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

: STAG2-insertion-molc - XML Representation

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<Observation xmlns="http://hl7.org/fhir">
  <id value="STAG2-insertion-molc"/>
  <meta>
    <profile
             value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence"/>
  </meta>
  <text>
    <status value="generated"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative: Observation</b><a name="STAG2-insertion-molc"> </a><a name="hcSTAG2-insertion-molc"> </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;STAG2-insertion-molc&quot; </p><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-molecular-consequence.html">Molecular Consequence</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>, Genetics <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.3.0/CodeSystem-v2-0074.html">diagnosticServiceSectionId</a>#GE)</span></p><p><b>code</b>: Molecular Consequence <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="CodeSystem-tbd-codes-cs.html">To Be Determined Codes</a>#molecular-consequence)</span></p><p><b>subject</b>: <a href="Patient-CGPatientExample01.html">Patient/CGPatientExample01</a> &quot; EVERYMAN&quot;</p><p><b>effective</b>: 2023-02-01</p><p><b>performer</b>: <a href="Practitioner-pathologistPractitioner.html">Practitioner/pathologistPractitioner</a> &quot; DOLIN&quot;</p><p><b>derivedFrom</b>: <a href="Observation-STAG2-insertion-var.html">Observation/STAG2-insertion-var</a></p><blockquote><p><b>component</b></p><p><b>code</b>: coding HGVS <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_006603.5:c.3530_3531insGTGACTATTAATAT <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_006603.5:c.3530_3531insGTGACTATTAATAT)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Transcript reference 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_006603.5 <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_006603.5)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Feature Consequence <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="CodeSystem-tbd-codes-cs.html">To Be Determined Codes</a>#feature-consequence)</span></p><p><b>value</b>: frameshift_variant <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (sequenceontology.org#SO:0001589)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Amino acid change (pHGVS) <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_006594.3:p.S1178* <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_006594.3:p.S1178*)</span></p></blockquote></div>
  </text>
  <status value="final"/>
  <category>
    <coding>
      <system
              value="http://terminology.hl7.org/CodeSystem/observation-category"/>
      <code value="laboratory"/>
    </coding>
  </category>
  <category>
    <coding>
      <system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
      <code value="GE"/>
    </coding>
  </category>
  <code>
    <coding>
      <system
              value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
      <code value="molecular-consequence"/>
    </coding>
  </code>
  <subject>🔗 
    <reference value="Patient/CGPatientExample01"/>
  </subject>
  <effectiveDateTime value="2023-02-01"/>
  <performer>🔗 
    <reference value="Practitioner/pathologistPractitioner"/>
  </performer>
  <derivedFrom>🔗 
    <reference value="Observation/STAG2-insertion-var"/>
  </derivedFrom>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="48004-6"/>
      </coding>
      <text value="coding HGVS"/>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://varnomen.hgvs.org"/>
        <code value="NM_006603.5:c.3530_3531insGTGACTATTAATAT"/>
        <display value="NM_006603.5:c.3530_3531insGTGACTATTAATAT"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="51958-7"/>
        <display value="Transcript reference sequence [ID]"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://www.ncbi.nlm.nih.gov/refseq"/>
        <code value="NM_006603.5"/>
        <display value="NM_006603.5"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system
                value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
        <code value="feature-consequence"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://sequenceontology.org"/>
        <code value="SO:0001589"/>
        <display value="frameshift_variant"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="48005-3"/>
        <display value="Amino acid change (pHGVS)"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://varnomen.hgvs.org"/>
        <code value="NP_006594.3:p.S1178*"/>
        <display value="NP_006594.3:p.S1178*"/>
      </coding>
    </valueCodeableConcept>
  </component>
</Observation>