This page is part of the Genetic Reporting Implementation Guide (v1.0.0: STU 1) based on FHIR R4. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions

Example - Variant with ACMG Screening - JSON Representation

(back to narrative)

Raw json

{
  "resourceType" : "DiagnosticReport",
  "id" : "AnnotationExample",
  "meta" : {
    "profile" : [
      "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-report"
    ]
  },
  "text" : {
    "status" : "generated",
    "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: AnnotationExample</p><p><b>meta</b>: </p><p><b>contained</b>: , </p><p><b>status</b>: final</p><p><b>code</b>: Master HL7 genetic variant reporting panel <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '81247-9' = 'Master HL7 genetic variant reporting panel', given as 'Master HL7 genetic variant reporting panel'})</span></p><p><b>result</b>: </p><ul><li>unknown resource contained</li><li>unknown resource contained</li></ul></div>"
  },
  "contained" : [
    {
      "resourceType" : "Observation",
      "id" : "1",
      "meta" : {
        "profile" : [
          "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/inherited-disease-pathogenicity"
        ]
      },
      "status" : "final",
      "category" : [
        {
          "coding" : [
            {
              "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
              "code" : "laboratory",
              "display" : "LABORATORY"
            }
          ]
        }
      ],
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "53037-8",
            "display" : "Genetic variation clinical significance [Imp]"
          }
        ]
      },
      "subject" : {
        "reference" : "urn:uuid:13f34265-335c-4853-bc38-0815315edafa"
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "LA6668-3",
            "display" : "Pathogenic"
          }
        ]
      },
      "derivedFrom" : [
        {
          "reference" : "#2"
        }
      ],
      "component" : [
        {
          "code" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "81259-4",
                "display" : "Associated phenotype"
              }
            ]
          },
          "valueCodeableConcept" : {
            "coding" : [
              {
                "system" : "http://snomed.info/sct",
                "code" : "398036000",
                "display" : "Familial hypercholesterolemia (disorder)"
              }
            ]
          }
        }
      ]
    },
    {
      "resourceType" : "Observation",
      "id" : "2",
      "meta" : {
        "profile" : [
          "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
        ]
      },
      "status" : "final",
      "category" : [
        {
          "coding" : [
            {
              "system" : "http://terminology.hl7.org/CodeSystem/observation-category",
              "code" : "laboratory",
              "display" : "LABORATORY"
            }
          ]
        }
      ],
      "code" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "69548-6",
            "display" : "Genetic variant assessment"
          }
        ]
      },
      "subject" : {
        "reference" : "urn:uuid:13f34265-335c-4853-bc38-0815315edafa"
      },
      "valueCodeableConcept" : {
        "coding" : [
          {
            "system" : "http://loinc.org",
            "code" : "LA9633-4",
            "display" : "present"
          }
        ]
      },
      "component" : [
        {
          "code" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "62374-4",
                "display" : "Human reference sequence assembly version"
              }
            ]
          },
          "valueCodeableConcept" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "LA14029-5",
                "display" : "GRCh37"
              }
            ]
          }
        },
        {
          "code" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "81252-9",
                "display" : "Discrete genetic variant"
              }
            ]
          },
          "valueCodeableConcept" : {
            "coding" : [
              {
                "system" : "http://www.ncbi.nlm.nih.gov/clinvar",
                "code" : "3683"
              }
            ]
          }
        },
        {
          "code" : {
            "coding" : [
              {
                "system" : "http://loinc.org",
                "code" : "48013-7",
                "display" : "Genomic reference sequence ID"
              }
            ]
          },
          "valueCodeableConcept" : {
            "coding" : [
              {
                "system" : "http://www.ncbi.nlm.nih.gov/nuccore",
                "code" : "NC_000019.9"
              }
            ]
          }
        },
        {
          "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" : "69547-8",
                "display" : "Genomic ref allele [ID]"
              }
            ]
          },
          "valueString" : "C"
        },
        {
          "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" : "LA30102-0"
              }
            ]
          }
        },
        {
          "code" : {
            "coding" : [
              {
                "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes",
                "code" : "exact-start-end",
                "display" : "Variant exact start and end"
              }
            ]
          },
          "valueRange" : {
            "low" : {
              "value" : 11210928
            }
          }
        }
      ]
    }
  ],
  "status" : "final",
  "code" : {
    "coding" : [
      {
        "system" : "http://loinc.org",
        "code" : "81247-9",
        "display" : "Master HL7 genetic variant reporting panel"
      }
    ]
  },
  "result" : [
    {
      "reference" : "#1"
    },
    {
      "reference" : "#2"
    }
  ]
}