Genomics Reporting Implementation Guide
3.0.0-ballot - Ballot
Genomics Reporting Implementation Guide
3.0.0-ballot - Ballot
This page is part of the Genetic Reporting Implementation Guide (v3.0.0-ballot: STU 3 Ballot 1) based on FHIR (HL7® FHIR® Standard) R4. The current version which supersedes this version is 2.0.0. For a full list of available versions, see the Directory of published versions
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"id" : "MC1",
"meta" : {
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🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence"
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"text" : {
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"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">NM_001395525.1:c.-281+2T>C - intronic_variant:loss_of_function_variant</div>"
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"effectiveDateTime" : "2023-04-01",
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🔗 "reference" : "Organization/ExampleOrg"
}
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"code" : "SO:0001627",
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},
{
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code" : "functional-effect"
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{
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"id" : "MC2",
"meta" : {
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🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence"
]
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"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">NM_001366781.1:c.90T>C - synonymous_variant</div>"
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"status" : "final",
"category" : [
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"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
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"coding" : [
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"system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
"code" : "GE"
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"code" : {
"coding" : [
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"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code" : "molecular-consequence"
}
]
},
"subject" : {
🔗 "reference" : "Patient/HG00403"
},
"effectiveDateTime" : "2023-04-01",
"performer" : [
{
🔗 "reference" : "Organization/ExampleOrg"
}
],
"interpretation" : [
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"coding" : [
{
"system" : "http://example.org/pcingola.github.io/SnpEff/se_inputoutput/#impact-prediction",
"code" : "LOW",
"display" : "Low"
}
]
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"derivedFrom" : [
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"reference" : "Observation/variantExampleMC"
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"component" : [
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"code" : {
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"code" : "48004-6"
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"text" : "coding HGVS"
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"code" : {
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"code" : "51958-7",
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"code" : {
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"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
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"valueCodeableConcept" : {
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}
},
{
"name" : "consequence",
"resource" : {
"resourceType" : "Observation",
"id" : "MC3",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">Molecular Consequence</div>"
},
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
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"coding" : [
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"system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
"code" : "GE"
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"subject" : {
🔗 "reference" : "Patient/HG00403"
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"effectiveDateTime" : "2023-04-01",
"performer" : [
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🔗 "reference" : "Organization/ExampleOrg"
}
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"display" : "Modifier"
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"component" : [
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"code" : "51958-7",
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"code" : {
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"valueCodeableConcept" : {
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"system" : "http://sequenceontology.org",
"code" : "SO:0001623",
"display" : "5_prime_UTR_variant"
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]
}
}
]
}
},
{
"name" : "consequence",
"resource" : {
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"id" : "MC4",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/molecular-consequence"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">Molecular Consequence</div>"
},
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
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{
"coding" : [
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"system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
"code" : "GE"
}
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],
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs",
"code" : "molecular-consequence"
}
]
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"subject" : {
🔗 "reference" : "Patient/HG00403"
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"effectiveDateTime" : "2023-04-01",
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},
{
"name" : "variant",
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"resourceType" : "Observation",
"id" : "variantExampleMC",
"meta" : {
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🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
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"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">Variant</div>"
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"status" : "final",
"category" : [
{
"coding" : [
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"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
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"coding" : [
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"code" : "GE"
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]
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],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "69548-6",
"display" : "Genetic variant assessment"
}
]
},
"subject" : {
🔗 "reference" : "Patient/HG00403"
},
"effectiveDateTime" : "2023-04-01",
"performer" : [
{
🔗 "reference" : "Organization/ExampleOrg"
}
],
"valueCodeableConcept" : {
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"system" : "http://loinc.org",
"code" : "LA9633-4",
"display" : "Present"
}
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"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "48002-0",
"display" : "Genomic source class"
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},
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"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA6683-2",
"display" : "Germline"
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"code" : {
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"system" : "http://loinc.org",
"code" : "48013-7",
"display" : "Genomic reference sequence ID"
}
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},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "53034-5",
"display" : "Allelic state"
}
]
},
"valueCodeableConcept" : {
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"system" : "http://loinc.org",
"code" : "LA6706-1",
"display" : "Heterozygous"
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},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81252-9",
"display" : "Discrete genetic variant"
}
]
},
"valueCodeableConcept" : {
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"system" : "http://varnomen.hgvs.org",
"code" : "NC_000001.10:g.86852621A>G",
"display" : "NC_000001.10:g.86852621A>G"
}
]
}
},
{
"code" : {
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"system" : "http://loinc.org",
"code" : "81258-6",
"display" : "Sample VAF"
}
]
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"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",
"display" : "Genomic allele start-end"
}
]
},
"valueRange" : {
"low" : {
"value" : 86852620
}
}
}
]
}
}
]
}
IG © 2022+ HL7 International / Clinical Genomics. Package hl7.fhir.uv.genomics-reporting#3.0.0-ballot based on FHIR 4.0.1. Generated 2023-12-18
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