If your project is research only and not for commercial gain, then use ANNOVAR.
I recommend that you devote time to learning how to use ANNOVAR because the developer constantly updates it and acts rapidly on any bugs that are found. Following the Quick Start-up Guide is probably the best place to go first.
Variant effect predictor (VEP)
Another option is Ensembl's Variant Effect Predictor (VEP). I mainly like VEP because it provides consequemces and predictions over all known transcript isoforms, which is useful when you are doing such an analysis. Of much benefit to you with only 2 variants, VEP has an Online Tool that you can use without the requirement to install anything locally.