The data aren't that hard, really, as far as I can tell:
You got genetic abberations: Deletions, Inserts, with and without frameshift, duplications or higher copy numbers, translocations on the DNA level. All this is at a location, which is within a gene, wich is coding or not. You have expression on the mRNA level. All those have a likelihood, but usally they get called: a threshold gets applied, turning into a binary yes or no (at which point the abberation disappears from the data.
That's about it.
The vocabulary has to know about the genes the abberation or variant is either in, or is affecting. And, if it is good, also the pathway or network information. But that's a nice to have.
There is a standard to report the DNA-level abberations: VCF. There are also standards to report the actual sequence and mRNA-level changes, which are much simpler.
What do you exactly need?