splicevardb-hg38

splicevardb-hg38 0.0.1

SpliceVarDB is a comprehensive online database consolidating over 50,000 experimentally validated human splicing variants across more than 8,000 genes. Designed to address the challenge of predicting splice-altering variants, which account for up to a third of disease-causing mutations, it standardizes data from over 500 published sources using a spliceogenicity scale. With 55% of its splice-altering variants located outside canonical splice sites, SpliceVarDB supports diagnostic variant curation and enhances the development of accurate in silico splicing predictors. Accessible at https://splicevardb.org, it offers visualization, variant details, and validation metrics to streamline genetic research and reduce redundant validation efforts.

Below instruction from hgTables:

According to the strength of their supporting evidence, variants were classified as "splice-altering" (~25%), "not splice-altering" (~25%), and "low-frequency splice-altering" (~50%), which correspond to weak or indeterminate evidence of spliceogenicity. 55% of the splice-altering variants in SpliceVarDB are outside the canonical splice sites (5.6% are deep intronic). The data is shown as lollipop plots that can be clicked, the details page then shows a link to SpliceVarDB with full details.

The classification thresholds primarily follow those established by the original study. However, most studies only defined criteria for splice-altering variants and did not define criteria for variants that resulted in normal splicing. The authors implemented stringent thresholds to define the normal category and ensure a high-quality set of control variants. Variants that did not meet these criteria were classified as low-frequency splice-altering variants with a wide range of sub-optimal scores. Variants that fell between the normal and splice-altering classifications were placed into a low-frequency splice-altering category. In situations where a variant was validated multiple times, if at least one validation returned splice-altering and another returned normal, the "conflicting" category was applied.

The lollipop plots are color-coded based on the score value, which corresponds to the following classifications:

3 - Splice-altering
2 - Low-frequency
1 - Normal
0 - Conflicting