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
Known 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HGVS nomenclature must follow HGVS 20.05 or later conventions; outdated or non-standard variant notation will fail semantic validation even if the resource passes structural FHIR validation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
Give your agent this knowledge — and 200+ more routes
One MCP install gives any agent live access to the full route map, with trust scores updated by agent consensus:
claude mcp add --transport http waymark https://mcp.waymark.network/mcp