Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 4.0.0-cibuild 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

## : ATR-insertion-var - XML Representation

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    <Observation xmlns="http://hl7.org/fhir">
      <id value="ATR-insertion-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 ATR-insertion-var</b></p><a name="ATR-insertion-var"> </a><a name="hcATR-insertion-var"> </a><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"/><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>: <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 51958-7}">Transcript reference sequence [ID]</span></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_001184.4}">NM_001184.4</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>: 131 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 48019-4}">DNA change type</span></p><p><b>value</b>: <span title="Codes:{http://www.sequenceontology.org SO:0000667}">insertion</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_001184.4:c.2878_2879insAGTAA}">NM_001184.4:c.2878_2879insAGTAA</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:882}">ATR</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>: TTACT</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 LA21256-5}">Chromosome 3</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>: 142269071-142269071</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_000003.11}">NC_000003.11</span></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_000003.11:g.142269071_142269072insTTACT}">NC_000003.11:g.142269071_142269072insTTACT</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>: 0.075 decimal</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 conclusion-string}">Conclusion Text</span></p><p><b>value</b>: Gene: ATR; Exon: 14; Nucleotide: NM_001184.4:c.2878_2879insAGTAA; Genomic Location: NC_000003.11:g.142269071_142269072insTTACT; Amino acid: NP_001175.2:p.R960fs*2; Function: loss; Assessment: Likely Pathogenic; Classification: Tier 2C; Allele Fraction: 5.34% (of 131 reads); Variation: Insertion; Interpretation: The protein encoded by this gene is a serine/threonine kinase and DNA damage sensor, activating cell cycle checkpoint signaling upon DNA stress. The encoded protein can phosphorylate and activate several proteins involved ... more</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>
            <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_001184.4"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="82121-5"/>
          </coding>
        </code>
        <valueQuantity>
          <value value="131"/>
          <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="48019-4"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://www.sequenceontology.org"/>
            <code value="SO:0000667"/>
            <display value="insertion"/>
          </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_001184.4:c.2878_2879insAGTAA"/>
          </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:882"/>
            <display value="ATR"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="69551-0"/>
          </coding>
        </code>
        <valueString value="TTACT"/>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="48000-4"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA21256-5"/>
            <display value="Chromosome 3"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="81254-5"/>
          </coding>
        </code>
        <valueRange>
          <low>
            <value value="142269071"/>
          </low>
          <high>
            <value value="142269071"/>
          </high>
        </valueRange>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="48013-7"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://www.ncbi.nlm.nih.gov/refseq"/>
            <code value="NC_000003.11"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="81290-9"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://varnomen.hgvs.org"/>
            <code value="NC_000003.11:g.142269071_142269072insTTACT"/>
          </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="0.075"/>
          <unit value="decimal"/>
          <system value="http://unitsofmeasure.org"/>
        </valueQuantity>
      </component>
      <component>
        <code>
          <coding>
            <system
                    value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
            <code value="conclusion-string"/>
          </coding>
        </code>
        <valueString
                     value="Gene: ATR; Exon: 14; Nucleotide: NM_001184.4:c.2878_2879insAGTAA; Genomic Location: NC_000003.11:g.142269071_142269072insTTACT; Amino acid: NP_001175.2:p.R960fs*2; Function: loss; Assessment: Likely Pathogenic; Classification: Tier 2C; Allele Fraction: 5.34% (of 131 reads); Variation: Insertion; Interpretation: The protein encoded by this gene is a serine/threonine kinase and DNA damage sensor, activating cell cycle checkpoint signaling upon DNA stress. The encoded protein can phosphorylate and activate several proteins involved ... more"/>
      </component>
    </Observation>