Clinical Genomics Resource Incubator
0.1.0-ci-build - CI Build International flag

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

CodeSystem: Coordinate System Normalization Method CodeSystem (Experimental)

Official URL: http://hl7.org/fhir/uv/cg-incubator/CodeSystem/coordinatesystem-normalizationmethod Version: 0.1.0-ci-build
Standards status: Informative Draft as of 2026-03-13 Maturity Level: 0 Computable Name: CoordinateSystemNormalizationMethod
Other Identifiers: OID:2.16.840.1.113883.4.642.4.3005

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.

This Code system is referenced in the definition of the following value sets:

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

Profile: Shareable CodeSystem

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

CodeDisplayDefinition
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.

Description of the above table(s).