interpretation model
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| { | |
| "cg:id": "VarInterp001", | |
| "cg:type": "VariantInterpretation", | |
| "variant": { | |
| "cg:id": "CanAll035", | |
| "cg:type": "CanonicalAllele", | |
| "preferredCtxAllele": "CtxAll039", | |
| "identifier": "http://reg.genome.network/allele/CA090919" | |
| }, | |
| "condition": { | |
| "cg:id": "Cond004", | |
| "cg:type": "Condition", | |
| "name": "Primary Ciliary Dyskenisia", | |
| "code": "244" | |
| }, | |
| "interpretationCode": "LN:LA6669-1", | |
| "assertionMethod": { | |
| "cg:id": "AssertMeth01", | |
| "cg:type": "AssertionMethod", | |
| "description": "ACMG ISV guidelines 2015", | |
| "version": "1.0", | |
| "url": "https://www.acmg.net/docs/Standards_Guidelines_for_the_Interpretation_of_Sequence_Variants.pdf", | |
| "scoringAlgorithm": { | |
| "cg:id": "ScorAlg01", | |
| "cg:type": "ScoringAlgorithm", | |
| "description": "This is the description of how the weighting of the satisfied criterion are typically evaluated to arrive at a specific clinical significance." | |
| } | |
| }, | |
| "modeOfInheritance": "HP:0000007", | |
| "explanation": "The Trp2490_Leu2496del variant in DNAH5 leads to an in-frame deletion of 7 amino acids. This variant has been reported together with a second DNAH5 variant (Met2083Ile) in one individual with PCD and situs inversus (Berg 2011). In addition, this variant has been identified in trans configuration with a disease-causing variant in one affected proband (LMM unpublished data). Data from large population studies is insufficient to determine whether this variant is present in the general population. In summary, this variant is likely pathogenic, though additional studies are required to fully establish its clinical significance.", | |
| "used": { | |
| "AssertionMethod": [ | |
| null | |
| ], | |
| "CriterionAssessment": [ | |
| { | |
| "cg:id": "CritAssess031", | |
| "cg:type": "CriterionAssessment", | |
| "criterion": { | |
| "cg:id": "PM2", | |
| "cg:type": "Criterion", | |
| "description": "Absent from controls (or at extremely low frequency if recessive) (Table 6) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium", | |
| "shortDescription": "Absent from controls", | |
| "defaultOutcome": "CG:M", | |
| "targetInterpretation": "LN:LA6668-3" | |
| }, | |
| "variant": { | |
| "cg:id": "CanAll035", | |
| "cg:type": "CanonicalAllele", | |
| "preferredCtxAllele": "CtxAll039", | |
| "identifier": "http://reg.genome.network/allele/CA090919" | |
| }, | |
| "outcome": "CG:I", | |
| "explanation": "while the variant is absent from exac, however\n1) very low coverage across this region (~5X) and usually 20X is used as a cut-off to say “absent”\n2) variant is 21 nt deletion - databases may not be able to call a variant of that size (I rarely see an indel of this size in ExAC).", | |
| "used": { | |
| "Data": [ | |
| { | |
| "cg:id": "PAF082", | |
| "cg:type": "PopulationAlleleFrequency", | |
| "ascertainment": "ExAC", | |
| "population": "CG:combined", | |
| "contextualAllele": { | |
| "cg:id": "CtxAll039", | |
| "cg:type": "ContextualAllele", | |
| "relatedCanonicalAllele": { | |
| "cg:id": "CanAll035", | |
| "cg:type": "CanonicalAllele", | |
| "preferredCtxAllele": "CtxAll039", | |
| "identifier": "http://reg.genome.network/allele/CA090919" | |
| }, | |
| "alleleName": "NM_001369.2(DNAH5):c.7468_7488del" | |
| }, | |
| "alleleCount": 0, | |
| "alleleFrequency": 0.0, | |
| "medianCoverage": 11.0, | |
| "used": { | |
| "DataSource": [ | |
| { | |
| "cg:id": "DataSrc009", | |
| "cg:type": "DataSource", | |
| "externalIdentifier": "EXAC v0.2", | |
| "linkedIRI": "ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.2/" | |
| } | |
| ] | |
| }, | |
| "startedAtTime": "2016-06-01T14:15:00+00:00", | |
| "endedAtTime": "2016-06-01T14:15:00+00:00", | |
| "wasAssociatedWith": [ | |
| { | |
| "cg:id": "Agent001", | |
| "cg:type": "Agent", | |
| "description": "SH", | |
| "name": "Steven Harrison" | |
| } | |
| ] | |
| } | |
| ], | |
| "Criterion": [ | |
| { | |
| "cg:id": "PM2", | |
| "cg:type": "Criterion", | |
| "description": "Absent from controls (or at extremely low frequency if recessive) (Table 6) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium", | |
| "shortDescription": "Absent from controls", | |
| "defaultOutcome": "CG:M", | |
| "targetInterpretation": "LN:LA6668-3" | |
| } | |
| ], | |
| "CanonicalAllele": [ | |
| { | |
| "cg:id": "CanAll035", | |
| "cg:type": "CanonicalAllele", | |
| "preferredCtxAllele": "CtxAll039", | |
| "identifier": "http://reg.genome.network/allele/CA090919" | |
| } | |
| ] | |
| }, | |
| "startedAtTime": "2016-07-01T10:53:00+00:00", | |
| "endedAtTime": "2016-07-01T10:53:00+00:00", | |
| "wasAssociatedWith": [ | |
| { | |
| "cg:id": "Agent001", | |
| "cg:type": "Agent", | |
| "description": "SH", | |
| "name": "Steven Harrison" | |
| }, | |
| { | |
| "cg:id": "Agent005", | |
| "cg:type": "Agent", | |
| "description": "CSER", | |
| "name": "CSER Bake Off Project" | |
| } | |
| ] | |
| }, | |
| { | |
| "cg:id": "CritAssess022", | |
| "cg:type": "CriterionAssessment", | |
| "criterion": { | |
| "cg:id": "PM3", | |
| "cg:type": "Criterion", | |
| "description": "For recessive disorders, detected in trans with a pathogenic variant", | |
| "shortDescription": "Recessive in trans w/ Path", | |
| "defaultOutcome": "CG:M", | |
| "targetInterpretation": "LN:LA6668-3" | |
| }, | |
| "variant": { | |
| "cg:id": "CanAll035", | |
| "cg:type": "CanonicalAllele", | |
| "preferredCtxAllele": "CtxAll039", | |
| "identifier": "http://reg.genome.network/allele/CA090919" | |
| }, | |
| "outcome": "CG:M", | |
| "used": { | |
| "Data": [ | |
| { | |
| "cg:id": "CondInh055", | |
| "cg:type": "ConditionInheritance", | |
| "condition": { | |
| "cg:id": "Cond004", | |
| "cg:type": "Condition", | |
| "name": "Primary Ciliary Dyskenisia", | |
| "code": "244" | |
| }, | |
| "modeOfInheritance": "HP:0000007", | |
| "used": { | |
| "DataSource": [ | |
| { | |
| "cg:id": "DataSrc004", | |
| "cg:type": "DataSource", | |
| "externalIdentifier": "OMIM:244400", | |
| "linkedIRI": "http://omim.org/entry/244400", | |
| "version": "alopez : 09/15/2016" | |
| } | |
| ] | |
| }, | |
| "startedAtTime": "2016-05-31T08:45:59+00:00", | |
| "endedAtTime": "2016-05-31T08:45:59+00:00", | |
| "wasAssociatedWith": [ | |
| { | |
| "cg:id": "Agent008", | |
| "cg:type": "Agent", | |
| "description": "MDS", | |
| "name": "Marina DiStefano" | |
| } | |
| ] | |
| }, | |
| { | |
| "cg:id": "IndCond056", | |
| "cg:type": "IndividualCondition", | |
| "individual": { | |
| "cg:id": "Indiv004", | |
| "cg:type": "Individual", | |
| "description": "individual #004" | |
| }, | |
| "condition": { | |
| "cg:id": "Cond014", | |
| "cg:type": "Condition", | |
| "name": "outer dynein arm (ODA) defects", | |
| "code": "0200106" | |
| }, | |
| "hasCondition": true, | |
| "used": { | |
| "DataSource": [ | |
| { | |
| "cg:id": "DataSrc005", | |
| "cg:type": "DataSource", | |
| "externalIdentifier": "LMM-CASE:CSER-SUBJECT-123" | |
| } | |
| ] | |
| }, | |
| "startedAtTime": "2016-05-31T09:14:59+00:00", | |
| "endedAtTime": "2016-05-31T09:14:59+00:00", | |
| "wasAssociatedWith": [ | |
| { | |
| "cg:id": "Agent001", | |
| "cg:type": "Agent", | |
| "description": "SH", | |
| "name": "Steven Harrison" | |
| } | |
| ] | |
| }, | |
| { | |
| "cg:id": "MenDisVarInterp057", | |
| "cg:type": "MendelianDiseaseVariantPathogenicityInterpretation", | |
| "canonicalAllele": { | |
| "cg:id": "CanAll036", | |
| "cg:type": "CanonicalAllele", | |
| "preferredCtxAllele": "CtxAll040", | |
| "identifier": "http://reg.genome.network/allele/CA273615" | |
| }, | |
| "condition": { | |
| "cg:id": "Cond004", | |
| "cg:type": "Condition", | |
| "name": "Primary Ciliary Dyskenisia", | |
| "code": "244" | |
| }, | |
| "clinicalSignificance": "LN:LA6668-3", | |
| "used": { | |
| "DataSource": [ | |
| { | |
| "cg:id": "DataSrc006", | |
| "cg:type": "DataSource", | |
| "externalIdentifier": "CLINVAR:SCV000205842.3", | |
| "linkedIRI": "https://www.ncbi.nlm.nih.gov/clinvar/SCV000205842.3" | |
| } | |
| ] | |
| }, | |
| "startedAtTime": "2016-05-31T11:00:59+00:00", | |
| "endedAtTime": "2016-05-31T11:00:59+00:00", | |
| "wasAssociatedWith": [ | |
| { | |
| "cg:id": "Agent008", | |
| "cg:type": "Agent", | |
| "description": "MDS", | |
| "name": "Marina DiStefano" | |
| } | |
| ] | |
| }, | |
| { | |
| "cg:id": "IndAll058", | |
| "cg:type": "IndividualAllele", | |
| "explanation": "Father was het for c.9449delG variant and negative for c.7468_7488del variant. Mother was het for c.7468_7488del variant and negative for c.9449delG variant. Thus, variants are in trans in this proband.", | |
| "individual": { | |
| "cg:id": "Indiv004", | |
| "cg:type": "Individual", | |
| "description": "individual #004" | |
| }, | |
| "primaryAllele": { | |
| "cg:id": "CanAll035", | |
| "cg:type": "CanonicalAllele", | |
| "preferredCtxAllele": "CtxAll039", | |
| "identifier": "http://reg.genome.network/allele/CA090919" | |
| }, | |
| "secondaryAllele": { | |
| "cg:id": "CanAll036", | |
| "cg:type": "CanonicalAllele", | |
| "preferredCtxAllele": "CtxAll040", | |
| "identifier": "http://reg.genome.network/allele/CA273615" | |
| }, | |
| "primaryZygosity": "CG:het", | |
| "secondaryZygosity": "CG:het", | |
| "phase": "CG:trans", | |
| "used": { | |
| "DataSource": [ | |
| { | |
| "cg:id": "DataSrc005", | |
| "cg:type": "DataSource", | |
| "externalIdentifier": "LMM-CASE:CSER-SUBJECT-123" | |
| } | |
| ] | |
| }, | |
| "startedAtTime": "2016-05-31T09:14:59+00:00", | |
| "endedAtTime": "2016-05-31T09:14:59+00:00", | |
| "wasAssociatedWith": [ | |
| { | |
| "cg:id": "Agent001", | |
| "cg:type": "Agent", | |
| "description": "SH", | |
| "name": "Steven Harrison" | |
| } | |
| ] | |
| } | |
| ], | |
| "Criterion": [ | |
| { | |
| "cg:id": "PM3", | |
| "cg:type": "Criterion", | |
| "description": "For recessive disorders, detected in trans with a pathogenic variant", | |
| "shortDescription": "Recessive in trans w/ Path", | |
| "defaultOutcome": "CG:M", | |
| "targetInterpretation": "LN:LA6668-3" | |
| } | |
| ], | |
| "CanonicalAllele": [ | |
| { | |
| "cg:id": "CanAll035", | |
| "cg:type": "CanonicalAllele", | |
| "preferredCtxAllele": "CtxAll039", | |
| "identifier": "http://reg.genome.network/allele/CA090919" | |
| } | |
| ], | |
| "Condition": [ | |
| { | |
| "cg:id": "Cond004", | |
| "cg:type": "Condition", | |
| "name": "Primary Ciliary Dyskenisia", | |
| "code": "244" | |
| }, | |
| { | |
| "cg:id": "Cond014", | |
| "cg:type": "Condition", | |
| "name": "outer dynein arm (ODA) defects", | |
| "code": "0200106" | |
| } | |
| ] | |
| }, | |
| "startedAtTime": "2016-06-02T08:00:59+00:00", | |
| "endedAtTime": "2016-06-02T08:00:59+00:00", | |
| "wasAssociatedWith": [ | |
| { | |
| "cg:id": "Agent001", | |
| "cg:type": "Agent", | |
| "description": "SH", | |
| "name": "Steven Harrison" | |
| } | |
| ] | |
| }, | |
| { | |
| "cg:id": "CritAssess025", | |
| "cg:type": "CriterionAssessment", | |
| "criterion": { | |
| "cg:id": "PM4", | |
| "cg:type": "Criterion", | |
| "description": "Protein length changes as a result of in-frame deletions/insertions in a nonrepeat region or stop-loss variants", | |
| "shortDescription": "Protein length changes or stop-loss", | |
| "defaultOutcome": "CG:M", | |
| "targetInterpretation": "LN:LA6668-3" | |
| }, | |
| "variant": { | |
| "cg:id": "CanAll035", | |
| "cg:type": "CanonicalAllele", | |
| "preferredCtxAllele": "CtxAll039", | |
| "identifier": "http://reg.genome.network/allele/CA090919" | |
| }, | |
| "outcome": "CG:M", | |
| "explanation": "leads to an in-frame deletion of 7 amino acids (not repeat region).", | |
| "used": { | |
| "Data": [ | |
| { | |
| "cg:id": "MolCon066", | |
| "cg:type": "MolecularConsequence", | |
| "contextualAllele": { | |
| "cg:id": "CtxAll044", | |
| "cg:type": "ContextualAllele", | |
| "relatedCanonicalAllele": { | |
| "cg:id": "CanAll040", | |
| "cg:type": "CanonicalAllele", | |
| "preferredCtxAllele": "CtxAll044", | |
| "identifier": "http://reg.genome.network/allele/CA273136" | |
| }, | |
| "alleleName": "NP_001360.1:p.Trp2490_Leu2496del" | |
| }, | |
| "consequence": "SO:0001825", | |
| "used": { | |
| "DataSource": [ | |
| { | |
| "cg:id": "DataSrc007", | |
| "cg:type": "DataSource", | |
| "externalIdentifier": "LMM:GENEINSIGHT-LAB v5.3.2", | |
| "linkedIRI": "https://geneinsight-lmm-test.partners.org" | |
| } | |
| ] | |
| }, | |
| "startedAtTime": "2016-06-01T14:03:00+00:00", | |
| "endedAtTime": "2016-06-01T14:03:00+00:00", | |
| "wasAssociatedWith": [ | |
| { | |
| "cg:id": "Agent001", | |
| "cg:type": "Agent", | |
| "description": "SH", | |
| "name": "Steven Harrison" | |
| } | |
| ] | |
| }, | |
| { | |
| "cg:id": "RegAnno069", | |
| "cg:type": "RegionAnnotation", | |
| "region": { | |
| "cg:id": "CtxReg004", | |
| "cg:type": "ContextualRegion", | |
| "referenceSequence": { | |
| "cg:id": "RefSeq005", | |
| "cg:type": "ReferenceSequence", | |
| "identifier": "NP_001360.1" | |
| }, | |
| "start": 2490, | |
| "stop": 2496 | |
| }, | |
| "value": true, | |
| "type": "CG:repeat", | |
| "used": { | |
| "DataSource": [ | |
| { | |
| "cg:id": "DataSrc008", | |
| "cg:type": "DataSource", | |
| "externalIdentifier": "LMM:ALAMUT-PROD v123", | |
| "linkedIRI": "https://pcpgm.partners.org/lmm" | |
| } | |
| ] | |
| }, | |
| "startedAtTime": "2016-06-01T14:10:00+00:00", | |
| "endedAtTime": "2016-06-01T14:10:00+00:00", | |
| "wasAssociatedWith": [ | |
| { | |
| "cg:id": "Agent008", | |
| "cg:type": "Agent", | |
| "description": "MDS", | |
| "name": "Marina DiStefano" | |
| } | |
| ] | |
| } | |
| ], | |
| "Criterion": [ | |
| { | |
| "cg:id": "PM4", | |
| "cg:type": "Criterion", | |
| "description": "Protein length changes as a result of in-frame deletions/insertions in a nonrepeat region or stop-loss variants", | |
| "shortDescription": "Protein length changes or stop-loss", | |
| "defaultOutcome": "CG:M", | |
| "targetInterpretation": "LN:LA6668-3" | |
| } | |
| ], | |
| "CanonicalAllele": [ | |
| { | |
| "cg:id": "CanAll035", | |
| "cg:type": "CanonicalAllele", | |
| "preferredCtxAllele": "CtxAll039", | |
| "identifier": "http://reg.genome.network/allele/CA090919" | |
| } | |
| ] | |
| }, | |
| "startedAtTime": "2016-06-12T07:30:00+00:00", | |
| "endedAtTime": "2016-06-12T07:30:00+00:00", | |
| "wasAssociatedWith": [ | |
| { | |
| "cg:id": "Agent003", | |
| "cg:type": "Agent", | |
| "description": "TS", | |
| "name": "Tasha Strande" | |
| } | |
| ] | |
| } | |
| ], | |
| "Condition": [ | |
| { | |
| "cg:id": "Cond004", | |
| "cg:type": "Condition", | |
| "name": "Primary Ciliary Dyskenisia", | |
| "code": "244" | |
| } | |
| ], | |
| "CanonicalAllele": [ | |
| { | |
| "cg:id": "CanAll035", | |
| "cg:type": "CanonicalAllele", | |
| "preferredCtxAllele": "CtxAll039", | |
| "identifier": "http://reg.genome.network/allele/CA090919" | |
| } | |
| ] | |
| }, | |
| "startedAtTime": "2016-07-12T11:00:59+00:00", | |
| "endedAtTime": "2016-07-12T11:00:59+00:00", | |
| "wasAssociatedWith": [ | |
| { | |
| "cg:id": "Agent007", | |
| "cg:type": "Agent", | |
| "description": "CPC", | |
| "name": "ClinGen Pathogenicity Calculator v1" | |
| }, | |
| { | |
| "cg:id": "Agent001", | |
| "cg:type": "Agent", | |
| "description": "SH", | |
| "name": "Steven Harrison" | |
| } | |
| ] | |
| } |
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