Real time-polymerase chain reaction (RT-PCR) is used routinely in clinical practice as a cost-effective method for molecular diagnostics. Research in pediatric B-cell Acute Lymphoblastic Leukemia (ped B-ALL) suggests that apart from cytogenetics and clinical features, there is a need to include Copy number variation (CNV) in select genes at diagnosis, for upfront stratification of patients. Using ped B-ALL as a model, we have developed a RT-PCR-based iterative probability scoring method for reporting CNVs, and relative gene-expression changes. Our work highlights that once genes of interest and hotspots of CNVs are identified in discovery phase, our proposed method can be used as a cost-effective and user-friendly diagnostic tool for the identification of changes at genomic or transcriptomic level. It has the potential to be incorporated in routine diagnostics in resource constrained settings and be tailored for different diseases as per need.