Genomics Reporting Implementation Guide
1.1.0 - Ballot

This page is part of the Genetic Reporting Implementation Guide (v1.1.0: STU 2 Ballot 1) based on FHIR R4. The current version which supercedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions

CodeSystem: TBD Code System

Summary

Defining URL:http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes
Version:1.1.0
Name:TbdCodes
Title:ToBeDeterminedCodes ('TbdCodes')
Status:Active as of 2021-04-13T19:13:37+00:00
Definition:

These codes are currently 'TBD-LOINC' codes. The CG WG is requesting formal LOINC codes.

Publisher:HL7 International Clinical Genomics Work Group
Content:Complete: All the concepts defined by the code system are included in the code system resource
Source Resource:XML / JSON / Turtle

This Code system is referenced in the content logical definition of the following value sets:

This code system http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/TbdCodes defines the following codes:

CodeDisplayDefinition
grouper grouperA means to bundle several observations such as one would find in a genetics test panel.
effect-transporter-function effect-transporter-functionPredicted phenotype for drug efficacy through transport mechanism. A single marker interpretation value known to increase or decrease the drug's performance.
effect-medication-efficacy Medication Efficacy
effect-medication-metabolism Medication Metabolism
effect-medication-transporter Medication Transporter Function
effect-high-risk-allele High Risk Allele
prognostic-implication Prognostic Implication componentFinding 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.
associated-cancer associated-cancer
associated-therapy Genomically linked therapyThe non-medication therapy (procedure) associated with this implication.
region-coverage region-coverageGiven 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.
molecular-consequence Molecular ConsequenceAnnotated changes to sequence features caused by this variant. Terms are from the sequence ontology under SO:0001537.
exact-start-end Variant exact start and endThe genomic coordinates of the exact genomic range in which the variant resides.
inner-start-end Variant inner start and endThe genomic coordinates of the inner genomic range in which the variant might reside.
outer-start-end Variant outer start and endThe genomic coordinates of the outer genomic range in which the variant might reside.
variant-inheritance Variant inheritanceA quality inhering in a variant by virtue of its origin. The terms are in the sequence ontology under SO:0001762.
diagnostic-implication Diagnostic ImplicationAn observation linking a genomic finding with a knowledge base, providing context that may aid in diagnosing a patient with a particular phenotype or condition.
therapeutic-implication Therapeutic ImplicationAn observation linking a genomic finding with a knowledge base, providing potential evidence of an interaction with a specified medication or non-medicinal therapy.
uncallable-regions Uncallable RegionsContiguous regions where a call was not made. Must be inside the range given by 'ranges examined' in the given reference sequence and coordinate system.
functional-effect Functional EffectThe effect of a variant on downstream biological products or pathways (from Sequence Ontology).
conclusion-string Conclusion textClinical conclusion (interpretation) of the observation.
condition-inheritance Condition InheritanceThe transmission pattern of the condition/phenotype in a pedigree.