Genomics Reporting Implementation Guide
3.0.0 - STU3 International flag

This page is part of the Genetic Reporting Implementation Guide (v3.0.0: STU3) based on FHIR (HL7® FHIR® Standard) R4. This is the current published version in its permanent home (it will always be available at this URL). For a full list of available versions, see the Directory of published versions

: NOTCH1-uncertain-var - XML Representation

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<Observation xmlns="http://hl7.org/fhir">
  <id value="NOTCH1-uncertain-var"/>
  <meta>
    <profile
             value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
  </meta>
  <text>
    <status value="generated"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><p class="res-header-id"><b>Generated Narrative: Observation NOTCH1-uncertain-var</b></p><a name="NOTCH1-uncertain-var"> </a><a name="hcNOTCH1-uncertain-var"> </a><a name="NOTCH1-uncertain-var-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://loinc.org 69548-6}">Genetic variant assessment</span></p><p><b>subject</b>: <a href="Patient-somaticPatient.html">Substance Junior Hamsburg (official) Male, DoB: 1987-09-01 ( Medical record number: 1234567 (use: temp, period: 2021-01-01 --&gt; (ongoing)))</a></p><p><b>effective</b>: 2023-02-01</p><p><b>performer</b>: <a href="Practitioner-pathologistPractitioner.html">Practitioner Test Dolin </a></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA9633-4}">Present</span></p><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 48005-3}">Amino acid change (pHGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NP_060087.3:p.A1931T}">NP_060087.3:p.A1931T</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_017617.5}">NM_017617.5</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>: 221 reads per base pair<span style="background: LightGoldenRodYellow"> (Details: UCUM  code1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48004-6}">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NM_017617.5:c.5791G&gt;A}">NM_017617.5:c.5791G&gt;A</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:7881}">NOTCH1</span></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>: T</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48000-4}">Chromosome [Identifier] in Blood or Tissue by Molecular genetics method</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA21262-3}">Chromosome 9</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>: 139395147-139395147</p></blockquote><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_000009.11}">NC_000009.11</span></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>: C</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81290-9}">Genomic DNA change (gHGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NC_000009.11:g.139395147C&gt;T}">NC_000009.11:g.139395147C&gt;T</span></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 LA6684-0}">Somatic</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81258-6}">Sample variant allelic frequency [NFr]</span></p><p><b>value</b>: 0.15 decimal</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"/>
    </coding>
  </code>
  <subject>🔗 
    <reference value="Patient/somaticPatient"/>
  </subject>
  <effectiveDateTime value="2023-02-01"/>
  <performer>🔗 
    <reference value="Practitioner/pathologistPractitioner"/>
  </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>
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        <code value="48005-3"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
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        <code value="NP_060087.3:p.A1931T"/>
      </coding>
    </valueCodeableConcept>
  </component>
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    <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_017617.5"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="82121-5"/>
      </coding>
    </code>
    <valueQuantity>
      <value value="221"/>
      <unit value="reads per base pair"/>
      <system value="http://unitsofmeasure.org"/>
      <code value="1"/>
    </valueQuantity>
  </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_017617.5:c.5791G&gt;A"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <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:7881"/>
        <display value="NOTCH1"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="69551-0"/>
      </coding>
    </code>
    <valueString value="T"/>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="48000-4"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://loinc.org"/>
        <code value="LA21262-3"/>
        <display value="Chromosome 9"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="81254-5"/>
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    </code>
    <valueRange>
      <low>
        <value value="139395147"/>
      </low>
      <high>
        <value value="139395147"/>
      </high>
    </valueRange>
  </component>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="48013-7"/>
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    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://www.ncbi.nlm.nih.gov/refseq"/>
        <code value="NC_000009.11"/>
      </coding>
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  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="69547-8"/>
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    <valueString value="C"/>
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  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="81290-9"/>
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    <valueCodeableConcept>
      <coding>
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    <code>
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      <coding>
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        <code value="LA6684-0"/>
        <display value="Somatic"/>
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      <coding>
        <system value="http://loinc.org"/>
        <code value="81258-6"/>
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    <valueQuantity>
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      <unit value="decimal"/>
      <system value="http://unitsofmeasure.org"/>
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</Observation>