minimal Common Oncology Data Elements (mCODE) Implementation Guide
3.0.0-ballot - 2023May United States of America flag

minimal Common Oncology Data Elements (mCODE) Implementation Guide, published by HL7 International Clinical Interoperability Council. This is not an authorized publication; it is the continuous build for version 3.0.0-ballot). This version is based on the current content of and changes regularly. See the Directory of published versions

Example Observation: gx-genomic-variant-somatic-bap1-indel

Generated Narrative: Observation

Resource Observation "gx-genomic-variant-somatic-bap1-indel"

Profile: Genomic Variant Profile

status: final

category: Laboratory (Observation Category Codes#laboratory)

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

subject: Patient/gx-cancer-patient-adam-anyperson " ANYPERSON"

value: Present (LOINC#LA9633-4)

method: Sequencing (LOINC#LA26398-0)


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

value: BAP1 (HUGO Gene Nomenclature Committee Genes#HGNC:950; gene#3815)


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

value: NM_004656.4 (Gene Reference Sequence Collection#NM_004656)


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

value: NC_000003.11(NM_004656.4):c.1768C>T (Human Genome Variation Society nomenclature#NM_004656.4:c.1768C>T)


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

value: NP_004647.1:p.(Gln590Ter) (Human Genome Variation Society nomenclature#NP_004647.1:p.(Gln590Ter))


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

value: Somatic (LOINC#LA6684-0)


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

value: 57.4 % (Details: UCUM code % = '%')


code: Molecular Consequence (To Be Determined Codes#molecular-consequence)

value: stop_gained (#SO:0001587)


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

value: GRCh37 (LOINC#LA14029-5)