Genomics Reporting Implementation Guide
3.0.0-ballot - Ballot International flag

This page is part of the Genetic Reporting Implementation Guide (v3.0.0-ballot: STU 3 Ballot 1) based on FHIR (HL7® FHIR® Standard) R4. The current version which supersedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions

: RepeatExpansion - XML Representation

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<Observation xmlns="http://hl7.org/fhir">
  <id value="RepeatExpansion"/>
  <meta>
    <profile
             value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
  </meta>
  <text>
    <status value="extensions"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative: Observation</b><a name="RepeatExpansion"> </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;RepeatExpansion&quot; </p><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>: 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>: Genetic variant assessment <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-ExamplePatient.html">Patient/ExamplePatient</a></p><p><b>effective</b>: 2023-06-01</p><p><b>performer</b>: <a href="Organization-ExampleLab.html">Organization/ExampleLab</a> &quot;Some lab&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><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>: PABPN1 <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:8565)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Cytogenetic (chromosome) location <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#48001-2)</span></p><p><b>value</b>: chr14 <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> ()</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_004643.4 <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_004643.4)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: DNA change (c.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_004643.3:c.3GGC[14] <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_004643.3:c.3GGC[14])</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic allele start-end <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#81254-5)</span></p><p><b>value</b>: 3-?</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Discrete genetic variant <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#81252-9)</span></p><p><b>value</b>: NM_004643.3(PABPN1):c.3GGC[11] (p.Ala11_Gly12insAlaAlaAlaAla) <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.3.0/CodeSystem-ClinVarV.html">ClinVar Variant ID</a>#503634)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 1</p><p><b>code</b>: Repeat Expansion Motif <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="CodeSystem-tbd-codes-cs.html">To Be Determined Codes</a>#repeat-motif)</span></p><p><b>value</b>: GGC</p></blockquote><blockquote><p><b>component</b></p><p><b>Repeat Motif Order</b>: 1</p><p><b>code</b>: Number of Repeat Expansions <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="CodeSystem-tbd-codes-cs.html">To Be Determined Codes</a>#repeat-number)</span></p><p><b>value</b>: 11</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://loinc.org"/>
      <code value="69548-6"/>
      <display value="Genetic variant assessment"/>
    </coding>
  </code>
  <subject>🔗 
    <reference value="Patient/ExamplePatient"/>
  </subject>
  <effectiveDateTime value="2023-06-01"/>
  <performer>🔗 
    <reference value="Organization/ExampleLab"/>
  </performer>
  <valueCodeableConcept>
    <coding>
      <system value="http://loinc.org"/>
      <code value="LA9633-4"/>
      <display value="Present"/>
    </coding>
  </valueCodeableConcept>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="48018-6"/>
        <display value="Gene studied ID"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://www.genenames.org"/>
        <code value="HGNC:8565"/>
        <display value="PABPN1"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="48001-2"/>
        <display value="Cytogenetic (chromosome) location"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <text value="chr14"/>
    </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_004643.4"/>
        <display value="NM_004643.4"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="48004-6"/>
        <display value="DNA change (c.HGVS)"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://varnomen.hgvs.org"/>
        <code value="NM_004643.3:c.3GGC[14]"/>
        <display value="NM_004643.3:c.3GGC[14]"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="81254-5"/>
        <display value="Genomic allele start-end"/>
      </coding>
    </code>
    <valueRange>
      <low>
        <value value="3"/>
      </low>
    </valueRange>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="81252-9"/>
        <display value="Discrete genetic variant"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://www.ncbi.nlm.nih.gov/clinvar"/>
        <code value="503634"/>
        <display
                 value="NM_004643.3(PABPN1):c.3GGC[11] (p.Ala11_Gly12insAlaAlaAlaAla)"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <extension
               url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order">
      <valuePositiveInt value="1"/>
    </extension>
    <code>
      <coding>
        <system
                value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
        <code value="repeat-motif"/>
        <display value="Repeat Expansion Motif"/>
      </coding>
    </code>
    <valueString value="GGC"/>
  </component>
  <component>
    <extension
               url="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order">
      <valuePositiveInt value="1"/>
    </extension>
    <code>
      <coding>
        <system
                value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
        <code value="repeat-number"/>
        <display value="Number of Repeat Expansions"/>
      </coding>
    </code>
    <valueQuantity>
      <value value="11"/>
    </valueQuantity>
  </component>
</Observation>