Genomics Reporting Implementation Guide
4.0.0-ballot - STU 4 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 4.0.0-ballot 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

CodeSystem: To Be Determined Codes (Experimental)

Official URL: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs Version: 4.0.0-ballot
Standards status: Informative Computable Name: TbdCodesCS

These codes are ‘TBD’ codes, meaning they are important concepts but codes have not been identifed in available code systems. The CG WG anticpates these codes maturing over time. We may remove some codes as we refine the concepts, or identify suitable replacement codes from other code systems. As we approach normative and these concepts are validated, for codes that remain, we plan to request formal LOINC codes to replace these temporary codes.

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

This case-sensitive code system http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs defines the following codes:

CodeDisplayDefinition
associated-therapy Associated Therapy The non-medication therapy (procedure) associated with this implication.
molecular-consequence Molecular Consequence The calculated or observed effect of a DNA variant on its downstream transcript and, if applicable, ensuing protein sequence.
feature-consequence Feature Consequence The structural implications of a variant (e.g. the variant disrupts a regulatory region, the variant is an inframe insertion).
diagnostic-implication Diagnostic 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-implication Therapeutic 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.
genomic-annotation Genomic Annotation Profile for communicating the genome annotation derived from a genomic finding. Annotations are obtained from different databases (Clinvar,gnomad3,thousandgenomes etc.). NOTE: The bound Annotation Module value set is extensible. New annotation programs are being developed and old programs are being upodated/revised, meaning some annotation modules are outside the value set.
functional-effect Functional Effect The effect of a variant on downstream biological products or pathways (from Sequence Ontology).
conclusion-string Conclusion Text Clinical conclusion (interpretation) of the observation.
condition-inheritance Condition Inheritance The transmission pattern of the condition/phenotype in a pedigree.
variant-confidence-status Variant Confidence Status The confidence of a true positive variant call.
repeat-motif Repeat Expansion Motif Nucleotides of a repeat expansion motif.
repeat-number Number of Repeat Expansions Number of repeats of a repeat expansion.
biomarker-category A characterization of a given biomarker observation.
protein-ref-seq An identifier for the protein reference sequence.
conservation-score Conservation Score The conservation score calculated
annotation-pipeline Annotation Pipeline The name of the data pipeline that processed the genomic data file
knowledge-base Knowledge Base The database from which the annotation is derived