FHIR IG analytics| Package | fhir.nwgenomics.nhs.uk |
| Resource Type | Observation |
| Id | Observation-igene-seqv1.json |
| FHIR Version | R4 |
No resources found
No resources found
Note: links and images are rebased to the (stated) source
Generated Narrative: Observation igene-seqv1
Profile: Variant (Observation)
status: Final
category: Laboratory, Genetics
code: Genetic variant assessment
subject: Patient/example-patient
effective: 2026-08-15
performer: Organization/igene-laboratory
value: Present
method: Sequencing
component
code: Gene studied [ID]
value: BRCA1
component
code: Genomic source class [Type]
value: Germline
component
code: Genomic reference sequence [ID]
value: NC_000017.10
component
code: Genomic coordinate system [Type]
value: 1-based character counting
component
code: Genomic ref allele [ID]
value: TCT
component
code: Genomic alt allele [ID]
value: T
component
code: DNA change type
value: deletion
component
code: Transcript reference sequence [ID]
value: NM_007294.3
component
code: DNA change (c.HGVS)
value: NM_007294.3(BRCA1):c.68_69del
component
code: Amino acid change (pHGVS)
value: p.(Glu23ValfsTer17)
component
code: Genomic DNA change (gHGVS)
value: g.41276047_41276048del
component
code: Genetic variation clinical significance [Imp]
value: Pathogenic
component
code: Origin of germline genetic variant [Type]
value: Maternal
component
code: Genomic allele start-end
value: 41276046-?
component
code: Sample variant allelic frequency
value: 0.33 decimal
component
code: Allelic state
value: heterozygous
FHIR
FHIRsmith{
"resourceType": "Observation",
"id": "igene-seqv1",
"meta": {
"profile": [
"https://fhir.nwgenomics.nhs.uk/StructureDefinition/Variant"
]
},
"text": {
"status": "generated",
"div": "<!-- snip (see above) -->"
},
"status": "final",
"category": [
{
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/observation-category",
"code": "laboratory"
}
]
},
{
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/v2-0074",
"code": "GE"
}
]
}
],
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "69548-6",
"display": "Genetic variant assessment"
}
]
},
"subject": {
"reference": "Patient/example-patient"
},
"effectiveDateTime": "2026-08-15",
"performer": [
{
"reference": "Organization/igene-laboratory"
}
],
"valueCodeableConcept": {
"coding": [
{
"system": "http://loinc.org",
"code": "LA9633-4",
"display": "Present"
}
]
},
"method": {
"coding": [
{
"system": "http://loinc.org",
"code": "LA26398-0",
"display": "Sequencing"
}
]
},
"component": [
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "48018-6",
"display": "Gene studied [ID]"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://www.genenames.org",
"code": "HGNC:1100",
"display": "BRCA1"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "48002-0",
"display": "Genomic source class [Type]"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://loinc.org",
"code": "LA6683-2",
"display": "Germline"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "48013-7",
"display": "Genomic reference sequence [ID]"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://www.ncbi.nlm.nih.gov/refseq",
"code": "NC_000017.10"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "92822-6",
"display": "Genomic coordinate system [Type]"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://loinc.org",
"code": "LA30102-0",
"display": "1-based character counting"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "69547-8",
"display": "Genomic ref allele [ID]"
}
]
},
"valueString": "TCT"
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "69551-0",
"display": "Genomic alt allele [ID]"
}
]
},
"valueString": "T"
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "48019-4",
"display": "DNA change type"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://www.sequenceontology.org",
"code": "SO:0000159",
"display": "deletion"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "51958-7",
"display": "Transcript reference sequence [ID]"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://www.ncbi.nlm.nih.gov/refseq",
"code": "NM_007294.3"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "48004-6",
"display": "DNA change (c.HGVS)"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://varnomen.hgvs.org",
"code": "NM_007294.3(BRCA1):c.68_69del"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "48005-3",
"display": "Amino acid change (pHGVS)"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://varnomen.hgvs.org",
"code": "p.(Glu23ValfsTer17)"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "81290-9",
"display": "Genomic DNA change (gHGVS)"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://varnomen.hgvs.org",
"code": "g.41276047_41276048del"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "53037-8",
"display": "Genetic variation clinical significance [Imp]"
}
]
},
"valueCodeableConcept": {
"text": "Pathogenic"
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "94186-4",
"display": "Origin of germline genetic variant [Type]"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://loinc.org",
"code": "LA26320-4",
"display": "Maternal"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "81254-5",
"display": "Genomic allele start-end"
}
]
},
"valueRange": {
"low": {
"value": 41276046
}
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "81258-6",
"display": "Sample variant allelic frequency"
}
]
},
"valueQuantity": {
"value": 0.33,
"unit": "decimal",
"system": "http://unitsofmeasure.org"
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "53034-5",
"display": "Allelic state"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://loinc.org",
"code": "LA6706-1",
"display": "heterozygous"
}
]
}
}
]
}