Genomics Reporting Implementation Guide
4.0.0-cibuild - CI Build

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-cibuild 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

Page standards status: Informative

Profile: Variant

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: Transcript reference sequence [ID]

> value: NM_001184.4

> component

> code: Allelic read depth

> value: 131 reads per base pair (Details: UCUM code1 = '1')

> component

> code: DNA change type

> value: insertion

> component

> code: DNA change (c.HGVS)

> value: NM_001184.4:c.2878_2879insAGTAA

> component

> code: Gene studied [ID]

> value: ATR

> component

> code: Genomic alt allele [ID]

> value: TTACT

> component

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

> value: Chromosome 3

> component

> code: Genomic allele start-end

> value: 142269071-142269071

> component

> code: Genomic reference sequence [ID]

> value: NC_000003.11

> component

> code: Genomic DNA change (gHGVS)

> value: NC_000003.11:g.142269071_142269072insTTACT

> component

> code: Genomic source class [Type]

> value: Somatic

> component

> code: Sample variant allelic frequency [NFr]

> value: 0.075 decimal

> component

> code: Conclusion Text

> 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