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
{
"resourceType" : "Observation",
"id" : "ZFHX3-uncertain-var",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/variant"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p><b>Generated Narrative: Observation</b><a name=\"ZFHX3-uncertain-var\"> </a></p><div style=\"display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%\"><p style=\"margin-bottom: 0px\">Resource Observation "ZFHX3-uncertain-var" </p><p style=\"margin-bottom: 0px\">Profile: <a href=\"StructureDefinition-variant.html\">Variant</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-observation-category.html\">Observation Category Codes</a>#laboratory)</span>, Genetics <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v2-0074.html\">diagnosticServiceSectionId</a>#GE)</span></p><p><b>code</b>: Genetic variant assessment <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69548-6)</span></p><p><b>subject</b>: <a href=\"Patient-somaticPatient.html\">Patient/somaticPatient</a> " HAMSBURG"</p><p><b>effective</b>: 2023-02-01</p><p><b>performer</b>: <a href=\"Practitioner-pathologistPractitioner.html\">Practitioner/pathologistPractitioner</a> " DOLIN"</p><p><b>value</b>: Present <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA9633-4)</span></p><p><b>method</b>: Sequencing <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA26398-0)</span></p><blockquote><p><b>component</b></p><p><b>code</b>: Amino acid change (pHGVS) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48005-3)</span></p><p><b>value</b>: NP_008816.3:p.G585S <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-hgvs.html\">Human Genome Variation Society nomenclature</a>#NP_008816.3:p.G585S)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Transcript reference sequence [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#51958-7)</span></p><p><b>value</b>: NM_006885.4 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-refSeq.html\">Gene Reference Sequence Collection</a>#NM_006885.4)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Allelic read depth <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#82121-5)</span></p><p><b>value</b>: 212 reads per base pair<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM code 1 = '1')</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: DNA change (c.HGVS) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48004-6)</span></p><p><b>value</b>: NM_006885.4:c.1753G>A <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-hgvs.html\">Human Genome Variation Society nomenclature</a>#NM_006885.4:c.1753G>A)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Gene studied [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48018-6)</span></p><p><b>value</b>: ZFHX3 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-hgnc.html\">HUGO Gene Nomenclature Committee Genes</a>#HGNC:777)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic alt allele [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69551-0)</span></p><p><b>value</b>: T</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Chromosome [Identifier] in Blood or Tissue by Molecular genetics method <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48000-4)</span></p><p><b>value</b>: Chromosome 16 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA21269-8)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic allele start-end <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81254-5)</span></p><p><b>value</b>: 72992292-72992292</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic reference sequence [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48013-7)</span></p><p><b>value</b>: NC_000016.9 <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-refSeq.html\">Gene Reference Sequence Collection</a>#NC_000016.9)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic ref allele [ID] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#69547-8)</span></p><p><b>value</b>: C</p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic DNA change (gHGVS) <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81290-9)</span></p><p><b>value</b>: NC_000016.9:g.72992292C>T <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"http://terminology.hl7.org/5.3.0/CodeSystem-v3-hgvs.html\">Human Genome Variation Society nomenclature</a>#NC_000016.9:g.72992292C>T)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Genomic source class [Type] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#48002-0)</span></p><p><b>value</b>: Somatic <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#LA6684-0)</span></p></blockquote><blockquote><p><b>component</b></p><p><b>code</b>: Sample variant allelic frequency [NFr] <span style=\"background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki\"> (<a href=\"https://loinc.org/\">LOINC</a>#81258-6)</span></p><p><b>value</b>: 0.1 decimal</p></blockquote></div>"
},
"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"
}
]
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"component" : [
{
"code" : {
"coding" : [
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"system" : "http://loinc.org",
"code" : "48005-3"
}
]
},
"valueCodeableConcept" : {
"coding" : [
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"system" : "http://varnomen.hgvs.org",
"code" : "NP_008816.3:p.G585S"
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]
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"code" : {
"coding" : [
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"system" : "http://loinc.org",
"code" : "51958-7"
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"valueCodeableConcept" : {
"coding" : [
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"system" : "http://www.ncbi.nlm.nih.gov/refseq",
"code" : "NM_006885.4"
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{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "82121-5"
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]
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"valueQuantity" : {
"value" : 212,
"unit" : "reads per base pair",
"system" : "http://unitsofmeasure.org",
"code" : "1"
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"code" : {
"coding" : [
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"system" : "http://loinc.org",
"code" : "48004-6"
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"valueCodeableConcept" : {
"coding" : [
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"system" : "http://varnomen.hgvs.org",
"code" : "NM_006885.4:c.1753G>A"
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{
"code" : {
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"system" : "http://loinc.org",
"code" : "48018-6"
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},
"valueCodeableConcept" : {
"coding" : [
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"system" : "http://www.genenames.org",
"code" : "HGNC:777",
"display" : "ZFHX3"
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},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "69551-0"
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]
},
"valueString" : "T"
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{
"code" : {
"coding" : [
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"system" : "http://loinc.org",
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"valueCodeableConcept" : {
"coding" : [
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"system" : "http://loinc.org",
"code" : "LA21269-8",
"display" : "Chromosome 16"
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{
"code" : {
"coding" : [
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"system" : "http://loinc.org",
"code" : "81254-5"
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"valueRange" : {
"low" : {
"value" : 72992292
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"high" : {
"value" : 72992292
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{
"code" : {
"coding" : [
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"system" : "http://loinc.org",
"code" : "48013-7"
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"valueCodeableConcept" : {
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"system" : "http://www.ncbi.nlm.nih.gov/refseq",
"code" : "NC_000016.9"
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"code" : {
"coding" : [
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"system" : "http://loinc.org",
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"valueString" : "C"
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"valueCodeableConcept" : {
"coding" : [
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"system" : "http://varnomen.hgvs.org",
"code" : "NC_000016.9:g.72992292C>T"
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{
"code" : {
"coding" : [
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"system" : "http://loinc.org",
"code" : "48002-0"
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]
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"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA6684-0",
"display" : "Somatic"
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},
{
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "81258-6"
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]
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"valueQuantity" : {
"value" : 0.1,
"unit" : "decimal",
"system" : "http://unitsofmeasure.org"
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}
]
}
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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