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

CodeSystem: Coordinate System Origin CodeSystem (Experimental)

Official URL: http://hl7.org/fhir/uv/cg-incubator/CodeSystem/coordinatesystem-origin Version: 0.1.0-ci-build
Standards status: Informative Draft as of 2026-03-13 Maturity Level: 0 Computable Name: CoordinateSystemOrigin
Other Identifiers: OID:2.16.840.1.113883.4.642.4.3004

The reference landmark (origin) from which coordinates are measured in a coordinateInterval. This identifies the conceptual anchor point on the molecule where numbering begins, independent of whether numbering is 0-based or 1-based (which is captured in coordinateSystem.system). 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-origin defines the following codes:

CodeDisplayDefinition
sequence-start Sequence Start Coordinates are measured from the start of the molecule: the 5' end of a nucleotide sequence or the N-terminus of a polypeptide. This is the default for genomic, chromosomal, and transcript-level coordinate systems (e.g., NC_ or NG_ accession-based positions).
cds-start CDS Start (A of ATG) Coordinates are measured from the adenine of the translation initiation codon (A of ATG = position 1, or 0 in 0-based systems). This is the origin used by the HGVS coding DNA reference sequence (c. prefix). Positions upstream of the ATG are negative (5' UTR); positions downstream of the stop codon are marked with an asterisk (3' UTR).
feature-start Feature Start Coordinates are measured from the start of a named genomic feature, such as the first base of an exon. This is used for HGVS exon-relative or feature-relative position expressions.
feature-end Feature End Coordinates are measured from the end of a named genomic feature, such as the last base of an exon. A positive offset extends into the downstream intron; a negative offset extends upstream into the exon. This origin is used for HGVS intronic positions (e.g., c.100+3, where 100 is the last coding base and +3 is the offset into the intron).

Description of the above table(s).