This page is part of the Genetic Reporting Implementation Guide (v3.0.0-ballot: STU 3 Ballot 1) based on FHIR (HL7® FHIR® Standard) R4. The current version which supersedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions
: molec-conseq1 - XML Representation
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<Observation xmlns="http://hl7.org/fhir">
<id value="molec-conseq1"/>
<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><b>Generated Narrative: Observation</b><a name="molec-conseq1"> </a></p><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">Resource Observation "molec-conseq1" </p><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>: Laboratory <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.3.0/CodeSystem-observation-category.html">Observation Category Codes</a>#laboratory)</span>, Genetics <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.3.0/CodeSystem-v2-0074.html">diagnosticServiceSectionId</a>#GE)</span></p><p><b>code</b>: Molecular Consequence <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="CodeSystem-tbd-codes-cs.html">To Be Determined Codes</a>#molecular-consequence)</span></p><p><b>subject</b>: <a href="Patient-HG00403.html">Patient/HG00403</a> " EVERYONE"</p><p><b>effective</b>: 2023-06-01</p><p><b>performer</b>: <a href="Organization-ExampleLab.html">Organization/ExampleLab</a> "Some lab"</p><p><b>interpretation</b>: High <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (#impact-prediction#HIGH)</span></p><p><b>derivedFrom</b>: <a href="Observation-variant-with-molec-consequences.html">Observation/variant-with-molec-consequences</a></p><blockquote><p><b>component</b></p><p><b>code</b>: Transcript reference sequence [ID] <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#51958-7)</span></p><p><b>value</b>: NM_001395525.1 <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.3.0/CodeSystem-v3-refSeq.html">Gene Reference Sequence Collection</a>#NM_001395525.1)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Feature Consequence <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="CodeSystem-tbd-codes-cs.html">To Be Determined Codes</a>#feature-consequence)</span></p><p><b>value</b>: splice_donor_variant <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (sequenceontology.org#SO:0001575; sequenceontology.org#SO:0001627 "intron_variant")</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Functional Effect <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="CodeSystem-tbd-codes-cs.html">To Be Determined Codes</a>#functional-effect)</span></p><p><b>value</b>: loss_of_function_variant <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (sequenceontology.org#SO_0002054)</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="HIGH"/>
<display value="High"/>
</coding>
</interpretation>
<derivedFrom>🔗
<reference value="Observation/variant-with-molec-consequences"/>
</derivedFrom>
<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_001395525.1"/>
<display value="NM_001395525.1"/>
</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://sequenceontology.org"/>
<code value="SO:0001575"/>
<display value="splice_donor_variant"/>
</coding>
<coding>
<system value="http://sequenceontology.org"/>
<code value="SO:0001627"/>
<display value="intron_variant"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system
value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
<code value="functional-effect"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://sequenceontology.org"/>
<code value="SO_0002054"/>
<display value="loss_of_function_variant"/>
</coding>
</valueCodeableConcept>
</component>
</Observation>
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