Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 4.0.0-cibuild built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions

## : FindSubjectMolecConseqOutput - JSON Representation

Raw json | Download

    {
      "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&gt;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&gt;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
                  }
                }
              }
            ]
          }
        }
      ]
    }