Abstract: The present disclosure is generally relates to technique for scoring variants to evaluate an effect of the variants on gene function. The present system and method assigns scores for the plurality of variants that are occurred in a particular transcript corresponding to a protein coding gene comprised in the exome. The plurality of variants including the synonymous variants, the non-synonymous variants, the frameshift indels and the non-frameshift indels, the variants that spans into a coding exonic intronic boundary region, and the splice site variants, considering an interplay between a pair of alleles in order to understand as to what extent the variant may impact the gene, based on number of risk alleles present in the gene. The final score of the variant indicate probable effect of the variant, higher the score more will be the effect of the variant on gene.