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Narrative

Note: links and images are rebased to the (stated) source

Source1

{
  "resourceType": "Observation",
  "id": "ATR-insertion-molc",
  "meta": {
    "profile": [
      "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence"
    ]
  },
  "text": {
    "status": "generated",
    "div": "<!-- snip (see above) -->"
  },
  "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/CGPatientExample01"
  },
  "effectiveDateTime": "2023-02-01",
  "performer": [
    {
      "reference": "Practitioner/pathologistPractitioner"
    }
  ],
  "derivedFrom": [
    {
      "reference": "Observation/ATR-insertion-var"
    }
  ],
  "component": [
    {
      "code": {
        "coding": [
          {
            "system": "http://loinc.org",
            "code": "48004-6"
          }
        ],
        "text": "coding HGVS"
      },
      "valueCodeableConcept": {
        "coding": [
          {
            "system": "http://varnomen.hgvs.org",
            "code": "NM_001184.4:c.2878_2879insAGTAA",
            "display": "NM_001184.4:c.2878_2879insAGTAA"
          }
        ]
      }
    },
    {
      "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_001184.4",
            "display": "NM_001184.4"
          }
        ]
      }
    },
    {
      "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:0001589",
            "display": "frameshift_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"
          }
        ]
      }
    }
  ]
}