GenomeX Data Exchange FHIR IG
0.2.0 - draft
GenomeX Data Exchange FHIR IG, published by MITRE. This guide is not an authorized publication; it is the continuous build for version 0.2.0 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/CodeX-HL7-FHIR-Accelerator/GenomeX-DataExchange/ and changes regularly. See the Directory of published versions
<Observation xmlns="http://hl7.org/fhir">
<id value="PrenatalVariant1SNPAlpha1ADPatientMale"/>
<meta>
<versionId value="1"/>
<lastUpdated value="2024-09-25T00:01:34.798+00:00"/>
<source value="#hrQE3dHjuHuJ5zkf"/>
<profile
value="http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><p class="res-header-id"><b>Generated Narrative: Observation PrenatalVariant1SNPAlpha1ADPatientMale</b></p><a name="PrenatalVariant1SNPAlpha1ADPatientMale"> </a><a name="hcPrenatalVariant1SNPAlpha1ADPatientMale"> </a><a name="PrenatalVariant1SNPAlpha1ADPatientMale-en-US"> </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">version: 1; Last updated: 2024-09-25 00:01:34+0000; </p><p style="margin-bottom: 0px">Information Source: #hrQE3dHjuHuJ5zkf</p><p style="margin-bottom: 0px">Profile: <a href="http://hl7.org/fhir/uv/genomics-reporting/2024Jan/StructureDefinition-variant.html">Variant</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://loinc.org 69548-6}">Genetic variant assessment</span></p><p><b>subject</b>: <a href="Patient-PatientMale.html">Higado Sobreviviente (official) Male, DoB: 1996-05-13 ( Patient ID: fec6172efdca41b4a13341e75cb62e0f (use: official, ))</a></p><p><b>effective</b>: 2024-07-09</p><p><b>performer</b>: <a href="Practitioner-PractitionerLabDirector.html">Practitioner PractitionerJane Smith </a></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA9633-4}">Present</span></p><p><b>method</b>: <span title="Codes:{http://loinc.org LA26398-0}">Sequencing</span></p><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 53037-8}">Genetic variation clinical significance [Imp]</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA6668-3}">Pathogenic</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48002-0}">Genomic source class [Type]</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 83005-9}">Variant category</span></p><p><b>value</b>: <span title="Codes:{http://loinc.org LA26801-3}">Simple variant</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 48004-6}">DNA change (c.HGVS)</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org NM_000295.4:c.1096G>A}">NM_000295.4(SERPINA1):c.1096G>A(E366K, aka Z allele) heterozygote</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://varnomen.hgvs.org NM_000295.4}">NM_000295.4</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48019-4}">DNA change type</span></p><p><b>value</b>: <span title="Codes:{http://varnomen.hgvs.org LA6690-7}">Substitution</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48013-7}">Genomic reference sequence identifier</span></p><p><b>value</b>: <span title="Codes:{http://www.ncbi.nlm.nih.gov/refseq NM_000295.4}">NM_000295.4</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: <span title="Codes:{http://loinc.org 48018-6}">Gene studied [ID]</span></p><p><b>value</b>: <span title="Codes:{http://www.genenames.org HGNC:8941}">SERPINA1</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://loinc.org"/>
<code value="69548-6"/>
<display value="Genetic variant assessment"/>
</coding>
</code>
<subject>🔗
<reference value="Patient/PatientMale"/>
</subject>
<effectiveDateTime value="2024-07-09"/>
<performer>🔗
<reference value="Practitioner/PractitionerLabDirector"/>
</performer>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA9633-4"/>
<display value="Present"/>
</coding>
</valueCodeableConcept>
<method>
<coding>
<system value="http://loinc.org"/>
<code value="LA26398-0"/>
<display value="Sequencing"/>
</coding>
</method>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="53037-8"/>
<display value="Genetic variation clinical significance [Imp]"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA6668-3"/>
<display value="Pathogenic"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48002-0"/>
<display value="Genomic source class [Type]"/>
</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="83005-9"/>
<display value="Variant category"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA26801-3"/>
<display value="Simple variant"/>
</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="48004-6"/>
<display value="DNA change (c.HGVS)"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://varnomen.hgvs.org"/>
<code value="NM_000295.4:c.1096G>A"/>
<display
value="NM_000295.4(SERPINA1):c.1096G>A(E366K, aka Z allele) heterozygote"/>
</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://varnomen.hgvs.org"/>
<code value="NM_000295.4"/>
<display value="NM_000295.4"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48019-4"/>
<display value="DNA change type"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://varnomen.hgvs.org"/>
<code value="LA6690-7"/>
<display value="Substitution"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48013-7"/>
<display value="Genomic reference sequence identifier"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.ncbi.nlm.nih.gov/refseq"/>
<code value="NM_000295.4"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48018-6"/>
<display value="Gene studied [ID]"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.genenames.org"/>
<code value="HGNC:8941"/>
<display value="SERPINA1"/>
</coding>
</valueCodeableConcept>
</component>
</Observation>