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 
<CodeSystem xmlns="http://hl7.org/fhir">
<id value="TbdCodes"/>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><p>This code system http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes defines the following codes:</p><table class="codes"><tr><td style="white-space:nowrap"><b>Code</b></td><td><b>Display</b></td><td><b>Definition</b></td></tr><tr><td style="white-space:nowrap">grouper<a name="TbdCodes-grouper"> </a></td><td>grouper</td><td>A means to bundle several observations such as one would find in a genetics test panel.</td></tr><tr><td style="white-space:nowrap">effect-transporter-function<a name="TbdCodes-effect-transporter-function"> </a></td><td>effect-transporter-function</td><td>Predicted phenotype for drug efficacy through transport mechanism. A single marker interpretation value known to increase or decrease the drug's performance.</td></tr><tr><td style="white-space:nowrap">effect-medication-efficacy<a name="TbdCodes-effect-medication-efficacy"> </a></td><td>Medication Efficacy</td><td/></tr><tr><td style="white-space:nowrap">effect-medication-metabolism<a name="TbdCodes-effect-medication-metabolism"> </a></td><td>Medication Metabolism</td><td/></tr><tr><td style="white-space:nowrap">effect-medication-transporter<a name="TbdCodes-effect-medication-transporter"> </a></td><td>Medication Transporter Function</td><td/></tr><tr><td style="white-space:nowrap">effect-high-risk-allele<a name="TbdCodes-effect-high-risk-allele"> </a></td><td>High Risk Allele</td><td/></tr><tr><td style="white-space:nowrap">prognostic-implication<a name="TbdCodes-prognostic-implication"> </a></td><td>Prognostic Implication component</td><td>Finding of whether a particular somatic genotype/haplotype/variation or combination-thereof predicts a particular outcome for the specified cancer - either on its own or in conjunction with one or more interventions.</td></tr><tr><td style="white-space:nowrap">associated-cancer<a name="TbdCodes-associated-cancer"> </a></td><td>associated-cancer</td><td/></tr><tr><td style="white-space:nowrap">associated-therapy<a name="TbdCodes-associated-therapy"> </a></td><td>Genomically linked therapy</td><td>The non-medication therapy (procedure) associated with this implication.</td></tr><tr><td style="white-space:nowrap">region-coverage<a name="TbdCodes-region-coverage"> </a></td><td>region-coverage</td><td>Given as a number between 0 and 100. Mean mapped read depth. Obtained by counting total number of mapped reads and divided by the number of bases in the region sequence.</td></tr><tr><td style="white-space:nowrap">molecular-consequence<a name="TbdCodes-molecular-consequence"> </a></td><td>Molecular Consequence</td><td>Annotated changes to sequence features caused by this variant. Terms are from the sequence ontology under SO:0001537.</td></tr><tr><td style="white-space:nowrap">exact-start-end<a name="TbdCodes-exact-start-end"> </a></td><td>Variant exact start and end</td><td>The genomic coordinates of the exact genomic range in which the variant resides.</td></tr><tr><td style="white-space:nowrap">inner-start-end<a name="TbdCodes-inner-start-end"> </a></td><td>Variant inner start and end</td><td>The genomic coordinates of the inner genomic range in which the variant might reside.</td></tr><tr><td style="white-space:nowrap">outer-start-end<a name="TbdCodes-outer-start-end"> </a></td><td>Variant outer start and end</td><td>The genomic coordinates of the outer genomic range in which the variant might reside.</td></tr><tr><td style="white-space:nowrap">variant-inheritance<a name="TbdCodes-variant-inheritance"> </a></td><td>Variant inheritance</td><td>A quality inhering in a variant by virtue of its origin. The terms are in the sequence ontology under SO:0001762.</td></tr><tr><td style="white-space:nowrap">diagnostic-implication<a name="TbdCodes-diagnostic-implication"> </a></td><td>Diagnostic Implication</td><td>An observation linking a genomic finding with a knowledge base, providing context that may aid in diagnosing a patient with a particular phenotype or condition.</td></tr><tr><td style="white-space:nowrap">therapeutic-implication<a name="TbdCodes-therapeutic-implication"> </a></td><td>Therapeutic Implication</td><td>An observation linking a genomic finding with a knowledge base, providing potential evidence of an interaction with a specified medication or non-medicinal therapy.</td></tr><tr><td style="white-space:nowrap">uncallable-regions<a name="TbdCodes-uncallable-regions"> </a></td><td>Uncallable Regions</td><td>Contiguous regions where a call was not made. Must be inside the range given by 'ranges examined' in the given reference sequence and coordinate system.</td></tr><tr><td style="white-space:nowrap">functional-effect<a name="TbdCodes-functional-effect"> </a></td><td>Functional Effect</td><td>The effect of a variant on downstream biological products or pathways (from Sequence Ontology).</td></tr><tr><td style="white-space:nowrap">conclusion-string<a name="TbdCodes-conclusion-string"> </a></td><td>Conclusion text</td><td>Clinical conclusion (interpretation) of the observation.</td></tr><tr><td style="white-space:nowrap">condition-inheritance<a name="TbdCodes-condition-inheritance"> </a></td><td>Condition Inheritance</td><td>The transmission pattern of the condition/phenotype in a pedigree.</td></tr></table></div>
</text>
<url value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes"/>
<version value="1.1.0"/>
<name value="TbdCodes"/>
<title value="ToBeDeterminedCodes ('TbdCodes')"/>
<status value="active"/>
<date value="2021-04-13T19:13:37+00:00"/>
<publisher value="HL7 International Clinical Genomics Work Group"/>
<contact>
<telecom>
<system value="url"/>
<value value="http://www.hl7.org/Special/committees/clingenomics"/>
</telecom>
</contact>
<description
value="These codes are currently 'TBD-LOINC' codes. The CG WG is requesting formal LOINC codes."/>
<jurisdiction>
<coding>
<system value="http://unstats.un.org/unsd/methods/m49/m49.htm"/>
<code value="001"/>
</coding>
</jurisdiction>
<content value="complete"/>
<count value="21"/>
<concept>
<code value="grouper"/>
<display value="grouper"/>
<definition
value="A means to bundle several observations such as one would find in a genetics test panel."/>
</concept>
<concept>
<code value="effect-transporter-function"/>
<display value="effect-transporter-function"/>
<definition
value="Predicted phenotype for drug efficacy through transport mechanism. A single marker interpretation value known to increase or decrease the drug's performance."/>
</concept>
<concept>
<code value="effect-medication-efficacy"/>
<display value="Medication Efficacy"/>
</concept>
<concept>
<code value="effect-medication-metabolism"/>
<display value="Medication Metabolism"/>
</concept>
<concept>
<code value="effect-medication-transporter"/>
<display value="Medication Transporter Function"/>
</concept>
<concept>
<code value="effect-high-risk-allele"/>
<display value="High Risk Allele"/>
</concept>
<concept>
<code value="prognostic-implication"/>
<display value="Prognostic Implication component"/>
<definition
value="Finding of whether a particular somatic genotype/haplotype/variation or combination-thereof predicts a particular outcome for the specified cancer - either on its own or in conjunction with one or more interventions."/>
</concept>
<concept>
<code value="associated-cancer"/>
<display value="associated-cancer"/>
</concept>
<concept>
<code value="associated-therapy"/>
<display value="Genomically linked therapy"/>
<definition
value="The non-medication therapy (procedure) associated with this implication."/>
</concept>
<concept>
<code value="region-coverage"/>
<display value="region-coverage"/>
<definition
value="Given as a number between 0 and 100. Mean mapped read depth. Obtained by counting total number of mapped reads and divided by the number of bases in the region sequence."/>
</concept>
<concept>
<code value="molecular-consequence"/>
<display value="Molecular Consequence"/>
<definition
value="Annotated changes to sequence features caused by this variant. Terms are from the sequence ontology under SO:0001537."/>
</concept>
<concept>
<code value="exact-start-end"/>
<display value="Variant exact start and end"/>
<definition
value="The genomic coordinates of the exact genomic range in which the variant resides."/>
</concept>
<concept>
<code value="inner-start-end"/>
<display value="Variant inner start and end"/>
<definition
value="The genomic coordinates of the inner genomic range in which the variant might reside."/>
</concept>
<concept>
<code value="outer-start-end"/>
<display value="Variant outer start and end"/>
<definition
value="The genomic coordinates of the outer genomic range in which the variant might reside."/>
</concept>
<concept>
<code value="variant-inheritance"/>
<display value="Variant inheritance"/>
<definition
value="A quality inhering in a variant by virtue of its origin. The terms are in the sequence ontology under SO:0001762."/>
</concept>
<concept>
<code value="diagnostic-implication"/>
<display value="Diagnostic Implication"/>
<definition
value="An observation linking a genomic finding with a knowledge base, providing context that may aid in diagnosing a patient with a particular phenotype or condition."/>
</concept>
<concept>
<code value="therapeutic-implication"/>
<display value="Therapeutic Implication"/>
<definition
value="An observation linking a genomic finding with a knowledge base, providing potential evidence of an interaction with a specified medication or non-medicinal therapy."/>
</concept>
<concept>
<code value="uncallable-regions"/>
<display value="Uncallable Regions"/>
<definition
value="Contiguous regions where a call was not made. Must be inside the range given by 'ranges examined' in the given reference sequence and coordinate system."/>
</concept>
<concept>
<code value="functional-effect"/>
<display value="Functional Effect"/>
<definition
value="The effect of a variant on downstream biological products or pathways (from Sequence Ontology)."/>
</concept>
<concept>
<code value="conclusion-string"/>
<display value="Conclusion text"/>
<definition value="Clinical conclusion (interpretation) of the observation."/>
</concept>
<concept>
<code value="condition-inheritance"/>
<display value="Condition Inheritance"/>
<definition
value="The transmission pattern of the condition/phenotype in a pedigree."/>
</concept>
</CodeSystem>
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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