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
<Observation xmlns="http://hl7.org/fhir">
<id value="ATR-insertion-var"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
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<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative: Observation</b><a name="ATR-insertion-var"> </a><a name="hcATR-insertion-var"> </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 "ATR-insertion-var" </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 var assess <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-somaticPatient.html">Patient/somaticPatient</a> " HAMSBURG"</p><p><b>effective</b>: 2023-02-01</p><p><b>performer</b>: <a href="Practitioner-pathologistPractitioner.html">Practitioner/pathologistPractitioner</a> " DOLIN"</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><p><b>method</b>: Sequencing <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#LA26398-0)</span></p><blockquote><p><b>component</b></p><p><b>code</b>: Transcript ref 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_001184.4 <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_001184.4)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Allelic read depth <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#82121-5)</span></p><p><b>value</b>: 131 reads per base pair<span style="background: LightGoldenRodYellow"> (Details: UCUM code 1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: DNA Change Type <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#48019-4)</span></p><p><b>value</b>: insertion <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (sequenceontology.org#SO:0000667)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: DNA change <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#48004-6)</span></p><p><b>value</b>: NM_001184.4:c.2878_2879insAGTAA <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>#NM_001184.4:c.2878_2879insAGTAA)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Gene studied ID <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#48018-6)</span></p><p><b>value</b>: ATR <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.3.0/CodeSystem-v3-hgnc.html">HUGO Gene Nomenclature Committee Genes</a>#HGNC:882)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Alt allele <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>: TTACT</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Chromosome Bld/T <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#48000-4)</span></p><p><b>value</b>: Chromosome 3 <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#LA21256-5)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Gen allele loc ID <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>: 142269071-142269071</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_000003.11 <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_000003.11)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Struct var HGVS name <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#81290-9)</span></p><p><b>value</b>: NC_000003.11:g.142269071_142269072insTTACT <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_000003.11:g.142269071_142269072insTTACT)</span></p></blockquote><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>: Somatic <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#LA6684-0)</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>: 0.075 decimal</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Conclusion Text <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="CodeSystem-tbd-codes-cs.html">To Be Determined Codes</a>#conclusion-string)</span></p><p><b>value</b>: Gene: ATR; Exon: 14; Nucleotide: NM_001184.4:c.2878_2879insAGTAA; Genomic Location: NC_000003.11:g.142269071_142269072insTTACT; Amino acid: NP_001175.2:p.R960fs*2; Function: loss; Assessment: Likely Pathogenic; Classification: Tier 2C; Allele Fraction: 5.34% (of 131 reads); Variation: Insertion; Interpretation: The protein encoded by this gene is a serine/threonine kinase and DNA damage sensor, activating cell cycle checkpoint signaling upon DNA stress. The encoded protein can phosphorylate and activate several proteins involved ... more</p></blockquote></div>
</text>
<status value="final"/>
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value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
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<category>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
<code value="GE"/>
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<code>
<coding>
<system value="http://loinc.org"/>
<code value="69548-6"/>
</coding>
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<subject>🔗
<reference value="Patient/somaticPatient"/>
</subject>
<effectiveDateTime value="2023-02-01"/>
<performer>🔗
<reference value="Practitioner/pathologistPractitioner"/>
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<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA9633-4"/>
<display value="Present"/>
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<method>
<coding>
<system value="http://loinc.org"/>
<code value="LA26398-0"/>
<display value="Sequencing"/>
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<coding>
<system value="http://loinc.org"/>
<code value="51958-7"/>
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<valueCodeableConcept>
<coding>
<system value="http://www.ncbi.nlm.nih.gov/refseq"/>
<code value="NM_001184.4"/>
</coding>
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<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="82121-5"/>
</coding>
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<valueQuantity>
<value value="131"/>
<unit value="reads per base pair"/>
<system value="http://unitsofmeasure.org"/>
<code value="1"/>
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<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48019-4"/>
</coding>
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<valueCodeableConcept>
<coding>
<system value="http://sequenceontology.org"/>
<code value="SO:0000667"/>
<display value="insertion"/>
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<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48004-6"/>
</coding>
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<valueCodeableConcept>
<coding>
<system value="http://varnomen.hgvs.org"/>
<code value="NM_001184.4:c.2878_2879insAGTAA"/>
</coding>
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<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48018-6"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.genenames.org"/>
<code value="HGNC:882"/>
<display value="ATR"/>
</coding>
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<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69551-0"/>
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<valueString value="TTACT"/>
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<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48000-4"/>
</coding>
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<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA21256-5"/>
<display value="Chromosome 3"/>
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<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81254-5"/>
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<valueRange>
<low>
<value value="142269071"/>
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<high>
<value value="142269071"/>
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<component>
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<coding>
<system value="http://loinc.org"/>
<code value="48013-7"/>
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<valueCodeableConcept>
<coding>
<system value="http://www.ncbi.nlm.nih.gov/refseq"/>
<code value="NC_000003.11"/>
</coding>
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<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81290-9"/>
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<valueCodeableConcept>
<coding>
<system value="http://varnomen.hgvs.org"/>
<code value="NC_000003.11:g.142269071_142269072insTTACT"/>
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<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48002-0"/>
</coding>
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<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA6684-0"/>
<display value="Somatic"/>
</coding>
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</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81258-6"/>
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<valueQuantity>
<value value="0.075"/>
<unit value="decimal"/>
<system value="http://unitsofmeasure.org"/>
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<component>
<code>
<coding>
<system
value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
<code value="conclusion-string"/>
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<valueString
value="Gene: ATR; Exon: 14; Nucleotide: NM_001184.4:c.2878_2879insAGTAA; Genomic Location: NC_000003.11:g.142269071_142269072insTTACT; Amino acid: NP_001175.2:p.R960fs*2; Function: loss; Assessment: Likely Pathogenic; Classification: Tier 2C; Allele Fraction: 5.34% (of 131 reads); Variation: Insertion; Interpretation: The protein encoded by this gene is a serine/threonine kinase and DNA damage sensor, activating cell cycle checkpoint signaling upon DNA stress. The encoded protein can phosphorylate and activate several proteins involved ... more"/>
</component>
</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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