Variation class organizes submissions by allele definition
Note: dbSNP has an allele length limitation of <=50bp. Submit alleles >50 nucleotides in length to the Database of Genomic Structural Variation (dbVAR).
| Variation Class a, b | Allele Class Assignment Rules |
Sample Allele
Definition | Class Codec |
|---|---|---|---|
| Single Nucleotide Variation (SNV) a | Single base substitutions involving A, T, C, or G. | A/G | 1 |
| Deletion/Insertion Variations (DIVs)a | Designated by the full sequence of the insertion as one allele, and either a fully defined string for the variant allele or a “-” character to specify the deleted allele. This class will be assigned to a variation if the variation alleles are of different lengths or if one of the alleles is deleted (“-”). | -/AA/CCT/GCC/GCCTG ss149071 | 2 |
| Heterozygousa | The term heterozygous is used to specify a region detected by certain methods that do not resolve the variation into a specific sequence motif. In these cases, a unique flanking sequence must be provided to define a sequence context for the variation. | (heterozygous) | 3 |
| Microsatellite or short tandem repeat (STR)a | Alleles are designated by providing the repeat motif and the copy number for each allele. Expansion of the allele repeat motif designated in dbSNP into full-length sequence will be only an approximation of the true genomic sequence because many microsatellite markers are not fully sequenced and are resolved as size variants only. | (CAC)8/9/10/11 | 4 |
| Nameda | Applies to insertion/deletion variants of longer sequence features, such as retroposon dimorphism for Alu or line elements. These variations frequently include a deletion “-” indicator for the absent allele. Observed field starts with '(', but is not class 3 or 4 | (alu) / - | 5 |
| NoVariationa | Reports may be submitted for segments of sequence that are assayed and determined to be invariant in the sample. | (NoVariation) | 6 |
| Mixedb | The refSNP cluster contains submissions from 2 or more allelic classes | Mix of allelic classes | 7 |
| Multi-Nucleotide Variation (MNV)a | Multi-base variations of a single, common length. | AT/GA ss2421179 | 8 |
| Exception | The submitted variation needs to be checked | The submitted variation does not contain “/” to indicate presence of variant. | 9 |
a) Seven of the classes apply to both submissions of variations (submitted SNP assay, or ss#) and the non-redundant refSNP clusters (rs#'s) created in dbSNP. b) The “Mixed” class is assigned to refSNP clusters that group submissions from different variation classes. c) Class codes have a numeric representation in the database itself and in the export versions of the data (VCF and XML).
From: The Database of Short Genetic Variation (dbSNP)
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