minimal Common Oncology Data Elements (mCODE) Implementation Guide
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This page is part of the HL7 FHIR Implementation Guide: minimal Common Oncology Data Elements (mCODE) Release 1 - US Realm | STU1 (v4.0.0-ballot: STU4 Ballot 1) based on FHIR (HL7® FHIR® Standard) R4. The current version which supersedes this version is 3.0.0. For a full list of available versions, see the Directory of published versions

: gx-genomic-variant-somatic-bap1-indel - XML Representation

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<Observation xmlns="http://hl7.org/fhir">
  <id value="gx-genomic-variant-somatic-bap1-indel"/>
  <meta>
    <profile
             value="http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomic-variant"/>
  </meta>
  <text>
    <status value="generated"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative: Observation</b><a name="gx-genomic-variant-somatic-bap1-indel"> </a><a name="hcgx-genomic-variant-somatic-bap1-indel"> </a></p><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">Resource Observation &quot;gx-genomic-variant-somatic-bap1-indel&quot; </p><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-mcode-genomic-variant.html">Genomic Variant Profile</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.3.0/CodeSystem-observation-category.html">Observation Category Codes</a>#laboratory)</span></p><p><b>code</b>: Genetic var assess <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#69548-6)</span></p><p><b>subject</b>: <a href="Patient-gx-cancer-patient-adam-anyperson.html">Patient/gx-cancer-patient-adam-anyperson</a> &quot; ANYPERSON&quot;</p><p><b>effective</b>: 2019-04-01</p><p><b>performer</b>: <a href="Practitioner-us-core-practitioner-owen-oncologist.html">Practitioner/us-core-practitioner-owen-oncologist</a> &quot; ONCOLOGIST&quot;</p><p><b>value</b>: Present <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#LA9633-4)</span></p><p><b>method</b>: Sequencing <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#LA26398-0)</span></p><blockquote><p><b>component</b></p><p><b>code</b>: Gene studied ID <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#48018-6)</span></p><p><b>value</b>: BAP1 <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.3.0/CodeSystem-v3-hgnc.html">HUGO Gene Nomenclature Committee Genes</a>#HGNC:950; gene#3815)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Transcript ref sequence ID <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#51958-7)</span></p><p><b>value</b>: NM_004656.4 <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.3.0/CodeSystem-v3-refSeq.html">Gene Reference Sequence Collection</a>#NM_004656)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: DNA change <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#48004-6)</span></p><p><b>value</b>: NM_004656.4:c.1768C&gt;T <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.3.0/CodeSystem-v3-hgvs.html">Human Genome Variation Society nomenclature</a>#NM_004656.4:c.1768C&gt;T)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Amino acid change <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#48005-3)</span></p><p><b>value</b>: NP_004647.1:p.(Gln590Ter) <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.3.0/CodeSystem-v3-hgvs.html">Human Genome Variation Society nomenclature</a>#NP_004647.1:p.(Gln590Ter))</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic source class <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#48002-0)</span></p><p><b>value</b>: Somatic <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#LA6684-0)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Sample VAF <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#81258-6)</span></p><p><b>value</b>: 57.4 %<span style="background: LightGoldenRodYellow"> (Details: UCUM code % = '%')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Molecular Consequence <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://hl7.org/fhir/uv/genomics-reporting/STU2/CodeSystem-tbd-codes-cs.html">To Be Determined Codes</a>#molecular-consequence)</span></p><p><b>value</b>: stop_gained <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (#SO:0001587)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Human ref seq assembly+build <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#62374-4)</span></p><p><b>value</b>: GRCh37 <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#LA14029-5)</span></p></blockquote></div>
  </text>
  <status value="final"/>
  <category>
    <coding>
      <system
              value="http://terminology.hl7.org/CodeSystem/observation-category"/>
      <code value="laboratory"/>
    </coding>
  </category>
  <code>
    <coding>
      <system value="http://loinc.org"/>
      <code value="69548-6"/>
    </coding>
  </code>
  <subject>🔗 
    <reference value="Patient/gx-cancer-patient-adam-anyperson"/>
  </subject>
  <effectiveDateTime value="2019-04-01"/>
  <performer>🔗 
    <reference value="Practitioner/us-core-practitioner-owen-oncologist"/>
  </performer>
  <valueCodeableConcept>
    <coding>
      <system value="http://loinc.org"/>
      <code value="LA9633-4"/>
      <display value="Present"/>
    </coding>
  </valueCodeableConcept>
  <method>
    <coding>
      <system value="http://loinc.org"/>
      <code value="LA26398-0"/>
      <display value="Sequencing"/>
    </coding>
  </method>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="48018-6"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://www.genenames.org"/>
        <code value="HGNC:950"/>
        <display value="BAP1"/>
      </coding>
      <coding>
        <system value="https://www.ncbi.nlm.nih.gov/gene"/>
        <code value="3815"/>
        <display value="BAP1"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="51958-7"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://www.ncbi.nlm.nih.gov/refseq"/>
        <code value="NM_004656"/>
        <display value="NM_004656.4"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="48004-6"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://varnomen.hgvs.org"/>
        <code value="NM_004656.4:c.1768C&gt;T"/>
        <display value="NM_004656.4:c.1768C&gt;T"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="48005-3"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://varnomen.hgvs.org"/>
        <code value="NP_004647.1:p.(Gln590Ter)"/>
        <display value="NP_004647.1:p.(Gln590Ter)"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="48002-0"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://loinc.org"/>
        <code value="LA6684-0"/>
        <display value="Somatic"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="81258-6"/>
      </coding>
    </code>
    <valueQuantity>
      <value value="57.4"/>
      <unit value="%"/>
      <system value="http://unitsofmeasure.org"/>
      <code value="%"/>
    </valueQuantity>
  </component>
  <component>
    <code>
      <coding>
        <system
                value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
        <code value="molecular-consequence"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://www.sequenceontology.org/"/>
        <code value="SO:0001587"/>
        <display value="stop_gained"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="62374-4"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://loinc.org"/>
        <code value="LA14029-5"/>
        <display value="GRCh37"/>
      </coding>
    </valueCodeableConcept>
  </component>
</Observation>