Intronic mutations can interact with the splicing process either by disrupting a wild type donor or acceptor splice sits but also a branch point. In addition, it can result in the creation of a new (cryptic) site that can be used in place of the wt site. (Note that an intronic mutation can also interacts with regulatory sequences).
The consensus value (CV) of splice sites is calculated with the UMD algorithm. A value >70 is associated with a potentially functional site. When a mutation affects a site both the CV of the mutant sequence and the variation of the CV (in comparison to the wt) should be taken into account. Usually, a variation of 10% or more is associated with a splice recognition alteration (*).
A color code allows a rapid interpretation of CVs: Strong splice site; Medium splice site; weak splice site and not a splice site.