Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build

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-cibuild 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

## : To Be Determined Codes - XML Representation

Page standards status: Informative

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    <CodeSystem xmlns="http://hl7.org/fhir">
      <id value="tbd-codes-cs"/>
      <text>
        <status value="generated"/>
        <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>Biomarker Category</td><td>A characterization of a given biomarker observation.</td></tr><tr><td style="white-space:nowrap">protein-ref-seq<a name="tbd-codes-cs-protein-ref-seq"> </a></td><td>Protein Reference Sequence</td><td>An identifier for the protein reference sequence.</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 for a genomic position or region indicating evolutionary conservation.</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>
      </text>
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                 url="http://hl7.org/fhir/StructureDefinition/structuredefinition-wg">
        <valueCode value="cg"/>
      </extension>
      <extension
                 url="http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status">
        <valueCode value="informative">
          <extension
                     url="http://hl7.org/fhir/StructureDefinition/structuredefinition-conformance-derivedFrom">
            <valueCanonical
                            value="http://hl7.org/fhir/uv/genomics-reporting/ImplementationGuide/genomics-reporting"/>
          </extension>
        </valueCode>
      </extension>
      <url
           value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
      <version value="4.0.0-cibuild"/>
      <name value="TbdCodesCS"/>
      <title value="To Be Determined Codes"/>
      <status value="active"/>
      <experimental value="true"/>
      <date value="2025-11-08T00:09:50+00:00"/>
      <publisher value="HL7 International / Clinical Genomics"/>
      <contact>
        <name value="HL7 International / Clinical Genomics"/>
        <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 'TBD' codes, meaning they are important concepts but codes have not been identifed in available code systems. The CG WG anticpates these codes maturing over time. We may remove some codes as we refine the concepts, or identify suitable replacement codes from other code systems. As we approach normative and these concepts are validated, for codes that remain, we plan to request formal LOINC codes to replace these temporary codes."/>
      <jurisdiction>
        <coding>
          <system value="http://unstats.un.org/unsd/methods/m49/m49.htm"/>
          <code value="001"/>
          <display value="World"/>
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      <caseSensitive value="true"/>
      <content value="complete"/>
      <count value="17"/>
      <concept>
        <code value="associated-therapy"/>
        <display value="Associated Therapy"/>
        <definition
                    value="The non-medication therapy (procedure) associated with this implication."/>
      </concept>
      <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."/>
      </concept>
      <concept>
        <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)."/>
      </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. 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="genomic-annotation"/>
        <display value="Genomic Annotation"/>
        <definition
                    value="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."/>
      </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>
      <concept>
        <code value="repeat-motif"/>
        <display value="Repeat Expansion Motif"/>
        <definition value="Nucleotides of a repeat expansion motif."/>
      </concept>
      <concept>
        <code value="repeat-number"/>
        <display value="Number of Repeat Expansions"/>
        <definition value="Number of repeats of a repeat expansion."/>
      </concept>
      <concept>
        <code value="biomarker-category"/>
        <display value="Biomarker Category"/>
        <definition value="A characterization of a given biomarker observation."/>
      </concept>
      <concept>
        <code value="protein-ref-seq"/>
        <display value="Protein Reference Sequence"/>
        <definition value="An identifier for the protein reference sequence."/>
      </concept>
      <concept>
        <code value="conservation-score"/>
        <display value="Conservation Score"/>
        <definition
                    value="The conservation score calculated for a genomic position or region indicating evolutionary conservation."/>
      </concept>
      <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"/>
      </concept>
    </CodeSystem>