Every one has been very helpful in answering my questions. Here i have one more.
I would like to know from detection of a variant in the vcf file , what are the steps to finally classify it as pathogenic or variant of unknown significance.(VUS).
What i am doing so far is filtering the genes based on read depth (>10), those that fit in heterozygous or homozygous category, gnomad frequency <1%., and phenotype match. After getting the short listed variants I will match the variant location on chromosome with the specific NM_ no. (transcript number). After that i will search that NM_ number in the literature to search if it is associated with disease or not. As i believe there are steps that I am missing like type of mutation, synonymous or non synonymous mutation etc Can some please tell me how to go about these steps after variant detection in vcf file. Also which databases I could use to get this extra information that i am missing.