Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot International flag

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.1-SNAPSHOT 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

: molec-conseq2 - JSON Representation

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{
  "resourceType" : "Observation",
  "id" : "molec-conseq2",
  "meta" : {
    "profile" : [
      🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence"
    ]
  },
  "text" : {
    "status" : "generated",
    "div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: Observation molec-conseq2</b></p><a name=\"molec-conseq2\"> </a><a name=\"hcmolec-conseq2\"> </a><a name=\"hcmolec-conseq2-en-US\"> </a><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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs molecular-consequence}\">Molecular Consequence</span></p><p><b>subject</b>: <a href=\"Patient-HG00403.html\">Alanine B. Everyone  Unknown, DoB: 1951-01-20 ( Medical Record Number: m234\u00a0(use:\u00a0usual,\u00a0))</a></p><p><b>effective</b>: 2023-06-01</p><p><b>performer</b>: <a href=\"Organization-ExampleLab.html\">Organization Some lab</a></p><p><b>interpretation</b>: <span title=\"Codes:{http://example.org/pcingola.github.io/SnpEff/se_inputoutput/#impact-prediction LOW}\">Low</span></p><p><b>derivedFrom</b>: <a href=\"Observation-variant-with-molec-consequences.html\">Observation Genetic variant assessment</a></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 48004-6}\">coding HGVS</span></p><p><b>value</b>: <span title=\"Codes:{http://varnomen.hgvs.org NM_001366781.1:c.90T&gt;C}\">NM_001366781.1:c.90T&gt;C</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 51958-7}\">Transcript reference sequence [ID]</span></p><p><b>value</b>: <span title=\"Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_001366781.1}\">NM_001366781.1</span></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 feature-consequence}\">Feature Consequence</span></p><p><b>value</b>: <span title=\"Codes:{http://sequenceontology.org SO:0001819}\">synonymous_variant</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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
        "code" : "molecular-consequence"
      }
    ]
  },
  "subject" : {
    🔗 "reference" : "Patient/HG00403"
  },
  "effectiveDateTime" : "2023-06-01",
  "performer" : [
    {
      🔗 "reference" : "Organization/ExampleLab"
    }
  ],
  "interpretation" : [
    {
      "coding" : [
        {
          "system" : "http://example.org/pcingola.github.io/SnpEff/se_inputoutput/#impact-prediction",
          "code" : "LOW",
          "display" : "Low"
        }
      ]
    }
  ],
  "derivedFrom" : [
    {
      🔗 "reference" : "Observation/variant-with-molec-consequences"
    }
  ],
  "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://sequenceontology.org",
            "code" : "SO:0001819",
            "display" : "synonymous_variant"
          }
        ]
      }
    }
  ]
}