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: variant-with-molec-consequences

Generated Narrative: Observation

ResourceObservation "variant-with-molec-consequences"

Profile: Variant

status: final

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

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

subject: Patient/HG00403 " EVERYONE"

effective: 2023-06-01

performer: Organization/ExampleLab "Some lab"

value: Present (LOINC#LA9633-4)

component

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

value: Germline (LOINC#LA6683-2)

component

code: Genomic reference sequence ID (LOINC#48013-7)

value: NC_000001.10 (Gene Reference Sequence Collection#NC_000001.10)

component

code: Allelic state (LOINC#53034-5)

value: Heterozygous (LOINC#LA6706-1)

component

code: Discrete genetic variant (LOINC#81252-9)

value: NC_000001.10:g.86852621A>G (Human Genome Variation Society nomenclature#NC_000001.10:g.86852621A>G)

component

code: Sample VAF (LOINC#81258-6)

value: 0.6 relative frequency of a particular allele in the specimen (Details: UCUM code 1 = '1')

component

code: Genomic Ref allele [ID] (LOINC#69547-8)

value: A

component

code: Genomic Alt allele [ID] (LOINC#69551-0)

value: G

component

code: Genomic coord system (LOINC#92822-6)

value: 0-based interval counting (LOINC#LA30100-4)

component

code: Variant exact start-end (LOINC#81254-5)

value: 86852620-?

component

code: Population allele frequency (LOINC#92821-8)

value: 0.327084 1 (Details: UCUM code 1 = '1')