A system for managing a CNV reference panel is disclosed, wherein the system includes a database arrangement configured to store a plurality of sample genomic DNA sequences and metadata associated with each of plurality of sample genomic DNA sequences. The system further includes a computing arrangement communicatively coupled to the database arrangement. The computing arrangement is configured to render a user interface to receive a target genomic DNA sequence along with interpretation request for calling CNVs in target genomic DNA sequence. The computing arrangement compares the plurality of characteristic attributes in the interpretation request with the metadata associated with each of plurality of sample genomic DNA sequences. Furthermore, the computing arrangement identifies a set of sample genomic DNA sequences as a reference panel, based on the comparison. Moreover, the computing arrangement utilise the reference panel for calling CNVs in the target genomic DNA sequence.