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 - JSON Representation
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{
"resourceType" : "CodeSystem",
"id" : "tbd-codes-cs",
"text" : {
"status" : "generated",
"div" : "<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>"
},
"extension" : [
{
"url" : "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg",
"valueCode" : "cg"
}
],
"url" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"version" : "3.0.0-ballot",
"name" : "TbdCodesCS",
"title" : "To Be Determined Codes",
"status" : "active",
"experimental" : false,
"date" : "2023-12-18T22:45:59+00:00",
"publisher" : "HL7 International / Clinical Genomics",
"contact" : [
{
"name" : "HL7 International / Clinical Genomics",
"telecom" : [
{
"system" : "url",
"value" : "http://www.hl7.org/Special/committees/clingenomics"
},
{
"system" : "email",
"value" : "cg@lists.HL7.org"
}
]
}
],
"description" : "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" : "http://unstats.un.org/unsd/methods/m49/m49.htm",
"code" : "001",
"display" : "World"
}
]
}
],
"caseSensitive" : true,
"content" : "complete",
"count" : 13,
"concept" : [
{
"code" : "associated-therapy",
"display" : "Associated Therapy",
"definition" : "The non-medication therapy (procedure) associated with this implication."
},
{
"code" : "molecular-consequence",
"display" : "Molecular Consequence",
"definition" : "The calculated or observed effect of a DNA variant on its downstream transcript and, if applicable, ensuing protein sequence."
},
{
"code" : "feature-consequence",
"display" : "Feature Consequence",
"definition" : "The structural implications of a variant (e.g. the variant disrupts a regulatory region, the variant is an inframe insertion)."
},
{
"code" : "diagnostic-implication",
"display" : "Diagnostic Implication",
"definition" : "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."
},
{
"code" : "therapeutic-implication",
"display" : "Therapeutic Implication",
"definition" : "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."
},
{
"code" : "functional-effect",
"display" : "Functional Effect",
"definition" : "The effect of a variant on downstream biological products or pathways (from Sequence Ontology)."
},
{
"code" : "conclusion-string",
"display" : "Conclusion Text",
"definition" : "Clinical conclusion (interpretation) of the observation."
},
{
"code" : "condition-inheritance",
"display" : "Condition Inheritance",
"definition" : "The transmission pattern of the condition/phenotype in a pedigree."
},
{
"code" : "variant-confidence-status",
"display" : "Variant Confidence Status",
"definition" : "The confidence of a true positive variant call."
},
{
"code" : "repeat-motif",
"display" : "Repeat Expansion Motif",
"definition" : "Nucleotides of a repeat expansion motif."
},
{
"code" : "repeat-number",
"display" : "Number of Repeat Expansions",
"definition" : "Number of repeats of a repeat expansion."
},
{
"code" : "biomarker-category",
"display" : "A characterization of a given biomarker observation."
},
{
"code" : "protein-ref-seq",
"display" : "An identifier for the protein reference sequence."
}
]
}
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