Notice
- Important: This guidance is under active development by NHS England and content may be added or updated on a regular basis.
- This Implementation Guide is currently in Draft and SHOULD NOT be used for development or active implementation without express direction from the NHS England Genomics Unit.
Observation-GenomicsVariantSLC52A2-Example
Example of an observation representing a Genomic variant.
| Observation |
| id : Observation-GenomicsVariantSLC52A2-Example |
| meta |
| profile : http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant |
| profile : http://hl7.eu/fhir/laboratory/StructureDefinition/Observation-resultslab-eu-lab |
| status : final |
| basedOn |
| reference : ServiceRequest/ServiceRequest-WGSTestOrderFormUpdated-TrioTesting-Example |
| category |
| coding |
| system : http://terminology.hl7.org/CodeSystem/observation-category |
| code : laboratory |
| category |
| coding |
| system : http://terminology.hl7.org/CodeSystem/v2-0074 |
| code : GE |
| code |
| coding |
| system : http://loinc.org |
| code : 69548-6 |
| coding |
| system : http://snomed.info/sct |
| code : 414755005 |
| display : Molecular, genetic AND/OR cellular observable |
| subject |
| reference : Patient/Patient-PheobeSmitham-Example |
| effective : 2023-09-16 |
| performer |
| identifier |
| system : https://fhir.nhs.uk/Id/ods-organization-code |
| value : R0A |
| value |
| coding |
| system : http://loinc.org |
| code : LA9633-4 |
| display : Present |
| coding |
| system : http://snomed.info/sct |
| code : 52101004 |
| display : Present |
| method |
| coding |
| system : http://loinc.org |
| code : LA26398-0 |
| display : Sequencing |
| coding |
| system : http://snomed.info/sct |
| code : 117040002 |
| display : Nucleic acid sequencing |
| specimen |
| reference : Specimen/Specimen-PheobeSmitham-Example |
| component |
| code |
| coding |
| system : http://loinc.org |
| code : 48004-6 |
| value |
| coding |
| system : http://varnomen.hgvs.org |
| code : NM_024531.4:c.9163>A p.(Gly306Arg) |
| component |
| code |
| coding |
| system : http://loinc.org |
| code : 81290-9 |
| value |
| coding |
| system : http://varnomen.hgvs.org |
| code : Chr8:g.1455840683>A |
| component |
| code |
| coding |
| system : http://loinc.org |
| code : 81252-9 |
| value |
| coding |
| system : http://www.sequenceontology.org |
| code : SO:0001583 |
| display : missense_variant |
| component |
| code |
| coding |
| system : http://loinc.org |
| code : 48018-6 |
| value |
| coding |
| system : http://www.genenames.org/ |
| code : HGNC:30224 |
| display : SLC52A2 |
| component |
| code |
| coding |
| system : http://loinc.org |
| code : 53034-5 |
| value |
| coding |
| system : http://loinc.org |
| code : LA6705-3 |
| display : homozygous |
| component |
| code |
| coding |
| system : http://loinc.org |
| code : 94186-4 |
| value |
| coding |
| system : http://loinc.org |
| code : LA4489-6 |
| display : Unknown |
| component |
| code |
| coding |
| system : http://loinc.org |
| code : 48002-0 |
| value |
| coding |
| system : http://loinc.org |
| code : LA6683-2 |
| display : Germline |
{
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant",
"http://hl7.eu/fhir/laboratory/StructureDefinition/Observation-resultslab-eu-lab"
]
},
],
{
]
},
{
}
],
{
},
{
}
]
},
},
],
{
},
{
}
]
},
{
},
{
}
]
},
},
{
},
]
}
},
{
},
}
},
{
},
{
}
]
}
},
{
},
}
},
{
},
}
},
{
},
}
},
{
},
}
}
]
}
</meta>
</basedOn>
</coding>
</category>
</coding>
</category>
</coding>
</coding>
</code>
</subject>
</identifier>
</performer>
</coding>
</coding>
</valueCodeableConcept>
</coding>
</coding>
</method>
</specimen>
</code>
</coding>
</valueCodeableConcept>
</component>
</code>
</valueCodeableConcept>
</component>
</code>
</coding>
</valueCodeableConcept>
</component>
</code>
</coding>
</valueCodeableConcept>
</component>
</code>
</coding>
</valueCodeableConcept>
</component>
</code>
</coding>
</valueCodeableConcept>
</component>
</code>
</coding>
</valueCodeableConcept>
</component>
</Observation>