Genomics Reporting Implementation Guide
4.0.0-ballot - STU 4 ballot
Genomics Reporting Implementation Guide
4.0.0-ballot - STU 4 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 4.0.0-ballot 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
| Page standards status: Informative |
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<div xmlns="http://www.w3.org/1999/xhtml"><p class="res-header-id"><b>Generated Narrative: CodeSystem tbd-codes-cs</b></p><a name="tbd-codes-cs"> </a><a name="hctbd-codes-cs"> </a><p>This case-sensitive code system <code>http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs</code> 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">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">molecular-consequence<a name="tbd-codes-cs-molecular-consequence"> </a></td><td>Molecular Consequence</td><td>The calculated or observed effect of a DNA variant on its downstream transcript and, if applicable, ensuing protein sequence.</td></tr><tr><td style="white-space:nowrap">feature-consequence<a name="tbd-codes-cs-feature-consequence"> </a></td><td>Feature Consequence</td><td>The structural implications of a variant (e.g. the variant disrupts a regulatory region, the variant is an inframe insertion).</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. 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">genomic-annotation<a name="tbd-codes-cs-genomic-annotation"> </a></td><td>Genomic Annotation</td><td>Profile for communicating the genome annotation derived from a genomic finding. Annotations are obtained from different databases (Clinvar,gnomad3,thousandgenomes etc.). NOTE: The bound Annotation Module value set is extensible. New annotation programs are being developed and old programs are being upodated/revised, meaning some annotation modules are outside the value set.</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><tr><td style="white-space:nowrap">repeat-motif<a name="tbd-codes-cs-repeat-motif"> </a></td><td>Repeat Expansion Motif</td><td>Nucleotides of a repeat expansion motif.</td></tr><tr><td style="white-space:nowrap">repeat-number<a name="tbd-codes-cs-repeat-number"> </a></td><td>Number of Repeat Expansions</td><td>Number of repeats of a repeat expansion.</td></tr><tr><td style="white-space:nowrap">biomarker-category<a name="tbd-codes-cs-biomarker-category"> </a></td><td>A characterization of a given biomarker observation.</td><td/></tr><tr><td style="white-space:nowrap">protein-ref-seq<a name="tbd-codes-cs-protein-ref-seq"> </a></td><td>An identifier for the protein reference sequence.</td><td/></tr><tr><td style="white-space:nowrap">conservation-score<a name="tbd-codes-cs-conservation-score"> </a></td><td>Conservation Score</td><td>The conservation score calculated</td></tr><tr><td style="white-space:nowrap">annotation-pipeline<a name="tbd-codes-cs-annotation-pipeline"> </a></td><td>Annotation Pipeline</td><td>The name of the data pipeline that processed the genomic data file</td></tr><tr><td style="white-space:nowrap">knowledge-base<a name="tbd-codes-cs-knowledge-base"> </a></td><td>Knowledge Base</td><td>The database from which the annotation is derived</td></tr></table></div>
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<display value="Associated Therapy"/>
<definition
value="The non-medication therapy (procedure) associated with this implication."/>
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<concept>
<code value="molecular-consequence"/>
<display value="Molecular Consequence"/>
<definition
value="The calculated or observed effect of a DNA variant on its downstream transcript and, if applicable, ensuing protein sequence."/>
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<code value="feature-consequence"/>
<display value="Feature Consequence"/>
<definition
value="The structural implications of a variant (e.g. the variant disrupts a regulatory region, the variant is an inframe insertion)."/>
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<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."/>
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<code value="therapeutic-implication"/>
<display value="Therapeutic Implication"/>
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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. 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."/>
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<display value="Functional Effect"/>
<definition
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<display value="Conclusion Text"/>
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<display value="Condition Inheritance"/>
<definition
value="The transmission pattern of the condition/phenotype in a pedigree."/>
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<code value="variant-confidence-status"/>
<display value="Variant Confidence Status"/>
<definition value="The confidence of a true positive variant call."/>
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<concept>
<code value="repeat-motif"/>
<display value="Repeat Expansion Motif"/>
<definition value="Nucleotides of a repeat expansion motif."/>
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<code value="repeat-number"/>
<display value="Number of Repeat Expansions"/>
<definition value="Number of repeats of a repeat expansion."/>
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<concept>
<code value="biomarker-category"/>
<display value="A characterization of a given biomarker observation."/>
</concept>
<concept>
<code value="protein-ref-seq"/>
<display value="An identifier for the protein reference sequence."/>
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<concept>
<code value="conservation-score"/>
<display value="Conservation Score"/>
<definition value="The conservation score calculated"/>
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<concept>
<code value="annotation-pipeline"/>
<display value="Annotation Pipeline"/>
<definition
value="The name of the data pipeline that processed the genomic data file"/>
</concept>
<concept>
<code value="knowledge-base"/>
<display value="Knowledge Base"/>
<definition value="The database from which the annotation is derived"/>
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IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#4.0.0-ballot based on FHIR 4.0.1. Generated 2025-09-22
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