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

## : Pgx-var-1012 - XML Representation

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    <Observation xmlns="http://hl7.org/fhir">
      <id value="Pgx-var-1012"/>
      <meta>
        <profile
                 value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
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      <text>
        <status value="generated"/>
        <div xmlns="http://www.w3.org/1999/xhtml"><p class="res-header-id"><b>Generated Narrative: Observation Pgx-var-1012</b></p><a name="Pgx-var-1012"> </a><a name="hcPgx-var-1012"> </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-CGPatientExample01.html">Adam B. Everyman  Male, DoB: 1951-01-20 ( Medical Record Number: m123 (use: usual, ))</a></p><p><b>effective</b>: 2019-04-01</p><p><b>performer</b>: <a href="Organization-ExampleOrg.html">Organization some lab</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 48013-7}">Genomic reference sequence [ID]</span></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/refseq NC_000010.10}">b37 Chr10</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 92822-6}">Genomic coordinate system [Type]</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA30102-0}">1-based character counting</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>: 96522463-96522463</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>: A</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>: A</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 LA6683-2}">Germline</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 53034-5}">Allelic state</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA6705-3}">homozygous</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:2621}">CYP2C19</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:0002073}">wild type</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>: &gt;20</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 variant-confidence-status}">Variant Confidence Status</span></p><p><b>value</b>: <span title="Codes:{http://terminology.hl7.org/CodeSystem/variant-confidence-status-cs high}">High</span></p></blockquote></div>
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          <code value="laboratory"/>
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      <category>
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          <system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
          <code value="GE"/>
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      </category>
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        <coding>
          <system value="http://loinc.org"/>
          <code value="69548-6"/>
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      </code>
      <subject>🔗
        <reference value="Patient/CGPatientExample01"/>
      </subject>
      <effectiveDateTime value="2019-04-01"/>
      <performer>🔗
        <reference value="Organization/ExampleOrg"/>
      </performer>
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          <system value="http://loinc.org"/>
          <code value="LA9633-4"/>
          <display value="Present"/>
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        <coding>
          <system value="http://loinc.org"/>
          <code value="LA26398-0"/>
          <display value="Sequencing"/>
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            <system value="http://loinc.org"/>
            <code value="48013-7"/>
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            <system value="http://www.ncbi.nlm.nih.gov/refseq"/>
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            <display value="b37 Chr10"/>
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        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="92822-6"/>
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          <coding>
            <system value="http://loinc.org"/>
            <code value="LA30102-0"/>
            <display value="1-based character counting"/>
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          <coding>
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          <low>
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          <coding>
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          <coding>
            <system value="http://loinc.org"/>
            <code value="48002-0"/>
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        <valueCodeableConcept>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA6683-2"/>
            <display value="Germline"/>
          </coding>
        </valueCodeableConcept>
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      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="53034-5"/>
          </coding>
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        <valueCodeableConcept>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA6705-3"/>
            <display value="homozygous"/>
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          <coding>
            <system value="http://loinc.org"/>
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        <valueCodeableConcept>
          <coding>
            <system value="http://www.genenames.org"/>
            <code value="HGNC:2621"/>
            <display value="CYP2C19"/>
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            <system value="http://loinc.org"/>
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        <valueCodeableConcept>
          <coding>
            <system value="http://www.sequenceontology.org"/>
            <code value="SO:0002073"/>
            <display value="wild type"/>
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        <code>
          <coding>
            <system value="http://loinc.org"/>
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        <valueQuantity>
          <value value="20"/>
          <comparator value="&gt;"/>
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      <component>
        <code>
          <coding>
            <system
                    value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
            <code value="variant-confidence-status"/>
          </coding>
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        <valueCodeableConcept>
          <coding>
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                    value="http://terminology.hl7.org/CodeSystem/variant-confidence-status-cs"/>
            <code value="high"/>
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