Clinical Genomics Resource Incubator
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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

ValueSet: Coordinate System Normalization Method ValueSet (Experimental)

Official URL: http://hl7.org/fhir/uv/cg-incubator/ValueSet/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:2.16.840.1.113883.4.642.3.3005

The normalization method applied when placing a variant within a repetitive sequence region. The binding is extensible to allow new alignment conventions as they emerge.

References

Logical Definition (CLD)

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

Profile: Shareable ValueSet

 

Expansion

Expansion performed internally based on codesystem Coordinate System Normalization Method CodeSystem v0.1.0-ci-build (CodeSystem)

This value set contains 4 concepts

SystemCodeDisplay (en)DefinitionJSONXML
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/coordinatesystem-normalizationmethod  left-shiftLeft ShiftThe 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.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/coordinatesystem-normalizationmethod  right-shiftRight ShiftThe 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.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/coordinatesystem-normalizationmethod  fully-justifiedFully JustifiedThe 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.
http://hl7.org/fhir/uv/cg-incubator/CodeSystem/coordinatesystem-normalizationmethod  no-normalizationNo NormalizationNo 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).