Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot
Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot
Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.1-SNAPSHOT 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
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<id value="variant-with-molec-consequences"/>
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<div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative: Observation</b><a name="variant-with-molec-consequences"> </a><a name="hcvariant-with-molec-consequences"> </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 "variant-with-molec-consequences" </p><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-variant.html">Variant</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>: Genetic variant assessment <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#69548-6)</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>value</b>: Present <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#LA9633-4)</span></p><blockquote><p><b>component</b></p><p><b>code</b>: Genomic source class <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#48002-0)</span></p><p><b>value</b>: Germline <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#LA6683-2)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic reference sequence ID <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#48013-7)</span></p><p><b>value</b>: NC_000001.10 <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>#NC_000001.10)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Allelic state <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#53034-5)</span></p><p><b>value</b>: Heterozygous <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#LA6706-1)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Discrete genetic variant <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#81252-9)</span></p><p><b>value</b>: NC_000001.10:g.86852621A>G <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.3.0/CodeSystem-v3-hgvs.html">Human Genome Variation Society nomenclature</a>#NC_000001.10:g.86852621A>G)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Sample VAF <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#81258-6)</span></p><p><b>value</b>: 0.6 relative frequency of a particular allele in the specimen<span style="background: LightGoldenRodYellow"> (Details: UCUM code 1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic Ref allele [ID] <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#69547-8)</span></p><p><b>value</b>: A</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic Alt allele [ID] <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#69551-0)</span></p><p><b>value</b>: G</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic coord system <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#92822-6)</span></p><p><b>value</b>: 0-based interval counting <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#LA30100-4)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Variant exact start-end <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#81254-5)</span></p><p><b>value</b>: 86852620-?</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Population allele frequency <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#92821-8)</span></p><p><b>value</b>: 0.327084 1<span style="background: LightGoldenRodYellow"> (Details: UCUM code 1 = '1')</span></p></blockquote></div>
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<subject>🔗
<reference value="Patient/HG00403"/>
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<effectiveDateTime value="2023-06-01"/>
<performer>🔗
<reference value="Organization/ExampleLab"/>
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<system value="http://loinc.org"/>
<code value="48002-0"/>
<display value="Genomic source class"/>
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<code value="LA6683-2"/>
<display value="Germline"/>
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<coding>
<system value="http://loinc.org"/>
<code value="48013-7"/>
<display value="Genomic reference sequence ID"/>
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<system value="http://www.ncbi.nlm.nih.gov/refseq"/>
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<component>
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<coding>
<system value="http://loinc.org"/>
<code value="53034-5"/>
<display value="Allelic state"/>
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<valueCodeableConcept>
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<code value="LA6706-1"/>
<display value="Heterozygous"/>
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<coding>
<system value="http://loinc.org"/>
<code value="81252-9"/>
<display value="Discrete genetic variant"/>
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<system value="http://varnomen.hgvs.org"/>
<code value="NC_000001.10:g.86852621A>G"/>
<display value="NC_000001.10:g.86852621A>G"/>
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<component>
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<coding>
<system value="http://loinc.org"/>
<code value="81258-6"/>
<display value="Sample VAF"/>
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<valueQuantity>
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<coding>
<system value="http://loinc.org"/>
<code value="69551-0"/>
<display value="Genomic Alt allele [ID]"/>
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<valueString value="G"/>
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<system value="http://loinc.org"/>
<code value="92822-6"/>
<display value="Genomic coord system"/>
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<coding>
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<coding>
<system value="http://loinc.org"/>
<code value="81254-5"/>
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<text value="Variant exact start-end"/>
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<valueRange>
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<coding>
<system value="http://loinc.org"/>
<code value="92821-8"/>
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<text value="Population allele frequency"/>
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<valueQuantity>
<value value="0.327084"/>
<system value="http://unitsofmeasure.org"/>
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</Observation>
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.1-SNAPSHOT based on FHIR 4.0.1. Generated 2024-04-09
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