<status value="draft"/> <experimental value="true"/> <date value="2026-03-13"/> <publisher value="HL7 International / Clinical Genomics"/> <contact> <name value="HL7 International / Clinical Genomics"/> <telecom> <system value="url"/> <value value="http://www.hl7.org/Special/committees/clingenomics"/> </telecom> <telecom> <system value="email"/> <value value="clingenomics@lists.hl7.org"/> </telecom> </contact> <description value="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."/> <jurisdiction> <coding> <system value="http://unstats.un.org/unsd/methods/m49/m49.htm"/> <code value="001"/> <display value="World"/> </coding> </jurisdiction> <caseSensitive value="true"/> <valueSet value="http://hl7.org/fhir/uv/cg-incubator/ValueSet/coordinatesystem-normalizationmethod"/> <content value="complete"/> <concept> <code value="left-shift"/> <display value="Left Shift"/> <definition value="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."/> </concept> <concept> <code value="right-shift"/> <display value="Right Shift"/> <definition value="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."/> </concept> <concept> <code value="fully-justified"/> <display value="Fully Justified"/> <definition value="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."/> </concept> <concept> <code value="no-normalization"/> <display value="No Normalization"/> <definition value="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."/> </concept> </CodeSystem>

Generated Narrative: CodeSystem coordinatesystem-normalizationmethod

Last updated: 2026-03-13 00:00:00+0000

This case-sensitive code system http://hl7.org/fhir/uv/cg-incubator/CodeSystem/coordinatesystem-normalizationmethod defines the following codes:

Code	Display	Definition
left-shift	Left Shift	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.
right-shift	Right Shift	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.
fully-justified	Fully Justified	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.
no-normalization	No Normalization	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.