Molecular codes for refSNPs in gene features
| Functional class | Definition/Example | dbSNP code | Sequence Ontology Code (term definition) |
|---|---|---|---|
| cds-synon | Synonymous change. Example: rs248, GAG->GAA, both produce amino acid: Glu | 3 |
SO |
| intron | Example: rs249 | 6 |
SO |
| cds-reference | Contig reference | 8 | |
| synonymy unknown | Coding: synonymy unknown. Not used since 2003 | 9 | |
| nearGene-3 | Within 3' 0.5kb to a gene. Example:rs3916027 is at NT_030737.9 pos7669796, within 500 bp of UTR starts 7669698 for NM_000237.2 | 13 |
SO |
| nearGene-5 | Within 5' 2kb to a gene. Example: rs7641128 is at NT_030737.9 pos7641128, with 2K bp of UTR starts 7641510 for NM_000237.2 | 15 |
SO |
| intergenic | Variant between two genes, outside of 2Kb upstream and 500bp downstream of a gene | 20 |
SO |
| ncRNA | Variant on non-coding RNA(NCBI Refseq prefix NR,XR) | 30 |
SO |
| STOP-GAIN | Changes to STOP codon. Example: rs328, TCA->TGA, Ser to terminator | 41 |
SO |
| missense | Alters codon to make an altered amino acid in protein product. Example: rs300, ACT->GCT, Thr->Ala | 42 |
SO |
| STOP-LOSS | Changes STOP codon to other non stop codon | 43 |
SO |
| frameshift | Indel snp causing frameshift | 44 |
SO |
| cds-indel | Indel snp with length of multiple of 3bp, not causing frameshift | 45 |
SO |
| UTR-3 | 3 prime untranslated region. Example: rs3289 | 53 |
SO |
| UTR-5 | 5 prime untranslated region. Example: rs1800590 | 55 |
SO |
| splice-3 | 3 prime acceptor dinucleotide. The last two bases in the 3 prime end of an intron. Most intron ends with AG. Example: rs193227 is in acceptor site. | 73 |
SO |
| splice-5 | 5 prime donor dinucleotide. 1st two bases in the 5 prime end of the intron. Most intron starts is GU. Example: rs8424 is in donor site. | 75 |
SO |
Most gene features are defined by the location of the variation with respect to transcript exon boundaries. Variations in coding regions, however, have a functional class assigned to each allele for the variation because these classes depend on allele sequence.
From: The Database of Short Genetic Variation (dbSNP)
NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health.