{
  "resourceType" : "Parameters",
  "id" : "FindSubjectMolecConseqOutput",
  "parameter" : [{
    "name" : "consequence",
    "resource" : {
      "resourceType" : "Observation",
      "id" : "MC1",
      "meta" : {
        "profile" : ["http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence"]
      },
      "text" : {
        "status" : "generated",
        "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">NM_001395525.1:c.-281+2T>C - intronic_variant:loss_of_function_variant</div>"
      },
      "status" : "final",
      "category" : [{
        "coding" : [{
          "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
          "code" : "laboratory"
        }]
      },
      {
        "coding" : [{
          "system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
          "code" : "GE"
        }]
      }],
      "code" : {
        "coding" : [{
          "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
          "code" : "molecular-consequence"
        }]
      },
      "subject" : {
        "reference" : "Patient/HG00403"
      },
      "effectiveDateTime" : "2023-04-01",
      "performer" : [{
        "reference" : "Organization/ExampleOrg"
      }],
      "interpretation" : [{
        "coding" : [{
          "system" : "http://example.org/pcingola.github.io/SnpEff/se_inputoutput/#impact-prediction",
          "code" : "HIGH",
          "display" : "High"
        }]
      }],
      "derivedFrom" : [{
        "reference" : "Observation/variantExampleMC"
      }],
      "component" : [{
        "code" : {
          "coding" : [{
            "system" : "http://loinc.org",
            "code" : "51958-7",
            "display" : "Transcript reference sequence [ID]"
          }]
        },
        "valueCodeableConcept" : {
          "coding" : [{
            "system" : "http://www.ncbi.nlm.nih.gov/refseq",
            "code" : "NM_001395525.1",
            "display" : "NM_001395525.1"
          }]
        }
      },
      {
        "code" : {
          "coding" : [{
            "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
            "code" : "feature-consequence"
          }]
        },
        "valueCodeableConcept" : {
          "coding" : [{
            "system" : "http://www.sequenceontology.org",
            "code" : "SO:0001575",
            "display" : "splice_donor_variant"
          },
          {
            "system" : "http://www.sequenceontology.org",
            "code" : "SO:0001627",
            "display" : "intron_variant"
          }]
        }
      },
      {
        "code" : {
          "coding" : [{
            "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
            "code" : "functional-effect"
          }]
        },
        "valueCodeableConcept" : {
          "coding" : [{
            "system" : "http://www.sequenceontology.org",
            "code" : "SO_0002054",
            "display" : "loss_of_function_variant"
          }]
        }
      }]
    }
  },
  {
    "name" : "consequence",
    "resource" : {
      "resourceType" : "Observation",
      "id" : "MC2",
      "meta" : {
        "profile" : ["http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence"]
      },
      "text" : {
        "status" : "generated",
        "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">NM_001366781.1:c.90T>C - synonymous_variant</div>"
      },
      "status" : "final",
      "category" : [{
        "coding" : [{
          "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
          "code" : "laboratory"
        }]
      },
      {
        "coding" : [{
          "system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
          "code" : "GE"
        }]
      }],
      "code" : {
        "coding" : [{
          "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
          "code" : "molecular-consequence"
        }]
      },
      "subject" : {
        "reference" : "Patient/HG00403"
      },
      "effectiveDateTime" : "2023-04-01",
      "performer" : [{
        "reference" : "Organization/ExampleOrg"
      }],
      "interpretation" : [{
        "coding" : [{
          "system" : "http://example.org/pcingola.github.io/SnpEff/se_inputoutput/#impact-prediction",
          "code" : "LOW",
          "display" : "Low"
        }]
      }],
      "derivedFrom" : [{
        "reference" : "Observation/variantExampleMC"
      }],
      "component" : [{
        "code" : {
          "coding" : [{
            "system" : "http://loinc.org",
            "code" : "48004-6"
          }],
          "text" : "coding HGVS"
        },
        "valueCodeableConcept" : {
          "coding" : [{
            "system" : "http://varnomen.hgvs.org",
            "code" : "NM_001366781.1:c.90T>C",
            "display" : "NM_001366781.1:c.90T>C"
          }]
        }
      },
      {
        "code" : {
          "coding" : [{
            "system" : "http://loinc.org",
            "code" : "51958-7",
            "display" : "Transcript reference sequence [ID]"
          }]
        },
        "valueCodeableConcept" : {
          "coding" : [{
            "system" : "http://www.ncbi.nlm.nih.gov/refseq",
            "code" : "NM_001366781.1",
            "display" : "NM_001366781.1"
          }]
        }
      },
      {
        "code" : {
          "coding" : [{
            "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
            "code" : "feature-consequence"
          }]
        },
        "valueCodeableConcept" : {
          "coding" : [{
            "system" : "http://www.sequenceontology.org",
            "code" : "SO:0001819",
            "display" : "synonymous_variant"
          }]
        }
      }]
    }
  },
  {
    "name" : "consequence",
    "resource" : {
      "resourceType" : "Observation",
      "id" : "MC3",
      "meta" : {
        "profile" : ["http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence"]
      },
      "text" : {
        "status" : "generated",
        "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">Molecular Consequence</div>"
      },
      "status" : "final",
      "category" : [{
        "coding" : [{
          "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
          "code" : "laboratory"
        }]
      },
      {
        "coding" : [{
          "system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
          "code" : "GE"
        }]
      }],
      "code" : {
        "coding" : [{
          "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
          "code" : "molecular-consequence"
        }]
      },
      "subject" : {
        "reference" : "Patient/HG00403"
      },
      "effectiveDateTime" : "2023-04-01",
      "performer" : [{
        "reference" : "Organization/ExampleOrg"
      }],
      "interpretation" : [{
        "coding" : [{
          "system" : "http://example.org/pcingola.github.io/SnpEff/se_inputoutput/#impact-prediction",
          "code" : "MOD",
          "display" : "Modifier"
        }]
      }],
      "derivedFrom" : [{
        "reference" : "Observation/variantExampleMC"
      }],
      "component" : [{
        "code" : {
          "coding" : [{
            "system" : "http://loinc.org",
            "code" : "48004-6"
          }],
          "text" : "coding HGVS"
        },
        "valueCodeableConcept" : {
          "coding" : [{
            "system" : "http://varnomen.hgvs.org",
            "code" : "NM_001395543.1:c.-171T>C",
            "display" : "NM_001395543.1:c.-171T>C"
          }]
        }
      },
      {
        "code" : {
          "coding" : [{
            "system" : "http://loinc.org",
            "code" : "51958-7",
            "display" : "Transcript reference sequence [ID]"
          }]
        },
        "valueCodeableConcept" : {
          "coding" : [{
            "system" : "http://www.ncbi.nlm.nih.gov/refseq",
            "code" : "NM_001395543.1",
            "display" : "NM_001395543.1"
          }]
        }
      },
      {
        "code" : {
          "coding" : [{
            "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
            "code" : "feature-consequence"
          }]
        },
        "valueCodeableConcept" : {
          "coding" : [{
            "system" : "http://www.sequenceontology.org",
            "code" : "SO:0001623",
            "display" : "5_prime_UTR_variant"
          }]
        }
      }]
    }
  },
  {
    "name" : "consequence",
    "resource" : {
      "resourceType" : "Observation",
      "id" : "MC4",
      "meta" : {
        "profile" : ["http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence"]
      },
      "text" : {
        "status" : "generated",
        "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">Molecular Consequence</div>"
      },
      "status" : "final",
      "category" : [{
        "coding" : [{
          "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
          "code" : "laboratory"
        }]
      },
      {
        "coding" : [{
          "system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
          "code" : "GE"
        }]
      }],
      "code" : {
        "coding" : [{
          "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
          "code" : "molecular-consequence"
        }]
      },
      "subject" : {
        "reference" : "Patient/HG00403"
      },
      "effectiveDateTime" : "2023-04-01",
      "performer" : [{
        "reference" : "Organization/ExampleOrg"
      }],
      "interpretation" : [{
        "coding" : [{
          "system" : "http://example.org/pcingola.github.io/SnpEff/se_inputoutput/#impact-prediction",
          "code" : "MOD",
          "display" : "Modifier"
        }]
      }],
      "derivedFrom" : [{
        "reference" : "Observation/variantExampleMC"
      }],
      "component" : [{
        "code" : {
          "coding" : [{
            "system" : "http://loinc.org",
            "code" : "51958-7",
            "display" : "Transcript reference sequence [ID]"
          }]
        },
        "valueCodeableConcept" : {
          "coding" : [{
            "system" : "http://www.ncbi.nlm.nih.gov/refseq",
            "code" : "NM_001395544.1",
            "display" : "NM_001395544.1"
          }]
        }
      },
      {
        "code" : {
          "coding" : [{
            "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
            "code" : "feature-consequence"
          }]
        },
        "valueCodeableConcept" : {
          "coding" : [{
            "system" : "http://www.sequenceontology.org",
            "code" : "SO:0001627",
            "display" : "intron_variant"
          }]
        }
      }]
    }
  },
  {
    "name" : "variant",
    "resource" : {
      "resourceType" : "Observation",
      "id" : "variantExampleMC",
      "meta" : {
        "profile" : ["http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"]
      },
      "text" : {
        "status" : "generated",
        "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">Variant</div>"
      },
      "status" : "final",
      "category" : [{
        "coding" : [{
          "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
          "code" : "laboratory"
        }]
      },
      {
        "coding" : [{
          "system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
          "code" : "GE"
        }]
      }],
      "code" : {
        "coding" : [{
          "system" : "http://loinc.org",
          "code" : "69548-6",
          "display" : "Genetic variant assessment"
        }]
      },
      "subject" : {
        "reference" : "Patient/HG00403"
      },
      "effectiveDateTime" : "2023-04-01",
      "performer" : [{
        "reference" : "Organization/ExampleOrg"
      }],
      "valueCodeableConcept" : {
        "coding" : [{
          "system" : "http://loinc.org",
          "code" : "LA9633-4",
          "display" : "Present"
        }]
      },
      "component" : [{
        "code" : {
          "coding" : [{
            "system" : "http://loinc.org",
            "code" : "48002-0",
            "display" : "Genomic source class"
          }]
        },
        "valueCodeableConcept" : {
          "coding" : [{
            "system" : "http://loinc.org",
            "code" : "LA6683-2",
            "display" : "Germline"
          }]
        }
      },
      {
        "code" : {
          "coding" : [{
            "system" : "http://loinc.org",
            "code" : "48013-7",
            "display" : "Genomic reference sequence ID"
          }]
        },
        "valueCodeableConcept" : {
          "coding" : [{
            "system" : "http://www.ncbi.nlm.nih.gov/refseq",
            "code" : "NC_000001.10"
          }]
        }
      },
      {
        "code" : {
          "coding" : [{
            "system" : "http://loinc.org",
            "code" : "53034-5",
            "display" : "Allelic state"
          }]
        },
        "valueCodeableConcept" : {
          "coding" : [{
            "system" : "http://loinc.org",
            "code" : "LA6706-1",
            "display" : "Heterozygous"
          }]
        }
      },
      {
        "code" : {
          "coding" : [{
            "system" : "http://loinc.org",
            "code" : "81252-9",
            "display" : "Discrete genetic variant"
          }]
        },
        "valueCodeableConcept" : {
          "coding" : [{
            "system" : "http://varnomen.hgvs.org",
            "code" : "NC_000001.10:g.86852621A>G",
            "display" : "NC_000001.10:g.86852621A>G"
          }]
        }
      },
      {
        "code" : {
          "coding" : [{
            "system" : "http://loinc.org",
            "code" : "81258-6",
            "display" : "Sample VAF"
          }]
        },
        "valueQuantity" : {
          "value" : 0.6,
          "unit" : "relative frequency of a particular allele in the specimen",
          "system" : "http://unitsofmeasure.org",
          "code" : "1"
        }
      },
      {
        "code" : {
          "coding" : [{
            "system" : "http://loinc.org",
            "code" : "69547-8",
            "display" : "Genomic Ref allele [ID]"
          }]
        },
        "valueString" : "A"
      },
      {
        "code" : {
          "coding" : [{
            "system" : "http://loinc.org",
            "code" : "69551-0",
            "display" : "Genomic Alt allele [ID]"
          }]
        },
        "valueString" : "G"
      },
      {
        "code" : {
          "coding" : [{
            "system" : "http://loinc.org",
            "code" : "92822-6",
            "display" : "Genomic coord system"
          }]
        },
        "valueCodeableConcept" : {
          "coding" : [{
            "system" : "http://loinc.org",
            "code" : "LA30100-4",
            "display" : "0-based interval counting"
          }]
        }
      },
      {
        "code" : {
          "coding" : [{
            "system" : "http://loinc.org",
            "code" : "81254-5",
            "display" : "Genomic allele start-end"
          }]
        },
        "valueRange" : {
          "low" : {
            "value" : 86852620
          }
        }
      }]
    }
  }]
}