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

## : FindSubjectVariantsOutput - JSON Representation

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    {
      "resourceType" : "Parameters",
      "id" : "FindSubjectVariantsOutput",
      "parameter" : [
        {
          "name" : "variants",
          "part" : [
            {
              "name" : "rangeItem",
              "valueString" : "NC_000017.11:39688093-39728660"
            },
            {
              "name" : "presence",
              "valueBoolean" : false
            }
          ]
        },
        {
          "name" : "variants",
          "part" : [
            {
              "name" : "rangeItem",
              "valueString" : "NC_000007.14:140713327-140924929"
            },
            {
              "name" : "presence",
              "valueBoolean" : true
            },
            {
              "name" : "variant",
              "resource" : {
                "resourceType" : "Observation",
                "id" : "dv-5a7f781e83514",
                "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" : "2023-07-01",
                "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 [Type]"
                        }
                      ]
                    },
                    "valueCodeableConcept" : {
                      "coding" : [
                        {
                          "system" : "http://loinc.org",
                          "code" : "LA6684-0",
                          "display" : "Somatic"
                        }
                      ]
                    }
                  },
                  {
                    "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_000007.14"
                        }
                      ]
                    }
                  },
                  {
                    "code" : {
                      "coding" : [
                        {
                          "system" : "http://loinc.org",
                          "code" : "81258-6",
                          "display" : "Sample VAF"
                        }
                      ]
                    },
                    "valueQuantity" : {
                      "value" : 0.1793,
                      "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" : "T"
                  },
                  {
                    "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"
                        }
                      ],
                      "text" : "Genomic allele start-end"
                    },
                    "valueRange" : {
                      "low" : {
                        "value" : 140753335
                      }
                    }
                  }
                ]
              }
            }
          ]
        }
      ]
    }