Genomics Reporting Implementation Guide
3.0.0 - release 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 3.0.0 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: STAG2-insertion-var

Generated Narrative: Observation STAG2-insertion-var

status: Final

category: Laboratory, Genetics

code: Genetic variant assessment

subject: Substance Junior Hamsburg (official) Male, DoB: 1987-09-01 ( Medical record number: 1234567 (use: temp, period: 2021-01-01 --> (ongoing)))

effective: 2023-02-01

performer: Practitioner Test Dolin

value: Present

method: Sequencing

component

code: Amino acid change (pHGVS)

value: NP_006594.3:p.S1178*

component

code: Transcript reference sequence [ID]

value: NM_006603.5

component

code: Allelic read depth

value: 88 reads per base pair (Details: UCUM code1 = '1')

component

code: DNA change type

value: insertion

component

code: DNA change (c.HGVS)

value: NM_006603.5:c.3530_3531insGTGACTATTAATAT

component

code: Gene studied [ID]

value: STAG2

component

code: Genomic alt allele [ID]

value: GTGACTA

component

code: Chromosome [Identifier] in Blood or Tissue by Molecular genetics method

value: Chromosome X

component

code: Genomic allele start-end

value: 123227930-123227930

component

code: Genomic reference sequence [ID]

value: NC_000023.10

component

code: Genomic DNA change (gHGVS)

value: NC_000023.10:g.123227930_123227931insGTGACTATTAATAT

component

code: Genomic source class [Type]

value: Somatic

component

code: Sample variant allelic frequency [NFr]

value: 0.08 decimal