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

Example Observation: SNVexample

Generated Narrative: Observation

ResourceObservation "SNVexample"

Profile: Variant

status: final

category: Laboratory (Observation Category Codes#laboratory), Genetics (diagnosticServiceSectionId#GE)

code: Genetic variant assessment (LOINC#69548-6)

subject: Patient/ExamplePatient

effective: 2023-06-01

performer: Organization/ExampleLab "Some lab"

value: Present (LOINC#LA9633-4)

method: Sequencing (LOINC#LA26398-0)

specimen: http://slk-kliniken.de/fhir/namingSystem/tissueID/16-123456-23

component

code: Gene studied ID (LOINC#48018-6)

value: AR (HUGO Gene Nomenclature Committee Genes#HGNC:644)

component

code: Cytogenetic (chromosome) location (LOINC#48001-2)

value: chrX ()

component

code: Human reference sequence assembly version (LOINC#62374-4)

value: GRCh37 (LOINC#LA14029-5)

component

code: Genomic source class (LOINC#48002-0)

value: Somatic (LOINC#LA6684-0)

component

code: DNA change (c.HGVS) (LOINC#48004-6)

value: NM_000044.6:c.7G>A (Human Genome Variation Society nomenclature#NM_000044.6:c.7G>A)

component

code: Amino acid change (pHGVS) (LOINC#48005-3)

value: NP_000035.2:p.Val3Met (Human Genome Variation Society nomenclature#NP_000035.2:p.Val3Met)

component

code: Transcript reference sequence [ID] (LOINC#51958-7)

value: NM_000044.6 (Gene Reference Sequence Collection#NM_000044.3)

component

code: Sample VAF (LOINC#81258-6)

value: 0.44 decimal

component

code: Allelic read depth (LOINC#82121-5)

value: 120 reads per base pair (Details: UCUM code 1 = '1')