Version 2.73

92822-6Genomic coordinate system [Type]Active

Term Description

A genomic coordinate is a position along a sequence. Coordinate systems can start counting from:

0-based interval counting
- Used by: GA4GH API, ClinGen data model, BED & BAM files, UCSC files, HLM 1.0 and NCBI's SPDI conversion format
- Akin to cursor positioning in modern text editors with cursor between characters
- A bit unnatural for humans, easier for computers
- Sequences have an inclusive start and exclusive end
- Insertions always go in the interval between characters

0-based character counting
- Used by: Genbank database & ASN files
- Sequences have an inclusive start, exclusive end
- Length = end - start
- A bit unnatural for human reading, easier for computers
- Sequences have an inclusive start and inclusive end
- Insertions not defined because GenBank and ASN do not model insertions to records they contain (historically ASN did internal to NCBI). SPDI was developed in part because of this inability to model insertions.

1-based character counting
- Used by: HGVS, VCF, NCBI's ClinVar (uses HGVS), Genbank files, IPD-IMGT/HLA, UCSC genome browser (note different from UCSC file, which uses 0-based interval counting)
- Akin to approach used in the earliest text processors
- Length = (end - start) + 1
- Sequences have inclusive start and inclusive end
- More natural for humans
- Insertions. Be careful in theory for 1-base, the insertion location could be defined in three ways: a) before position, b) after position, c) specify the di-nucleotide which where the insertion goes; but in practice there is only one way to do it per coordinate type.

Distinctions for describing sub sequences with the three approaches with examples
Consider ACGTAGTC as an example string and what nucleotides would be in the range 2-4
- 0-based interval counting (e.g..SPDI): GT
- 0-based character counting (i.e. GenBank): GTA
- 1-based character counting (i.e. VCF): CGT

Distinctions regarding insertions with examples. Insertions can be tricky with character counting.
Now consider that you want to describe an insertion between T&A (4th and 5th characters in the example string):
- 0-based interval counting (i.e. SPDI) insert at position 4.
- 0-based character counting. Insert between 3&4. Note: insertions are not supported in GenBank's model.
- 1-based character counting. Insert between 4&5. Note: HGVS requires specification of the dinucleotide between which the insertion goes. For VCF, this would be represented as insert after 4 and does not require other information but the result is the same.
Source: Regenstrief LOINC

Fully-Specified Name

Genomic coordinate system

Additional Names

Short Name
Genomic coord system
Display Name
Genomic coordinate system Molgen Nom (Specimen)
Consumer Name Alpha
Genomic coordinate system, Specimen

Preferred Answer List LL5323-2

Source: National Library of Medicine

Answer Code Score Answer ID
0-based interval counting LA30100-4
0-based character counting LA30101-2
1-based character counting LA30102-0

Basic Attributes

First Released
Version 2.66
Last Updated
Version 2.72
Order vs. Observation

Language Variants Get Info

zh-CNChinese (China)
fr-FRFrench (France)
System de coordination génomique:Type:Ponctuel:Milieux divers:Résultat nominal:Biologie moléculaire
it-ITItalian (Italy)
Coordinate genomiche, sistema:Tipo:Pt:XXX:Nom:Molgen
es-MXSpanish (Mexico)
Sistema de coordenadas genómicas:Tipo:Punto temporal:XXX:Nominal:Genética molecular
es-ESSpanish (Spain)
Sistema de coordenadas genómicas:Tipo:Punto temporal:XXX:Nom:Genética molecular

LOINC FHIR® API Example - CodeSystem Request Get Info