Genomics Reporting Implementation Guide
3.0.0-ballot - Ballot International flag

This page is part of the Genetic Reporting Implementation Guide (v3.0.0-ballot: STU 3 Ballot 1) based on FHIR (HL7® FHIR® Standard) R4. The current version which supersedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions

: To Be Determined Codes - XML Representation

Active as of 2023-12-18

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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>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">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></table></div>
  </text>
  <extension
             url="http://hl7.org/fhir/StructureDefinition/structuredefinition-wg">
    <valueCode value="cg"/>
  </extension>
  <url
       value="http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs"/>
  <version value="3.0.0-ballot"/>
  <name value="TbdCodesCS"/>
  <title value="To Be Determined Codes"/>
  <status value="active"/>
  <experimental value="false"/>
  <date value="2023-12-18T22:45:59+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 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="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="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="A characterization of a given biomarker observation."/>
  </concept>
  <concept>
    <code value="protein-ref-seq"/>
    <display value="An identifier for the protein reference sequence."/>
  </concept>
</CodeSystem>