Genomics Reporting Implementation Guide
3.0.0 - STU3
Genomics Reporting Implementation Guide
3.0.0 - STU3
This page is part of the Genetic Reporting Implementation Guide (v3.0.0: STU3) based on FHIR (HL7® FHIR® Standard) R4. This is the current published version. For a full list of available versions, see the Directory of published versions
<Observation xmlns="http://hl7.org/fhir">
<id value="variant-with-molec-consequences"/>
<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 variant-with-molec-consequences</b></p><a name="variant-with-molec-consequences"> </a><a name="hcvariant-with-molec-consequences"> </a><a name="variant-with-molec-consequences-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://loinc.org 69548-6}">Genetic variant assessment</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>value</b>: <span title="Codes:{http://loinc.org LA9633-4}">Present</span></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48002-0}">Genomic source class</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 48013-7}">Genomic reference sequence ID</span></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/refseq NC_000001.10}">NC_000001.10</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 LA6706-1}">Heterozygous</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81252-9}">Discrete genetic variant</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NC_000001.10:g.86852621A>G}">NC_000001.10:g.86852621A>G</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81258-6}">Sample VAF</span></p><p><b>value</b>: 0.6 relative frequency of a particular allele in the specimen<span style="background: LightGoldenRodYellow"> (Details: UCUM code1 = '1')</span></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>: G</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 92822-6}">Genomic coord system</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA30100-4}">0-based interval counting</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 81254-5}">Variant exact start-end</span></p><p><b>value</b>: 86852620-?</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 92821-8}">Population allele frequency</span></p><p><b>value</b>: 0.327084 1<span style="background: LightGoldenRodYellow"> (Details: UCUM code1 = '1')</span></p></blockquote></div>
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<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
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</category>
<category>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
<code value="GE"/>
</coding>
</category>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69548-6"/>
<display value="Genetic variant assessment"/>
</coding>
</code>
<subject>🔗
<reference value="Patient/HG00403"/>
</subject>
<effectiveDateTime value="2023-06-01"/>
<performer>🔗
<reference value="Organization/ExampleLab"/>
</performer>
<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="48002-0"/>
<display value="Genomic source class"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA6683-2"/>
<display value="Germline"/>
</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/refseq"/>
<code value="NC_000001.10"/>
</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="81252-9"/>
<display value="Discrete genetic variant"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://varnomen.hgvs.org"/>
<code value="NC_000001.10:g.86852621A>G"/>
<display value="NC_000001.10:g.86852621A>G"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81258-6"/>
<display value="Sample VAF"/>
</coding>
</code>
<valueQuantity>
<value value="0.6"/>
<unit
value="relative frequency of a particular allele in the specimen"/>
<system value="http://unitsofmeasure.org"/>
<code value="1"/>
</valueQuantity>
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<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69547-8"/>
<display value="Genomic Ref allele [ID]"/>
</coding>
</code>
<valueString value="A"/>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69551-0"/>
<display value="Genomic Alt allele [ID]"/>
</coding>
</code>
<valueString value="G"/>
</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="LA30100-4"/>
<display value="0-based interval counting"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81254-5"/>
</coding>
<text value="Variant exact start-end"/>
</code>
<valueRange>
<low>
<value value="86852620"/>
</low>
</valueRange>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="92821-8"/>
</coding>
<text value="Population allele frequency"/>
</code>
<valueQuantity>
<value value="0.327084"/>
<system value="http://unitsofmeasure.org"/>
<code value="1"/>
</valueQuantity>
</component>
</Observation>
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.0 based on FHIR 4.0.1. Generated 2024-12-12
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