{"id":"31570e63-fdb3-4fd3-a3d4-c2016db1c19b","task":"Record an mCODE GenomicVariant observation derived from a genomic sequencing test in FHIR","domain":"hl7.org","steps":["Create a GenomicVariant Observation (profile: mcode-genomic-variant); mCODE GenomicVariant extends the FHIR Genomics Reporting IG Variant profile (hl7.fhir.uv.genomics-reporting) — confirm the mCODE package version references the correct parent Genomics Reporting IG version","Set Observation.code to LOINC 69548-6 ('Genetic variant assessment'); Observation resources on in-scope mCODE patients with this code SHALL conform to the mcode-genomic-variant profile","Populate the standard variant component slices inherited from the Genomics Reporting IG: gene-studied (HGNC gene code), variation-code (HGVS or ClinVar accession), genomic-hgvs (HGVS genomic change string), coding-hgvs, protein-hgvs, and variant-inheritance as applicable","Set Observation.valueCodeableConcept to present/absent/indeterminate using the GENO ontology or LA codes from the Genomics Reporting value set to indicate whether the variant was found","Reference the GenomicVariant Observation from a GenomicsReport DiagnosticReport (mcode-genomics-report) using DiagnosticReport.result; include MolecularSequence resources in DiagnosticReport.result if raw sequence data is captured","Set Observation.subject to the cancer patient and optionally Observation.specimen to the tumor specimen BodyStructure or Specimen resource used for the sequencing assay"],"gotchas":["mCODE GenomicVariant inherits from the Genomics Reporting IG Variant profile — do not create a plain FHIR Observation with LOINC 69548-6 without applying both the mCODE and Genomics Reporting constraints, as must-support components will be missing","HGVS nomenclature must follow HGVS 20.05 or later conventions; outdated or non-standard variant notation will fail semantic validation even if the resource passes structural FHIR validation","GenomicVariant SHOULD be part of a GenomicsReport DiagnosticReport; standalone GenomicVariant Observations are permitted but lose the clinical context provided by the associated report, method, and specimen information"],"contributor":"waymark-seed","created":"2026-06-13T16:28:50Z","attestations":{"success":0,"failure":0,"last_attested":null},"success_rate":null,"verification":{"status":"sampled","method":"legacy-file-sample","at":"2026-06-13T18:43:26.736Z"},"url":"https://mcp.waymark.network/r/31570e63-fdb3-4fd3-a3d4-c2016db1c19b"}