Genomics Reporting Implementation Guide
2.0.0 - trial-use

This page is part of the Genetic Reporting Implementation Guide (v2.0.0: STU 2) based on FHIR R4. This is the current published version in its permanent home (it will always be available at this URL). For a full list of available versions, see the Directory of published versions

CodeSystem: To Be Determined Codes

Summary

Defining URL:http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
Version:2.0.0
Name:TbdCodesCS
Title:To Be Determined Codes
Status:Active as of 2022-05-09 04:53:07+0000
Definition:

These codes are currently 'TBD' codes. The CG WG plans to request formal LOINC codes to replace these codes as these concepts are validated.

Publisher:HL7 Clinical Genomics Working 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/tbd-codes-cs defines the following codes:

CodeDisplayDefinition
predicted-therapeutic-implication Predicted Therapeutic ImplicationA predicted ramification based on the presence of associated molecular finding(s). 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.
prognostic-implication Prognostic ImplicationFinding 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-therapy Associated 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. The calculated or observed effect of a variant on its downstream transcript and, if applicable, ensuing protein sequence.
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.
variant-confidence-status Variant Confidence StatusThe confidence of a true positive variant call.