Table 5. Function codes for refSNPs in gene features. a
| Functional class | Description | Database code |
|---|---|---|
| Locus region | Variation is within 2 Kb 5′ or 500 bp 3′ of a gene feature (on either strand), but the variation is not in the transcript for the gene. This class is indicated with an “L” in graphical summaries. As of build 127, function code 1 has been modified into a two digit code that will more precisely indicate the location of a SNP. The two digit code has function code 1as the first digit, which will keep the meaning as described above, and 3 or 5 as the second digit, which will indicate whether the SNP is 3’ or 5’ to the region of interest. See function codes 13 and 15 in this table. | 1 |
| Coding | Variation is in the coding region of the gene. This class is assigned if the allele-specific class is unknown. This class is indicated with a C in graphical summaries. This code was retired as of dbSNP build 127. | 2 |
| Coding-synon | The variation allele is synonymous with the contig codon in a gene. An allele receives this class when substitution and translation of the allele into the codon makes no change to the amino acid specified by the reference sequence. A variation is a synonymous substitution if all alleles are classified as contig reference or coding-synon. This class is indicated with a C in graphical summaries. | 3 |
| Coding-nonsynon | The variation allele is nonsynonymous for the contig codon in a gene. An allele receives this class when substitution and translation of the allele into the codon changes the amino acid specified by the reference sequence. A variation is a nonsynonymous substitution if any alleles are classified as coding-nonsynon. This class is indicated with a C or N in graphical summaries. As of build 128, function code 4 has been modified into a two digit code that will more precisely indicate the nonsynonymous nature of the SNP. The two digit code has function code 4 as the first digit, which will keep its original meaning, and 1, 2, or 4 as the second digit, which will indicate whether the SNP is nonsense, missense, or frameshift. See function codes 41, 42, and 44 in this table | 4 |
| mRNA-UTR | The variation is in the transcript of a gene but not in the coding region of the transcript. This class is indicated by a “T” in graphical summaries. As of build 127, function code 5 has been modified into a two digit code that will more precisely indicate the location of a SNP. The two digit code has function code 5 as the first digit, which will keep its original meaning, and 3 or 5 as the second digit, which will indicate whether the SNP is 3’ or 5’ to the region of interest. See function codes 53 and 55 in this table. | 5 |
| Intron | The variation is in the intron of a gene but not in the first two or last two bases of the intron. This class is indicated by an L in graphical summaries. | 6 |
| Splice-site | The variation is in the first two or last two bases of the intron. This class is indicated by a “T” in graphical summaries. As of build 127, function code 7 has been modified into a two digit code that will more precisely indicate the location of a SNP. The two digit code has function codes 7 as the first digit, which will keep its original meaning, and 3 or 5 as the second digit, which will indicate whether the SNP is 3’ or 5’ to the region of interest. See function codes 73 and 75 in this table. | 7 |
| Contig-reference | The variation allele is identical to the contig nucleotide. Typically, one allele of a variation is the same as the reference genome. The letter used to indicate the variation is a C or N, depending on the state of the alternative allele for the variation. | 8 |
| Coding-exception | The variation is in the coding region of a gene, but the precise location cannot be resolved because of an error in the alignment of the exon. The class is indicated by a C in graphical summaries. | 9 |
| NearGene–3 | Function Code 13, where: 1=locus region (see function code 1 in this table) 3=SNP is 3’to and 0.5kb away from gene | 13 |
| NearGene–5 | Function Code 15, where: 1=locus region (see function code 1 in this table) 5= SNP is 5’ to 2kb away from gene | 15 |
| Coding-nonsynonymous nonsense | Function Code 41, where: 4 =Coding- nonsynonymous (see function code 4 in this table) 1 = Nonsense (changes to the Stop codon) | 41 |
| Coding-nonsynonymous missense | Function Code 42, where: 4 =Coding- nonsynonymous (see function code 4 in this table) 2 = missense (alters codon to make an altered amino acid in protein product) | 42 |
| Coding-nonsynonymous frameshift | Function Code 44, where: 4 =Coding- nonsynonymous (see function code 4 in this table) 4 = frameshift (alters codon to make an altered amino acid in protein product) | 44 |
| UTR–3 | Function code 53, where: 5= UTR (untranslated region: see function code 5 in this table) 3= SNP located in the 3’ untranslated region | 53 |
| UTR–5 | Function code 55, where: 5= UTR (untranslated region: see function code 5 in this table) 5(as the second digit)= SNP located in the 5’ untranslated region | 55 |
| Splice–3 | Function code 73, where: 7=splice site (see function code 7 in this table) 3=3’ acceptor dinucleotide | 73 |
| Splice–5 | Function code 75, where: 7=splice site (see function code 7 in this table) 5=5’ donor dinucleotide | 75 |
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: Chapter 5, The Single Nucleotide Polymorphism Database (dbSNP) of Nucleotide Sequence Variation
NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health.