FHIR IG analytics| Package | hl7.fhir.uv.genomics-reporting.r4b |
| Resource Type | Observation |
| Id | Observation-RepeatExpansion.json |
| FHIR Version | R4B |
No resources found
No resources found
Note: links and images are rebased to the (stated) source
Generated Narrative: Observation RepeatExpansion
status: Final
category: Laboratory, Genetics
code: Genetic variant assessment
subject: Anonymous Patient (no stated gender), DoB Unknown
effective: 2023-06-01
performer: Organization Some lab
value: Present
component
code: Gene studied ID
value: PABPN1
component
code: Cytogenetic (chromosome) location
value: chr14
component
code: Transcript reference sequence [ID]
value: NM_004643.4
component
code: DNA change (c.HGVS)
value: NM_004643.3:c.3GGC[14]
component
code: Genomic allele start-end
value: 3-?
component
code: Discrete genetic variant
value: NM_004643.3(PABPN1):c.3GGC[11] (p.Ala11_Gly12insAlaAlaAlaAla)
component
Repeat Motif Order: 1
code: Repeat Expansion Motif
value: GGC
component
Repeat Motif Order: 1
code: Number of Repeat Expansions
value: 11
FHIR
FHIRsmith{
"resourceType": "Observation",
"id": "RepeatExpansion",
"meta": {
"profile": [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
]
},
"text": {
"status": "extensions",
"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/ExamplePatient"
},
"effectiveDateTime": "2023-06-01",
"performer": [
{
"reference": "Organization/ExampleLab"
}
],
"valueCodeableConcept": {
"coding": [
{
"system": "http://loinc.org",
"code": "LA9633-4",
"display": "Present"
}
]
},
"component": [
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "48018-6",
"display": "Gene studied ID"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://www.genenames.org",
"code": "HGNC:8565",
"display": "PABPN1"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "48001-2",
"display": "Cytogenetic (chromosome) location"
}
]
},
"valueCodeableConcept": {
"text": "chr14"
}
},
{
"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_004643.4",
"display": "NM_004643.4"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "48004-6",
"display": "DNA change (c.HGVS)"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://varnomen.hgvs.org",
"code": "NM_004643.3:c.3GGC[14]",
"display": "NM_004643.3:c.3GGC[14]"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "81254-5",
"display": "Genomic allele start-end"
}
]
},
"valueRange": {
"low": {
"value": 3
}
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "81252-9",
"display": "Discrete genetic variant"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://www.ncbi.nlm.nih.gov/clinvar",
"code": "503634",
"display": "NM_004643.3(PABPN1):c.3GGC[11] (p.Ala11_Gly12insAlaAlaAlaAla)"
}
]
}
},
{
"extension": [
{
"url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order",
"valuePositiveInt": 1
}
],
"code": {
"coding": [
{
"system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code": "repeat-motif",
"display": "Repeat Expansion Motif"
}
]
},
"valueString": "GGC"
},
{
"extension": [
{
"url": "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/repeat-motif-order",
"valuePositiveInt": 1
}
],
"code": {
"coding": [
{
"system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code": "repeat-number",
"display": "Number of Repeat Expansions"
}
]
},
"valueQuantity": {
"value": 11
}
}
]
}