Hi,

If you need to predict the effect of an SNP in clinical setting, you can follow the ACMG (American College of Medical Genetics and Genomics) Standards and guidelines https://www.acmg.net/docs/Standards_Guidelines_for_the_Interpretation_of_Sequence_Variants.pdf , in which you may find the classification criteria for your variants. You can look onto tools based on it's category (like missense, splice-site etc) and refer to population, disease specific and sequence databases.