FHIR IG analytics| Package | hl7.fhir.us.mcode.r4 |
| Resource Type | Observation |
| Id | Observation-gx-genomic-variant-somatic-bap1-indel.json |
| FHIR Version | R4 |
No resources found
No resources found
Note: links and images are rebased to the (stated) source
Generated Narrative: Observation gx-genomic-variant-somatic-bap1-indel
status: Final
category: Laboratory
code: Genetic variant assessment
subject: Adam Anyperson Male, DoB: 1990-01-01 ( Medical Record Number: 123456789)
effective: 2019-04-01
performer: Practitioner Owen Oncologist
value: Present
method: Sequencing
component
code: Gene studied [ID]
value: BAP1
component
code: Transcript reference sequence [ID]
value: NM_004656.4
component
code: DNA change (c.HGVS)
value: NM_004656.4:c.1768C>T
component
code: Amino acid change (pHGVS)
value: NP_004647.1:p.(Gln590Ter)
component
code: Genomic source class [Type]
value: Somatic
component
code: Sample variant allelic frequency [NFr]
value: 57.4 % (Details: UCUM code% = '%')
component
code: Molecular Consequence
value: stop_gained
component
code: Human reference sequence assembly version
value: GRCh37
FHIR
FHIRsmith{
"resourceType": "Observation",
"id": "gx-genomic-variant-somatic-bap1-indel",
"meta": {
"profile": [
"http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-genomic-variant"
]
},
"text": {
"status": "generated",
"div": "<!-- snip (see above) -->"
},
"status": "final",
"category": [
{
"coding": [
{
"system": "http://terminology.hl7.org/CodeSystem/observation-category",
"code": "laboratory"
}
]
}
],
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "69548-6"
}
]
},
"subject": {
"reference": "Patient/gx-cancer-patient-adam-anyperson"
},
"effectiveDateTime": "2019-04-01",
"performer": [
{
"reference": "Practitioner/us-core-practitioner-owen-oncologist"
}
],
"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"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://www.genenames.org",
"code": "HGNC:950",
"display": "BAP1"
},
{
"system": "https://www.ncbi.nlm.nih.gov/gene",
"code": "3815",
"display": "BAP1"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "51958-7"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://www.ncbi.nlm.nih.gov/refseq",
"code": "NM_004656",
"display": "NM_004656.4"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "48004-6"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://varnomen.hgvs.org",
"code": "NM_004656.4:c.1768C>T",
"display": "NM_004656.4:c.1768C>T"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "48005-3"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://varnomen.hgvs.org",
"code": "NP_004647.1:p.(Gln590Ter)",
"display": "NP_004647.1:p.(Gln590Ter)"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "48002-0"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://loinc.org",
"code": "LA6684-0",
"display": "Somatic"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "81258-6"
}
]
},
"valueQuantity": {
"value": 57.4,
"unit": "%",
"system": "http://unitsofmeasure.org",
"code": "%"
}
},
{
"code": {
"coding": [
{
"system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code": "molecular-consequence"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://www.sequenceontology.org/",
"code": "SO:0001587",
"display": "stop_gained"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "62374-4"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://loinc.org",
"code": "LA14029-5",
"display": "GRCh37"
}
]
}
}
]
}