This page is part of a downloaded copy of this specification. This page is part of the Genetic Reporting Implementation Guide (v1.0.0: STU 1) based on FHIR R4. For a full list of available versions, see the Directory of published versions 
{
"resourceType" : "Observation",
"id" : "obs-idh-ex",
"meta" : {
"profile" : [
"http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/inherited-disease-pathogenicity"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative with Details</b></p><p><b>id</b>: obs-idh-ex</p><p><b>meta</b>: </p><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style=\"background: LightGoldenRodYellow\">(Details : {http://terminology.hl7.org/CodeSystem/observation-category code 'laboratory' = 'Laboratory)</span></p><p><b>code</b>: Genetic variation clinical significance [Imp] <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '53037-8' = 'Genetic variation clinical significance [Imp]', given as 'Genetic variation clinical significance [Imp]'})</span></p><p><b>value</b>: Pathogenic <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code 'LA6668-3' = 'Pathogenic', given as 'Pathogenic'})</span></p><p><b>derivedFrom</b>: <a href=\"obs-idh-ex.html\">Generated Summary: id: SNVexample; <span title=\"Codes: {http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span>; <span title=\"Codes: {http://loinc.org 69548-6}\">Genetic variant assessment</span>; <span title=\"Codes: {http://loinc.org LA9633-4}\">Present</span>; <span title=\"Codes: {http://loinc.org LA26398-0}\">Sequencing</span></a></p><blockquote><p><b>component</b></p><p><b>code</b>: Associated phenotype <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '81259-4' = 'Associated phenotype', given as 'Associated phenotype'})</span></p><p><b>value</b>: Cystic fibrosis <span style=\"background: LightGoldenRodYellow\">(Details : {http://www.ncbi.nlm.nih.gov/medgen code 'C0010674' = 'C0010674', given as 'Cystic fibrosis'}; {http://www.orpha.net code 'ORPHA:586' = 'ORPHA:586; {http://www.omim.org code '219700' = '219700)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Associated phenotype <span style=\"background: LightGoldenRodYellow\">(Details : {LOINC code '81259-4' = 'Associated phenotype', given as 'Associated phenotype'})</span></p><p><b>value</b>: Congenital bilateral absence of the vas deferens <span style=\"background: LightGoldenRodYellow\">(Details : {http://www.ncbi.nlm.nih.gov/medgen code 'C0403814' = 'C0403814; {http://www.orpha.net code 'ORPHA:48' = 'ORPHA:48; {http://www.omim.org code '277180' = '277180; {http://www.omim.org code '300985' = '300985)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: mode-of-inheritance <span style=\"background: LightGoldenRodYellow\">(Details : {http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes code 'mode-of-inheritance' = 'mode-of-inheritance', given as 'mode-of-inheritance'})</span></p><p><b>value</b>: Autosomal recessive <span style=\"background: LightGoldenRodYellow\">(Details : {http://ghr.nlm.nih.gov/primer/inheritance/inheritancepatterns code 'Autosomal recessive' = 'Autosomal recessive', given as 'Autosomal recessive'})</span></p></blockquote></div>"
},
"extension" : [
{
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/RelatedArtifact",
"valueRelatedArtifact" : {
"type" : "citation",
"url" : "https://www.ncbi.nlm.nih.gov/clinvar/variation/53685/#clinical-assertions"
}
}
],
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "53037-8",
"display" : "Genetic variation clinical significance [Imp]"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA6668-3",
"display" : "Pathogenic"
}
]
},
"derivedFrom" : [
{
"reference" : "Observation/SNVexample"
}
],
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81259-4",
"display" : "Associated phenotype"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.ncbi.nlm.nih.gov/medgen",
"code" : "C0010674",
"display" : "Cystic fibrosis"
},
{
"system" : "http://www.orpha.net",
"code" : "ORPHA:586"
},
{
"system" : "http://www.omim.org",
"code" : "219700"
}
],
"text" : "Cystic fibrosis"
}
},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81259-4",
"display" : "Associated phenotype"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://www.ncbi.nlm.nih.gov/medgen",
"code" : "C0403814"
},
{
"system" : "http://www.orpha.net",
"code" : "ORPHA:48"
},
{
"system" : "http://www.omim.org",
"code" : "277180"
},
{
"system" : "http://www.omim.org",
"code" : "300985"
}
],
"text" : "Congenital bilateral absence of the vas deferens"
}
},
{
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes",
"code" : "mode-of-inheritance",
"display" : "mode-of-inheritance"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://ghr.nlm.nih.gov/primer/inheritance/inheritancepatterns",
"code" : "Autosomal recessive",
"display" : "Autosomal recessive"
}
]
}
}
]
}