Genomics Reporting Implementation Guide
3.0.0 - STU3 International flag

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.0 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

: molec-conseq2 - XML Representation

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<Observation xmlns="http://hl7.org/fhir">
  <id value="molec-conseq2"/>
  <meta>
    <profile
             value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence"/>
  </meta>
  <text>
    <status value="generated"/>
    <div xmlns="http://www.w3.org/1999/xhtml"><p class="res-header-id"><b>Generated Narrative: Observation molec-conseq2</b></p><a name="molec-conseq2"> </a><a name="hcmolec-conseq2"> </a><a name="molec-conseq2-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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs molecular-consequence}">Molecular Consequence</span></p><p><b>subject</b>: <a href="Patient-HG00403.html">Alanine B. Everyone  Unknown, DoB: 1951-01-20 ( Medical Record Number: m234 (use: usual, ))</a></p><p><b>effective</b>: 2023-06-01</p><p><b>performer</b>: <a href="Organization-ExampleLab.html">Organization Some lab</a></p><p><b>interpretation</b>: <span title="Codes:{http://example.org/pcingola.github.io/SnpEff/se_inputoutput/#impact-prediction LOW}">Low</span></p><p><b>derivedFrom</b>: <a href="Observation-variant-with-molec-consequences.html">Observation Genetic variant assessment</a></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48004-6}">coding HGVS</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NM_001366781.1:c.90T&gt;C}">NM_001366781.1:c.90T&gt;C</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_001366781.1}">NM_001366781.1</span></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 feature-consequence}">Feature Consequence</span></p><p><b>value</b>: <span title="Codes:{http://www.sequenceontology.org SO:0001819}">synonymous_variant</span></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://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
      <code value="molecular-consequence"/>
    </coding>
  </code>
  <subject>🔗 
    <reference value="Patient/HG00403"/>
  </subject>
  <effectiveDateTime value="2023-06-01"/>
  <performer>🔗 
    <reference value="Organization/ExampleLab"/>
  </performer>
  <interpretation>
    <coding>
      <system
              value="http://example.org/pcingola.github.io/SnpEff/se_inputoutput/#impact-prediction"/>
      <code value="LOW"/>
      <display value="Low"/>
    </coding>
  </interpretation>
  <derivedFrom>🔗 
    <reference value="Observation/variant-with-molec-consequences"/>
  </derivedFrom>
  <component>
    <code>
      <coding>
        <system value="http://loinc.org"/>
        <code value="48004-6"/>
      </coding>
      <text value="coding HGVS"/>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://varnomen.hgvs.org"/>
        <code value="NM_001366781.1:c.90T&gt;C"/>
        <display value="NM_001366781.1:c.90T&gt;C"/>
      </coding>
    </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_001366781.1"/>
        <display value="NM_001366781.1"/>
      </coding>
    </valueCodeableConcept>
  </component>
  <component>
    <code>
      <coding>
        <system
                value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
        <code value="feature-consequence"/>
      </coding>
    </code>
    <valueCodeableConcept>
      <coding>
        <system value="http://www.sequenceontology.org"/>
        <code value="SO:0001819"/>
        <display value="synonymous_variant"/>
      </coding>
    </valueCodeableConcept>
  </component>
</Observation>