This page is part of the Genetic Reporting Implementation Guide (v1.0.0: STU 1) based on FHIR R4. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions

Example - Variant with ACMG Screening - XML Representation

(back to narrative)

Raw xml

<DiagnosticReport xmlns="http://hl7.org/fhir">
  <id value="AnnotationExample"/>
  <meta>
    <profile
             value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomics-report"/>
  </meta>
  <text>
    <status value="generated"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: AnnotationExample</p><p><b>meta</b>: </p><p><b>contained</b>: , </p><p><b>status</b>: final</p><p><b>code</b>: Master HL7 genetic variant reporting panel <span style="background: LightGoldenRodYellow">(Details : {LOINC code '81247-9' = 'Master HL7 genetic variant reporting panel', given as 'Master HL7 genetic variant reporting panel'})</span></p><p><b>result</b>: </p><ul><li>unknown resource contained</li><li>unknown resource contained</li></ul></div>
  </text>
  <contained>
    <Observation>
      <id value="1"/>
      <meta>
        <profile
                 value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/inherited-disease-pathogenicity"/>
      </meta>
      <status value="final"/>
      <category>
        <coding>
          <system
                  value="http://terminology.hl7.org/CodeSystem/observation-category"/>
          <code value="laboratory"/>
          <display value="LABORATORY"/>
        </coding>
      </category>
      <code>
        <coding>
          <system value="http://loinc.org"/>
          <code value="53037-8"/>
          <display value="Genetic variation clinical significance [Imp]"/>
        </coding>
      </code>
      <subject>
        <reference value="urn:uuid:13f34265-335c-4853-bc38-0815315edafa"/>
      </subject>
      <valueCodeableConcept>
        <coding>
          <system value="http://loinc.org"/>
          <code value="LA6668-3"/>
          <display value="Pathogenic"/>
        </coding>
      </valueCodeableConcept>
      <derivedFrom>
        <reference value="#2"/>
      </derivedFrom>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="81259-4"/>
            <display value="Associated phenotype"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://snomed.info/sct"/>
            <code value="398036000"/>
            <display value="Familial hypercholesterolemia (disorder)"/>
          </coding>
        </valueCodeableConcept>
      </component>
    </Observation>
  </contained>
  <contained>
    <Observation>
      <id value="2"/>
      <meta>
        <profile
                 value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
      </meta>
      <status value="final"/>
      <category>
        <coding>
          <system
                  value="http://terminology.hl7.org/CodeSystem/observation-category"/>
          <code value="laboratory"/>
          <display value="LABORATORY"/>
        </coding>
      </category>
      <code>
        <coding>
          <system value="http://loinc.org"/>
          <code value="69548-6"/>
          <display value="Genetic variant assessment"/>
        </coding>
      </code>
      <subject>
        <reference value="urn:uuid:13f34265-335c-4853-bc38-0815315edafa"/>
      </subject>
      <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="62374-4"/>
            <display value="Human reference sequence assembly version"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA14029-5"/>
            <display value="GRCh37"/>
          </coding>
        </valueCodeableConcept>
      </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="3683"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="48013-7"/>
            <display value="Genomic reference sequence ID"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://www.ncbi.nlm.nih.gov/nuccore"/>
            <code value="NC_000019.9"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="53034-5"/>
            <display value="Allelic state"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA6706-1"/>
            <display value="heterozygous"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="69547-8"/>
            <display value="Genomic ref allele [ID]"/>
          </coding>
        </code>
        <valueString value="C"/>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="69551-0"/>
            <display value="Genomic alt allele [ID]"/>
          </coding>
        </code>
        <valueString value="T"/>
      </component>
      <component>
        <code>
          <coding>
            <system value="http://loinc.org"/>
            <code value="92822-6"/>
            <display value="Genomic coord system"/>
          </coding>
        </code>
        <valueCodeableConcept>
          <coding>
            <system value="http://loinc.org"/>
            <code value="LA30102-0"/>
          </coding>
        </valueCodeableConcept>
      </component>
      <component>
        <code>
          <coding>
            <system
                    value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes"/>
            <code value="exact-start-end"/>
            <display value="Variant exact start and end"/>
          </coding>
        </code>
        <valueRange>
          <low>
            <value value="11210928"/>
          </low>
        </valueRange>
      </component>
    </Observation>
  </contained>
  <status value="final"/>
  <code>
    <coding>
      <system value="http://loinc.org"/>
      <code value="81247-9"/>
      <display value="Master HL7 genetic variant reporting panel"/>
    </coding>
  </code>
  <result>
    <reference value="#1"/>
  </result>
  <result>
    <reference value="#2"/>
  </result>
</DiagnosticReport>