{
  "description": "These codes are currently 'TBD-LOINC' codes. The CG WG is requesting formal LOINC codes.",
  "_filename": "CodeSystem-TbdCodes.json",
  "package_name": "hl7.fhir.uv.genomics-reporting",
  "date": "2021-04-13T19:13:37+00:00",
  "publisher": "HL7 International Clinical Genomics Work Group",
  "jurisdiction": [ {
    "coding": [ {
      "code": "001",
      "system": "http://unstats.un.org/unsd/methods/m49/m49.htm"
    } ]
  } ],
  "content": "complete",
  "name": "TbdCodes",
  "type": null,
  "experimental": null,
  "resourceType": "CodeSystem",
  "title": "ToBeDeterminedCodes ('TbdCodes')",
  "package_version": "1.1.0",
  "status": "active",
  "id": "fc0311a5-b91a-4758-ada2-08ffb26e812e",
  "kind": null,
  "count": 21,
  "url": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes",
  "concept": [ {
    "code": "grouper",
    "display": "grouper",
    "definition": "A means to bundle several observations such as one would find in a genetics test panel."
  }, {
    "code": "effect-transporter-function",
    "display": "effect-transporter-function",
    "definition": "Predicted phenotype for drug efficacy through transport mechanism. A single marker interpretation value known to increase or decrease the drug's performance."
  }, {
    "code": "effect-medication-efficacy",
    "display": "Medication Efficacy"
  }, {
    "code": "effect-medication-metabolism",
    "display": "Medication Metabolism"
  }, {
    "code": "effect-medication-transporter",
    "display": "Medication Transporter Function"
  }, {
    "code": "effect-high-risk-allele",
    "display": "High Risk Allele"
  }, {
    "code": "prognostic-implication",
    "display": "Prognostic Implication component",
    "definition": "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."
  }, {
    "code": "associated-cancer",
    "display": "associated-cancer"
  }, {
    "code": "associated-therapy",
    "display": "Genomically linked therapy",
    "definition": "The non-medication therapy (procedure) associated with this implication."
  }, {
    "code": "region-coverage",
    "display": "region-coverage",
    "definition": "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."
  }, {
    "code": "molecular-consequence",
    "display": "Molecular Consequence",
    "definition": "Annotated changes to sequence features caused by this variant. Terms are from the sequence ontology under SO:0001537."
  }, {
    "code": "exact-start-end",
    "display": "Variant exact start and end",
    "definition": "The genomic coordinates of the exact genomic range in which the variant resides."
  }, {
    "code": "inner-start-end",
    "display": "Variant inner start and end",
    "definition": "The genomic coordinates of the inner genomic range in which the variant might reside."
  }, {
    "code": "outer-start-end",
    "display": "Variant outer start and end",
    "definition": "The genomic coordinates of the outer genomic range in which the variant might reside."
  }, {
    "code": "variant-inheritance",
    "display": "Variant inheritance",
    "definition": "A quality inhering in a variant by virtue of its origin. The terms are in the sequence ontology under SO:0001762."
  }, {
    "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."
  }, {
    "code": "uncallable-regions",
    "display": "Uncallable Regions",
    "definition": "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."
  }, {
    "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."
  } ],
  "version": "1.1.0",
  "contact": [ {
    "telecom": [ {
      "value": "http://www.hl7.org/Special/committees/clingenomics",
      "system": "url"
    } ]
  } ]
}