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

## : molec-conseq3 - XML Representation

Page standards status: Informative

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    <Observation xmlns="http://hl7.org/fhir">
      <id value="molec-conseq3"/>
      <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-conseq3</b></p><a name="molec-conseq3"> </a><a name="hcmolec-conseq3"> </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-molecular-consequence.html">Molecular Consequence</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://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 MOD}">Modifier</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_001395543.1:c.-171T&gt;C}">NM_001395543.1:c.-171T&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_001395543.1}">NM_001395543.1</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:0001623}">5_prime_UTR_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="MOD"/>
          <display value="Modifier"/>
        </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_001395543.1:c.-171T&gt;C"/>
            <display value="NM_001395543.1:c.-171T&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_001395543.1"/>
            <display value="NM_001395543.1"/>
          </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:0001623"/>
            <display value="5_prime_UTR_variant"/>
          </coding>
        </valueCodeableConcept>
      </component>
    </Observation>