FHIR IG analytics| Package | hl7.fhir.uv.genomics-reporting.r4b |
| Resource Type | Observation |
| Id | Observation-variant-with-molec-consequences.json |
| FHIR Version | R4B |
No resources found
No resources found
Note: links and images are rebased to the (stated) source
Generated Narrative: Observation variant-with-molec-consequences
status: Final
category: Laboratory, Genetics
code: Genetic variant assessment
subject: Alanine B. Everyone Unknown, DoB: 1951-01-20 ( Medical Record Number: m234 (use: usual, ))
effective: 2023-06-01
performer: Organization Some lab
value: Present
component
code: Genomic source class
value: Germline
component
code: Genomic reference sequence ID
value: NC_000001.10
component
code: Allelic state
value: Heterozygous
component
code: Discrete genetic variant
value: NC_000001.10:g.86852621A>G
component
code: Sample VAF
value: 0.6 relative frequency of a particular allele in the specimen (Details: UCUM code1 = '1')
component
code: Genomic Ref allele [ID]
value: A
component
code: Genomic Alt allele [ID]
value: G
component
code: Genomic coord system
value: 0-based interval counting
component
code: Variant exact start-end
value: 86852620-?
component
code: Population allele frequency
value: 0.327084 1 (Details: UCUM code1 = '1')
FHIR
FHIRsmith{
"resourceType": "Observation",
"id": "variant-with-molec-consequences",
"meta": {
"profile": [
"http://hl7.org/fhir/uv/genomics-reporting/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/HG00403"
},
"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": "48002-0",
"display": "Genomic source class"
}
]
},
"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_000001.10"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "53034-5",
"display": "Allelic state"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://loinc.org",
"code": "LA6706-1",
"display": "Heterozygous"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "81252-9",
"display": "Discrete genetic variant"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://varnomen.hgvs.org",
"code": "NC_000001.10:g.86852621A>G",
"display": "NC_000001.10:g.86852621A>G"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "81258-6",
"display": "Sample VAF"
}
]
},
"valueQuantity": {
"value": 0.6,
"unit": "relative frequency of a particular allele in the specimen",
"system": "http://unitsofmeasure.org",
"code": "1"
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "69547-8",
"display": "Genomic Ref allele [ID]"
}
]
},
"valueString": "A"
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "69551-0",
"display": "Genomic Alt allele [ID]"
}
]
},
"valueString": "G"
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "92822-6",
"display": "Genomic coord system"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://loinc.org",
"code": "LA30100-4",
"display": "0-based interval counting"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "81254-5"
}
],
"text": "Variant exact start-end"
},
"valueRange": {
"low": {
"value": 86852620
}
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "92821-8"
}
],
"text": "Population allele frequency"
},
"valueQuantity": {
"value": 0.327084,
"system": "http://unitsofmeasure.org",
"code": "1"
}
}
]
}