VARIANT effect retrieving

Question

[cocchi.e89]

Dear all, I am working on a database of several patients with relative variants (SNV and INDELS basically) VCF files. I know I can check for variant effect against VEP DB or similar, but for variants that are absent in such databases, how can I possibly categorize them in effect result? (e.g. missense vs nonsense etc)

Thanks a lot in advance for any help!