Annotation of genomic variants

Question

[onemoreuser]

Hi, I have a TAB file containing somatic and germline variants from RNA sequencing data. Using tools like: VEP, ANNOVAR or SNPEff, I can annotate the variants but these tools predict the impact variant by variant. They don't consider that different variants interact with each other and one can compensate the other.

Are there tools that predict the impact of variants considering the impact of several variants and not just one on the gene/transcript?

Right now the only tool that I know that predicts something like this is CooVar: Co-occurring variant analyzer. But is there more tools/softwares?

Thanks