Clinical Genomics Resource Incubator, published by HL7 International / Clinical Genomics. This guide is not an authorized publication; it is the continuous build for version 0.1.0-ci-build built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/cg-incubator/ and changes regularly. See the Directory of published versions
: Coordinate System Normalization Method CodeSystem
Raw ttl | Download
@prefix fhir: <http://hl7.org/fhir/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
# - resource -------------------------------------------------------------------
a fhir:CodeSystem ;
fhir:nodeRole fhir:treeRoot ;
fhir:id [ fhir:v "coordinatesystem-normalizationmethod"] ; #
fhir:meta [
fhir:lastUpdated [ fhir:v "2026-03-13T00:00:00Z"^^xsd:dateTime ] ;
( fhir:profile [
fhir:v "http://hl7.org/fhir/StructureDefinition/shareablecodesystem"^^xsd:anyURI ;
fhir:l <http://hl7.org/fhir/StructureDefinition/shareablecodesystem> ] )
] ; #
fhir:language [ fhir:v "en"] ; #
fhir:text [
fhir:status [ fhir:v "generated" ] ;
fhir:div [ fhir:v "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: CodeSystem coordinatesystem-normalizationmethod</b></p><a name=\"coordinatesystem-normalizationmethod\"> </a><a name=\"hccoordinatesystem-normalizationmethod\"> </a><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\">Last updated: 2026-03-13 00:00:00+0000</p><p style=\"margin-bottom: 0px\">Profile: <a href=\"http://hl7.org/fhir/R5/shareablecodesystem.html\">Shareable CodeSystem</a></p></div><p>This case-sensitive code system <code>http://hl7.org/fhir/uv/cg-incubator/CodeSystem/coordinatesystem-normalizationmethod</code> defines the following codes:</p><table class=\"codes\"><tr><td style=\"white-space:nowrap\"><b>Code</b></td><td><b>Display</b></td><td><b>Definition</b></td></tr><tr><td style=\"white-space:nowrap\">left-shift<a name=\"coordinatesystem-normalizationmethod-left-shift\"> </a></td><td>Left Shift</td><td>The variant is placed at the 5'-most (left-most on the forward strand) equivalent position within a repetitive sequence region. This is the VCF convention. For example, a single-base deletion in a homopolymer run is placed at the first occurrence of the repeated base.</td></tr><tr><td style=\"white-space:nowrap\">right-shift<a name=\"coordinatesystem-normalizationmethod-right-shift\"> </a></td><td>Right Shift</td><td>The variant is placed at the 3'-most (right-most on the forward strand) equivalent position within a repetitive sequence region. This is the HGVS convention for duplications and insertions (3' rule). For example, a duplicated base is assigned to the most 3' position of the repeat unit.</td></tr><tr><td style=\"white-space:nowrap\">fully-justified<a name=\"coordinatesystem-normalizationmethod-fully-justified\"> </a></td><td>Fully Justified</td><td>The variant is normalized to span the full repeat unit affected, anchored at the first position of the repeat. This is the VOCA (Variant Overprecision Correction Algorithm) convention, also aligned with GA4GH normalization guidelines. Fully justified representations are unique for a given repeat context.</td></tr><tr><td style=\"white-space:nowrap\">no-normalization<a name=\"coordinatesystem-normalizationmethod-no-normalization\"> </a></td><td>No Normalization</td><td>No alignment shifting has been applied. The variant position is recorded exactly as reported by the originating system or caller, without adjustment for repetitive sequence context.</td></tr></table></div>"^^rdf:XMLLiteral ]
] ; #
fhir:extension ( [
fhir:url [
fhir:v "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg"^^xsd:anyURI ;
fhir:l <http://hl7.org/fhir/StructureDefinition/structuredefinition-wg> ] ;
fhir:value [
a fhir:Code ;
fhir:v "cg" ]
] [
fhir:url [
fhir:v "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status"^^xsd:anyURI ;
fhir:l <http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status> ] ;
fhir:value [
a fhir:Code ;
fhir:v "informative" ]
] [
fhir:url [
fhir:v "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm"^^xsd:anyURI ;
fhir:l <http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm> ] ;
fhir:value [
a fhir:Integer ;
fhir:v 0 ]
] ) ; #
fhir:url [
fhir:v "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/coordinatesystem-normalizationmethod"^^xsd:anyURI ;
fhir:l <http://hl7.org/fhir/uv/cg-incubator/CodeSystem/coordinatesystem-normalizationmethod>
] ; #
fhir:identifier ( [
fhir:system [
fhir:v "urn:ietf:rfc:3986"^^xsd:anyURI ;
fhir:l <urn:ietf:rfc:3986> ] ;
fhir:value [ fhir:v "urn:oid:2.16.840.1.113883.4.642.4.3005" ]
] ) ; #
fhir:version [ fhir:v "0.1.0-ci-build"] ; #
fhir:name [ fhir:v "CoordinateSystemNormalizationMethod"] ; #
fhir:title [ fhir:v "Coordinate System Normalization Method CodeSystem"] ; #
fhir:status [ fhir:v "draft"] ; #
fhir:experimental [ fhir:v true] ; #
fhir:date [ fhir:v "2026-03-13"^^xsd:date] ; #
fhir:publisher [ fhir:v "HL7 International / Clinical Genomics"] ; #
fhir:contact ( [
fhir:name [ fhir:v "HL7 International / Clinical Genomics" ] ;
( fhir:telecom [
fhir:system [ fhir:v "url" ] ;
fhir:value [ fhir:v "http://www.hl7.org/Special/committees/clingenomics" ] ] [
fhir:system [ fhir:v "email" ] ;
fhir:value [ fhir:v "clingenomics@lists.hl7.org" ] ] )
] ) ; #
fhir:description [ fhir:v "The normalization method applied when a variant can be placed at multiple equivalent positions within a repetitive sequence region. Different community standards (VCF, HGVS, VOCA/GA4GH) apply different alignment conventions, and recording which was used is necessary for lossless round-tripping of variant representations across systems. No external vocabulary covers this domain-specific concept, so it is defined here by the CG Working Group."] ; #
fhir:jurisdiction ( [
( fhir:coding [
fhir:system [
fhir:v "http://unstats.un.org/unsd/methods/m49/m49.htm"^^xsd:anyURI ;
fhir:l <http://unstats.un.org/unsd/methods/m49/m49.htm> ] ;
fhir:code [ fhir:v "001" ] ;
fhir:display [ fhir:v "World" ] ] )
] ) ; #
fhir:caseSensitive [ fhir:v true] ; #
fhir:valueSet [
fhir:v "http://hl7.org/fhir/uv/cg-incubator/ValueSet/coordinatesystem-normalizationmethod"^^xsd:anyURI ;
fhir:l <http://hl7.org/fhir/uv/cg-incubator/ValueSet/coordinatesystem-normalizationmethod>
] ; #
fhir:content [ fhir:v "complete"] ; #
fhir:concept ( [
fhir:code [ fhir:v "left-shift" ] ;
fhir:display [ fhir:v "Left Shift" ] ;
fhir:definition [ fhir:v "The variant is placed at the 5'-most (left-most on the forward strand) equivalent position within a repetitive sequence region. This is the VCF convention. For example, a single-base deletion in a homopolymer run is placed at the first occurrence of the repeated base." ]
] [
fhir:code [ fhir:v "right-shift" ] ;
fhir:display [ fhir:v "Right Shift" ] ;
fhir:definition [ fhir:v "The variant is placed at the 3'-most (right-most on the forward strand) equivalent position within a repetitive sequence region. This is the HGVS convention for duplications and insertions (3' rule). For example, a duplicated base is assigned to the most 3' position of the repeat unit." ]
] [
fhir:code [ fhir:v "fully-justified" ] ;
fhir:display [ fhir:v "Fully Justified" ] ;
fhir:definition [ fhir:v "The variant is normalized to span the full repeat unit affected, anchored at the first position of the repeat. This is the VOCA (Variant Overprecision Correction Algorithm) convention, also aligned with GA4GH normalization guidelines. Fully justified representations are unique for a given repeat context." ]
] [
fhir:code [ fhir:v "no-normalization" ] ;
fhir:display [ fhir:v "No Normalization" ] ;
fhir:definition [ fhir:v "No alignment shifting has been applied. The variant position is recorded exactly as reported by the originating system or caller, without adjustment for repetitive sequence context." ]
] ) . #
|
Propose a change