open-cravat can handle unlimited number of variants. It can consume VCF format input files and produce tab-separated text output files as well as excel spreadsheets. It has visualization components which is still being polished but its command-line portion is quite solid. It is modular and open-source, and it is easy to write input and output format converters and custom report generators (you write only minimum specific parts since heavy lifting is done by open-cravat) or any annotation module for that matter. You can publish your converters, report generators, annotation modules, gene mappers, and etc with one command to cravat store for other people to install and use with one command or one click. It is Python based and installed with pip. Disclosure: I am the lead architect of open-cravat.
Sorry, I just now noticed that the question was from years ago.