Genomics Reporting Implementation Guide
2.0.0 - trial-use
Genomics Reporting Implementation Guide
2.0.0 - trial-use
This page is part of the Genetic Reporting Implementation Guide (v2.0.0: STU 2) based on FHIR R4. This is the current published version in its permanent home (it will always be available at this URL). For a full list of available versions, see the Directory of published versions 
<CodeSystem xmlns="http://hl7.org/fhir">
<id value="tbd-codes-cs"/>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><p>This code system http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs 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">predicted-therapeutic-implication<a name="tbd-codes-cs-predicted-therapeutic-implication"> </a></td><td>Predicted Therapeutic Implication</td><td>A predicted ramification based on the presence of associated molecular finding(s). Ramifications may include alterations in drug metabolism (or pharmacokinetics) that determine the concentration of the drug, prodrug, and/or break-down products over time; alterations in drug efficacy (or pharmacodynamics) that determine how effective a drug is at a given concentration; alterations that alter the risk of adverse drug events, or other types of implications that indicate altered responsiveness to other types of therapies.</td></tr><tr><td style="white-space:nowrap">prognostic-implication<a name="tbd-codes-cs-prognostic-implication"> </a></td><td>Prognostic Implication</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-therapy<a name="tbd-codes-cs-associated-therapy"> </a></td><td>Associated Therapy</td><td>The non-medication therapy (procedure) associated with this implication.</td></tr><tr><td style="white-space:nowrap">region-coverage<a name="tbd-codes-cs-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="tbd-codes-cs-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. The calculated or observed effect of a variant on its downstream transcript and, if applicable, ensuing protein sequence.</td></tr><tr><td style="white-space:nowrap">variant-inheritance<a name="tbd-codes-cs-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="tbd-codes-cs-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="tbd-codes-cs-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="tbd-codes-cs-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="tbd-codes-cs-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="tbd-codes-cs-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="tbd-codes-cs-condition-inheritance"> </a></td><td>Condition Inheritance</td><td>The transmission pattern of the condition/phenotype in a pedigree.</td></tr><tr><td style="white-space:nowrap">variant-confidence-status<a name="tbd-codes-cs-variant-confidence-status"> </a></td><td>Variant Confidence Status</td><td>The confidence of a true positive variant call.</td></tr></table></div>
</text>
<url value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
<version value="2.0.0"/>
<name value="TbdCodesCS"/>
<title value="To Be Determined Codes"/>
<status value="active"/>
<date value="2022-05-09T16:53:07+00:00"/>
<publisher value="HL7 Clinical Genomics Working Group"/>
<contact>
<name value="HL7 Clinical Genomics Working Group"/>
<telecom>
<system value="url"/>
<value value="http://www.hl7.org/Special/committees/clingenomics"/>
</telecom>
<telecom>
<system value="email"/>
<value value="cg@lists.HL7.org"/>
</telecom>
</contact>
<description
value="These codes are currently 'TBD' codes. The CG WG plans to request formal LOINC codes to replace these codes as these concepts are validated."/>
<jurisdiction>
<coding>
<system value="http://unstats.un.org/unsd/methods/m49/m49.htm"/>
<code value="001"/>
<display value="World"/>
</coding>
</jurisdiction>
<caseSensitive value="true"/>
<content value="complete"/>
<count value="13"/>
<concept>
<code value="predicted-therapeutic-implication"/>
<display value="Predicted Therapeutic Implication"/>
<definition
value="A predicted ramification based on the presence of associated molecular finding(s). Ramifications may include alterations in drug metabolism (or pharmacokinetics) that determine the concentration of the drug, prodrug, and/or break-down products over time; alterations in drug efficacy (or pharmacodynamics) that determine how effective a drug is at a given concentration; alterations that alter the risk of adverse drug events, or other types of implications that indicate altered responsiveness to other types of therapies."/>
</concept>
<concept>
<code value="prognostic-implication"/>
<display value="Prognostic Implication"/>
<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-therapy"/>
<display value="Associated 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. The calculated or observed effect of a variant on its downstream transcript and, if applicable, ensuing protein sequence."/>
</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>
<concept>
<code value="variant-confidence-status"/>
<display value="Variant Confidence Status"/>
<definition value="The confidence of a true positive variant call."/>
</concept>
</CodeSystem>
IG © 2022+ HL7 Clinical Genomics Working Group. Package hl7.fhir.uv.genomics-reporting#2.0.0 based on FHIR 4.0.1. Generated 2022-05-09
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