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: ATR-insertion-var

Generated Narrative: Observation

ResourceObservation "ATR-insertion-var"

Profile: Variant

status: final

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

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

subject: Patient/somaticPatient " HAMSBURG"

effective: 2023-02-01

performer: Practitioner/pathologistPractitioner " DOLIN"

value: Present (LOINC#LA9633-4)

method: Sequencing (LOINC#LA26398-0)

component

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

value: NM_001184.4 (Gene Reference Sequence Collection#NM_001184.4)

component

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

value: 131 reads per base pair (Details: UCUM code 1 = '1')

component

code: DNA change type (LOINC#48019-4)

value: insertion (sequenceontology.org#SO:0000667)

component

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

value: NM_001184.4:c.2878_2879insAGTAA (Human Genome Variation Society nomenclature#NM_001184.4:c.2878_2879insAGTAA)

component

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

value: ATR (HUGO Gene Nomenclature Committee Genes#HGNC:882)

component

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

value: TTACT

component

code: Chromosome [Identifier] in Blood or Tissue by Molecular genetics method (LOINC#48000-4)

value: Chromosome 3 (LOINC#LA21256-5)

component

code: Genomic allele start-end (LOINC#81254-5)

value: 142269071-142269071

component

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

value: NC_000003.11 (Gene Reference Sequence Collection#NC_000003.11)

component

code: Genomic DNA change (gHGVS) (LOINC#81290-9)

value: NC_000003.11:g.142269071_142269072insTTACT (Human Genome Variation Society nomenclature#NC_000003.11:g.142269071_142269072insTTACT)

component

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

value: Somatic (LOINC#LA6684-0)

component

code: Sample variant allelic frequency [NFr] (LOINC#81258-6)

value: 0.075 decimal

component

code: Conclusion Text (To Be Determined Codes#conclusion-string)

value: Gene: ATR; Exon: 14; Nucleotide: NM_001184.4:c.2878_2879insAGTAA; Genomic Location: NC_000003.11:g.142269071_142269072insTTACT; Amino acid: NP_001175.2:p.R960fs*2; Function: loss; Assessment: Likely Pathogenic; Classification: Tier 2C; Allele Fraction: 5.34% (of 131 reads); Variation: Insertion; Interpretation: The protein encoded by this gene is a serine/threonine kinase and DNA damage sensor, activating cell cycle checkpoint signaling upon DNA stress. The encoded protein can phosphorylate and activate several proteins involved ... more