Abstract: Diagnosis of rare human diseases using DNA sequencing is a fast growing area of research. Conventional methods carries a risk of incorrect phenotype interpretation. However, obtaining a correct genotype and phenotype matching is challenging. A system for matching phenotype descriptions and pathogenic variants provides a one to one mapping of the phenotype and genotypes of a plurality of subjects under test. Initially, a plurality of phenotypes and a plurality of genome sequences are segmented based on metadata. A phenotype driven gene prioritization and a variant prioritization is applied on the segmented data method. A similarity score is calculated between the phenotype driven gene prioritization output and the variant prioritization output. The similarity score is further utilized to obtain a one to one matching of the plurality of phenotypes and the plurality of genotype sequences of the plurality of subjects under test.