FHIR IG analytics| Package | hl7.fhir.uv.genomics-reporting.r4b |
| Resource Type | Observation |
| Id | Observation-ATR-insertion-var.json |
| FHIR Version | R4B |
No resources found
No resources found
Note: links and images are rebased to the (stated) source
Generated Narrative: Observation ATR-insertion-var
status: Final
category: Laboratory, Genetics
code: Genetic variant assessment
effective: 2023-02-01
performer: Practitioner Test Dolin
value: Present
method: Sequencing
component
code: Transcript reference sequence [ID]
value: NM_001184.4
component
code: Allelic read depth
value: 131 reads per base pair (Details: UCUM code1 = '1')
component
code: DNA change type
value: insertion
component
code: DNA change (c.HGVS)
value: NM_001184.4:c.2878_2879insAGTAA
component
code: Gene studied [ID]
value: ATR
component
code: Genomic alt allele [ID]
value: TTACT
component
code: Chromosome [Identifier] in Blood or Tissue by Molecular genetics method
value: Chromosome 3
component
code: Genomic allele start-end
value: 142269071-142269071
component
code: Genomic reference sequence [ID]
value: NC_000003.11
component
code: Genomic DNA change (gHGVS)
value: NC_000003.11:g.142269071_142269072insTTACT
component
code: Genomic source class [Type]
value: Somatic
component
code: Sample variant allelic frequency [NFr]
value: 0.075 decimal
component
code: Conclusion Text
value: Gene: ATR; Exon: 14; Nucleotide: NM_001184.4:c.2878_2879insAGTAA; Genomic Location: NC_000003.11:g.142269071_142269072insTTACT; Amino acid: NP_001175.2:p.R960fs*2; Function: loss; Assessment: Likely Pathogenic; Classification: Tier 2C; Allele Fraction: 5.34% (of 131 reads); Variation: Insertion; Interpretation: The protein encoded by this gene is a serine/threonine kinase and DNA damage sensor, activating cell cycle checkpoint signaling upon DNA stress. The encoded protein can phosphorylate and activate several proteins involved ... more
FHIR
FHIRsmith{
"resourceType": "Observation",
"id": "ATR-insertion-var",
"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"
}
]
},
"subject": {
"reference": "Patient/somaticPatient"
},
"effectiveDateTime": "2023-02-01",
"performer": [
{
"reference": "Practitioner/pathologistPractitioner"
}
],
"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": "51958-7"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://www.ncbi.nlm.nih.gov/refseq",
"code": "NM_001184.4"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "82121-5"
}
]
},
"valueQuantity": {
"value": 131,
"unit": "reads per base pair",
"system": "http://unitsofmeasure.org",
"code": "1"
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "48019-4"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://www.sequenceontology.org",
"code": "SO:0000667",
"display": "insertion"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "48004-6"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://varnomen.hgvs.org",
"code": "NM_001184.4:c.2878_2879insAGTAA"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "48018-6"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://www.genenames.org",
"code": "HGNC:882",
"display": "ATR"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "69551-0"
}
]
},
"valueString": "TTACT"
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "48000-4"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://loinc.org",
"code": "LA21256-5",
"display": "Chromosome 3"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "81254-5"
}
]
},
"valueRange": {
"low": {
"value": 142269071
},
"high": {
"value": 142269071
}
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "48013-7"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://www.ncbi.nlm.nih.gov/refseq",
"code": "NC_000003.11"
}
]
}
},
{
"code": {
"coding": [
{
"system": "http://loinc.org",
"code": "81290-9"
}
]
},
"valueCodeableConcept": {
"coding": [
{
"system": "http://varnomen.hgvs.org",
"code": "NC_000003.11:g.142269071_142269072insTTACT"
}
]
}
},
{
"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": 0.075,
"unit": "decimal",
"system": "http://unitsofmeasure.org"
}
},
{
"code": {
"coding": [
{
"system": "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code": "conclusion-string"
}
]
},
"valueString": "Gene: ATR; Exon: 14; Nucleotide: NM_001184.4:c.2878_2879insAGTAA; Genomic Location: NC_000003.11:g.142269071_142269072insTTACT; Amino acid: NP_001175.2:p.R960fs*2; Function: loss; Assessment: Likely Pathogenic; Classification: Tier 2C; Allele Fraction: 5.34% (of 131 reads); Variation: Insertion; Interpretation: The protein encoded by this gene is a serine/threonine kinase and DNA damage sensor, activating cell cycle checkpoint signaling upon DNA stress. The encoded protein can phosphorylate and activate several proteins involved ... more"
}
]
}