Genomics Reporting Implementation Guide
3.0.1-SNAPSHOT - Ballot International flag

Genomics Reporting Implementation Guide, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 3.0.1-SNAPSHOT built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/genomics-reporting/ and changes regularly. See the Directory of published versions

ValueSet: To Be Determined Value Set

Official URL: http://hl7.org/fhir/uv/genomics-reporting/ValueSet/tbd-codes-vs Version: 3.0.1-SNAPSHOT
Active as of 2024-07-15 Computable Name: TBDCodesVS

Value Set for codes yet to be defined in LOINC

References

This value set is not used here; it may be used elsewhere (e.g. specifications and/or implementations that use this content)

Logical Definition (CLD)

Generated Narrative: ValueSet tbd-codes-vs

 

Expansion

Generated Narrative: ValueSet

Expansion based on codesystem To Be Determined Codes v3.0.1-SNAPSHOT (CodeSystem)

This value set contains 13 concepts

CodeSystemDisplayDefinition
  associated-therapyhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-csAssociated Therapy

The non-medication therapy (procedure) associated with this implication.

  molecular-consequencehttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-csMolecular Consequence

The calculated or observed effect of a DNA variant on its downstream transcript and, if applicable, ensuing protein sequence.

  feature-consequencehttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-csFeature Consequence

The structural implications of a variant (e.g. the variant disrupts a regulatory region, the variant is an inframe insertion).

  diagnostic-implicationhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-csDiagnostic Implication

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.

  therapeutic-implicationhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-csTherapeutic Implication

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.

  functional-effecthttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-csFunctional Effect

The effect of a variant on downstream biological products or pathways (from Sequence Ontology).

  conclusion-stringhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-csConclusion Text

Clinical conclusion (interpretation) of the observation.

  condition-inheritancehttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-csCondition Inheritance

The transmission pattern of the condition/phenotype in a pedigree.

  variant-confidence-statushttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-csVariant Confidence Status

The confidence of a true positive variant call.

  repeat-motifhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-csRepeat Expansion Motif

Nucleotides of a repeat expansion motif.

  repeat-numberhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-csNumber of Repeat Expansions

Number of repeats of a repeat expansion.

  biomarker-categoryhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-csA characterization of a given biomarker observation.
  protein-ref-seqhttp://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-csAn identifier for the protein reference sequence.

Explanation of the columns that may appear on this page:

Level A few code lists that FHIR defines are hierarchical - each code is assigned a level. In this scheme, some codes are under other codes, and imply that the code they are under also applies
System The source of the definition of the code (when the value set draws in codes defined elsewhere)
Code The code (used as the code in the resource instance)
Display The display (used in the display element of a Coding). If there is no display, implementers should not simply display the code, but map the concept into their application
Definition An explanation of the meaning of the concept
Comments Additional notes about how to use the code