Genomics Reporting Implementation Guide
1.1.0 - Ballot
Genomics Reporting Implementation Guide
1.1.0 - Ballot
This page is part of the Genetic Reporting Implementation Guide (v1.1.0: STU 2 Ballot 1) based on FHIR R4. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions 
<Bundle xmlns="http://hl7.org/fhir">
<id value="complexVariant-nonHGVS"/>
<type value="transaction"/>
<entry>
<fullUrl value="urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d"/>
<resource>
<Observation>
<meta>
<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><b>Generated Narrative with Details</b></p><p><b>meta</b>: </p><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style="background: LightGoldenRodYellow">(Details : {http://terminology.hl7.org/CodeSystem/observation-category code 'laboratory' = 'Laboratory)</span></p><p><b>code</b>: Genetic variant assessment <span style="background: LightGoldenRodYellow">(Details : {LOINC code '69548-6' = 'Genetic variant assessment', given as 'Genetic variant assessment'})</span></p><p><b>value</b>: Present <span style="background: LightGoldenRodYellow">(Details : {LOINC code 'LA9633-4' = 'Present', given as 'Present'})</span></p><h3>Components</h3><table class="grid"><tr><td>-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td>*</td><td>DNA change (c.HGVS) <span style="background: LightGoldenRodYellow">(Details : {LOINC code '48004-6' = 'DNA change (c.HGVS)', given as 'DNA change (c.HGVS)'})</span></td><td>NM_022787.3:c.769G>A <span style="background: LightGoldenRodYellow">(Details : {http://varnomen.hgvs.org code 'null' = 'null', given as 'NM_022787.3:c.769G>A'})</span></td></tr></table></div>
</text>
<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69548-6"/>
<display value="Genetic variant assessment"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA9633-4"/>
<display value="Present"/>
</coding>
</valueCodeableConcept>
<!-- HGVS which was unpacked -->
<!-- component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48004-6"/>
<display value="DNA change (c.HGVS)"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
HGVS which was unpaceked
<system value="http://varnomen.hgvs.org"/>
<display value="NM_022787.3:c.769G>A"/>
</coding>
</valueCodeableConcept>
</component -->
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="51958-7"/>
<display value="Transcript ref sequence ID"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.ncbi.nlm.nih.gov/refseq"/>
<code value="NM_022787.3"/>
<display value="NM_022787.3"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system
value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes"/>
<code value="exact-start-end"/>
<display value="Variant exact start and end"/>
</coding>
</code>
<valueRange>
<low>
<value value="769"/>
</low>
<high>
<value value="769"/>
</high>
</valueRange>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69547-8"/>
<display value="Genomic ref allele [ID]"/>
</coding>
</code>
<valueString value="G"/>
</component>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69551-0"/>
<display value="Genomic alt allele [ID]"/>
</coding>
</code>
<valueString value="A"/>
</component>
</Observation>
</resource>
<request>
<method value="POST"/>
<url value="Observation"/>
</request>
</entry>
<entry>
<fullUrl value="urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12e"/>
<resource>
<Observation>
<meta>
<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><b>Generated Narrative with Details</b></p><p><b>meta</b>: </p><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style="background: LightGoldenRodYellow">(Details : {http://terminology.hl7.org/CodeSystem/observation-category code 'laboratory' = 'Laboratory)</span></p><p><b>code</b>: Genetic variant assessment <span style="background: LightGoldenRodYellow">(Details : {LOINC code '69548-6' = 'Genetic variant assessment', given as 'Genetic variant assessment'})</span></p><p><b>value</b>: Present <span style="background: LightGoldenRodYellow">(Details : {LOINC code 'LA9633-4' = 'Present', given as 'Present'})</span></p><h3>Components</h3><table class="grid"><tr><td>-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td>*</td><td>DNA change (c.HGVS) <span style="background: LightGoldenRodYellow">(Details : {LOINC code '48004-6' = 'DNA change (c.HGVS)', given as 'DNA change (c.HGVS)'})</span></td><td>NM_022787.3:c.53A>G <span style="background: LightGoldenRodYellow">(Details : {http://varnomen.hgvs.org code 'null' = 'null', given as 'NM_022787.3:c.53A>G'})</span></td></tr></table></div>
</text>
<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69548-6"/>
<display value="Genetic variant assessment"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA9633-4"/>
<display value="Present"/>
</coding>
</valueCodeableConcept>
<!-- HGVS which was unpaceked -->
<!-- component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="48004-6"/>
<display value="DNA change (c.HGVS)"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
HGVS which was unpaceked
<system value="http://varnomen.hgvs.org"/>
<display value="NM_022787.3:c.53A>G"/>
</coding>
</valueCodeableConcept>
</component -->
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="51958-7"/>
<display value="Transcript ref sequence ID"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://www.ncbi.nlm.nih.gov/refseq"/>
<code value="NM_022787.3"/>
<display value="NM_022787.3"/>
</coding>
</valueCodeableConcept>
</component>
<component>
<code>
<coding>
<system
value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes"/>
<code value="exact-start-end"/>
<display value="Variant exact start and end"/>
</coding>
</code>
<valueRange>
<low>
<value value="53"/>
</low>
<high>
<value value="53"/>
</high>
</valueRange>
</component>
<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>
</Observation>
</resource>
<request>
<method value="POST"/>
<url value="Observation"/>
</request>
</entry>
<entry>
<fullUrl value="urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12a"/>
<resource>
<Observation>
<meta>
<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><b>Generated Narrative with Details</b></p><p><b>meta</b>: </p><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style="background: LightGoldenRodYellow">(Details : {http://terminology.hl7.org/CodeSystem/observation-category code 'laboratory' = 'Laboratory)</span></p><p><b>code</b>: Genetic variant assessment <span style="background: LightGoldenRodYellow">(Details : {LOINC code '69548-6' = 'Genetic variant assessment', given as 'Genetic variant assessment'})</span></p><p><b>value</b>: Present <span style="background: LightGoldenRodYellow">(Details : {LOINC code 'LA9633-4' = 'Present', given as 'Present'})</span></p><p><b>hasMember</b>: </p><ul><li>NM_022787.3:c.53A>G</li><li/></ul><h3>Components</h3><table class="grid"><tr><td>-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td>*</td><td>Complex Variant Type <span style="background: LightGoldenRodYellow">(Details : {LOINC code '81263-6' = 'Complex variant type', given as 'Complex Variant Type'})</span></td><td>Compound heterozygous <span style="background: LightGoldenRodYellow">(Details : {LOINC code 'LA26217-2' = 'Compound heterozygous', given as 'Compound heterozygous'})</span></td></tr></table></div>
</text>
<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69548-6"/>
<display value="Genetic variant assessment"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA9633-4"/>
<display value="Present"/>
</coding>
</valueCodeableConcept>
<hasMember>
<reference value="urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12e"/>
<display value="unpacked representation of NM_022787.3:c.53A>G"/>
</hasMember>
<hasMember>
<reference value="urn:uuid:16fdd5fc-e665-48af-99e4-48d603f3e12d"/>
<display value="unpacked representation of NM_022787.3:c.769G>A"/>
</hasMember>
<component>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="81263-6"/>
<display value="Complex Variant Type"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA26217-2"/>
<display value="Compound heterozygous"/>
</coding>
</valueCodeableConcept>
</component>
</Observation>
</resource>
<request>
<method value="POST"/>
<url value="Observation"/>
</request>
</entry>
</Bundle>
IG © 2019+ HL7 International Clinical Genomics Work Group. Package hl7.fhir.uv.genomics-reporting#1.1.0 based on FHIR 4.0.1. Generated 2021-04-13
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