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Source1

{
  "resourceType": "CodeSystem",
  "id": "coordinatesystem-normalizationmethod",
  "meta": {
    "lastUpdated": "2026-03-13T00:00:00Z",
    "profile": [
      "http://hl7.org/fhir/StructureDefinition/shareablecodesystem"
    ]
  },
  "text": {
    "status": "generated",
    "div": "<!-- snip (see above) -->"
  },
  "extension": [
    {
      "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg",
      "valueCode": "cg"
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status",
      "valueCode": "informative"
    },
    {
      "url": "http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm",
      "valueInteger": 0
    }
  ],
  "url": "http://hl7.org/fhir/uv/cg-incubator/CodeSystem/coordinatesystem-normalizationmethod",
  "identifier": [
    {
      "system": "urn:ietf:rfc:3986",
      "value": "urn:oid:2.16.840.1.113883.4.642.4.3005"
    }
  ],
  "version": "0.1.0-ci-build",
  "name": "CoordinateSystemNormalizationMethod",
  "title": "Coordinate System Normalization Method CodeSystem",
  "status": "draft",
  "experimental": true,
  "date": "2026-03-13",
  "publisher": "HL7 International / Clinical Genomics",
  "contact": [
    {
      "name": "HL7 International / Clinical Genomics",
      "telecom": [
        {
          "system": "url",
          "value": "http://www.hl7.org/Special/committees/clingenomics"
        },
        {
          "system": "email",
          "value": "clingenomics@lists.hl7.org"
        }
      ]
    }
  ],
  "description": "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": "http://unstats.un.org/unsd/methods/m49/m49.htm",
          "code": "001",
          "display": "World"
        }
      ]
    }
  ],
  "caseSensitive": true,
  "valueSet": "http://hl7.org/fhir/uv/cg-incubator/ValueSet/coordinatesystem-normalizationmethod",
  "content": "complete",
  "concept": [
    {
      "code": "left-shift",
      "display": "Left Shift",
      "definition": "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."
    },
    {
      "code": "right-shift",
      "display": "Right Shift",
      "definition": "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."
    },
    {
      "code": "fully-justified",
      "display": "Fully Justified",
      "definition": "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."
    },
    {
      "code": "no-normalization",
      "display": "No Normalization",
      "definition": "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."
    }
  ]
}