{
  "resourceType" : "Observation",
  "id" : "Pgx-var-1021",
  "meta" : {
    "profile" : ["http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"]
  },
  "text" : {
    "status" : "generated",
    "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: Observation Pgx-var-1021</b></p><a name=\"Pgx-var-1021\"> </a><a name=\"hcPgx-var-1021\"> </a><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\"/><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-variant.html\">Variant</a></p></div><p><b>status</b>: Final</p><p><b>category</b>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>, <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}\">Genetics</span></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69548-6}\">Genetic variant assessment</span></p><p><b>subject</b>: <a href=\"Patient-CGPatientExample01.html\">Adam B. Everyman  Male, DoB: 1951-01-20 ( Medical Record Number: m123\u00a0(use:\u00a0usual,\u00a0))</a></p><p><b>effective</b>: 2019-04-01</p><p><b>performer</b>: <a href=\"Organization-ExampleOrg.html\">Organization some lab</a></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA9633-4}\">Present</span></p><p><b>note</b>: </p><blockquote><div><p>This variant was confirmed with SANGER sequencing</p>\n</div></blockquote><p><b>method</b>: <span title=\"Codes:{http://loinc.org LA26398-0}\">Sequencing</span></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48013-7}\">Genomic reference sequence [ID]</span></p><p><b>value</b>: <span title=\"Codes:{http://www.ncbi.nlm.nih.gov/refseq NC_000010.10}\">b37 Chr10</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 92822-6}\">Genomic coordinate system [Type]</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA30102-0}\">1-based character counting</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 81254-5}\">Genomic allele start-end</span></p><p><b>value</b>: 96741053-96741053</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69547-8}\">Genomic ref allele [ID]</span></p><p><b>value</b>: A</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 69551-0}\">Genomic alt allele [ID]</span></p><p><b>value</b>: A</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48002-0}\">Genomic source class [Type]</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA6683-2}\">Germline</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 53034-5}\">Allelic state</span></p><p><b>value</b>: <span title=\"Codes:{http://loinc.org LA6705-3}\">homozygous</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48018-6}\">Gene studied [ID]</span></p><p><b>value</b>: <span title=\"Codes:{http://www.genenames.org HGNC:2623}\">CYP2C9</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48019-4}\">DNA change type</span></p><p><b>value</b>: <span title=\"Codes:{http://www.sequenceontology.org SO:1000002}\">wild type</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 82121-5}\">Allelic read depth</span></p><p><b>value</b>: &gt;20</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs variant-confidence-status}\">Variant Confidence Status</span></p><p><b>value</b>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/variant-confidence-status-cs intermediate}\">Intermediate</span></p></blockquote></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"
    }]
  },
  "subject" : {
    "reference" : "Patient/CGPatientExample01"
  },
  "effectiveDateTime" : "2019-04-01",
  "performer" : [{
    "reference" : "Organization/ExampleOrg"
  }],
  "valueCodeableConcept" : {
    "coding" : [{
      "system" : "http://loinc.org",
      "code" : "LA9633-4",
      "display" : "Present"
    }]
  },
  "note" : [{
    "extension" : [{
      "url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/annotation-code",
      "valueCodeableConcept" : {
        "coding" : [{
          "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/coded-annotation-types-cs",
          "code" : "result-confirmation"
        }]
      }
    }],
    "text" : "This variant was confirmed with SANGER sequencing"
  }],
  "method" : {
    "coding" : [{
      "system" : "http://loinc.org",
      "code" : "LA26398-0",
      "display" : "Sequencing"
    }]
  },
  "component" : [{
    "code" : {
      "coding" : [{
        "system" : "http://loinc.org",
        "code" : "48013-7"
      }]
    },
    "valueCodeableConcept" : {
      "coding" : [{
        "system" : "http://www.ncbi.nlm.nih.gov/refseq",
        "code" : "NC_000010.10",
        "display" : "b37 Chr10"
      }]
    }
  },
  {
    "code" : {
      "coding" : [{
        "system" : "http://loinc.org",
        "code" : "92822-6"
      }]
    },
    "valueCodeableConcept" : {
      "coding" : [{
        "system" : "http://loinc.org",
        "code" : "LA30102-0",
        "display" : "1-based character counting"
      }]
    }
  },
  {
    "code" : {
      "coding" : [{
        "system" : "http://loinc.org",
        "code" : "81254-5"
      }]
    },
    "valueRange" : {
      "low" : {
        "value" : 96741053
      },
      "high" : {
        "value" : 96741053
      }
    }
  },
  {
    "code" : {
      "coding" : [{
        "system" : "http://loinc.org",
        "code" : "69547-8"
      }]
    },
    "valueString" : "A"
  },
  {
    "code" : {
      "coding" : [{
        "system" : "http://loinc.org",
        "code" : "69551-0"
      }]
    },
    "valueString" : "A"
  },
  {
    "code" : {
      "coding" : [{
        "system" : "http://loinc.org",
        "code" : "48002-0"
      }]
    },
    "valueCodeableConcept" : {
      "coding" : [{
        "system" : "http://loinc.org",
        "code" : "LA6683-2",
        "display" : "Germline"
      }]
    }
  },
  {
    "code" : {
      "coding" : [{
        "system" : "http://loinc.org",
        "code" : "53034-5"
      }]
    },
    "valueCodeableConcept" : {
      "coding" : [{
        "system" : "http://loinc.org",
        "code" : "LA6705-3",
        "display" : "homozygous"
      }]
    }
  },
  {
    "code" : {
      "coding" : [{
        "system" : "http://loinc.org",
        "code" : "48018-6"
      }]
    },
    "valueCodeableConcept" : {
      "coding" : [{
        "system" : "http://www.genenames.org",
        "code" : "HGNC:2623",
        "display" : "CYP2C9"
      }]
    }
  },
  {
    "code" : {
      "coding" : [{
        "system" : "http://loinc.org",
        "code" : "48019-4"
      }]
    },
    "valueCodeableConcept" : {
      "coding" : [{
        "system" : "http://www.sequenceontology.org",
        "code" : "SO:1000002",
        "display" : "wild type"
      }]
    }
  },
  {
    "code" : {
      "coding" : [{
        "system" : "http://loinc.org",
        "code" : "82121-5"
      }]
    },
    "valueQuantity" : {
      "value" : 20,
      "comparator" : ">"
    }
  },
  {
    "code" : {
      "coding" : [{
        "system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
        "code" : "variant-confidence-status"
      }]
    },
    "valueCodeableConcept" : {
      "coding" : [{
        "system" : "http://terminology.hl7.org/CodeSystem/variant-confidence-status-cs",
        "code" : "intermediate"
      }]
    }
  }]
}