Based on a WGS and deep targeted sequencing approach, this study identified recurrent pathogenic somatic variants in the genes ABL1, RUNX1 and ASXL1 driving blast‐phase transformation as well as a high number of ACAs (e.g. high‐risk ACA, small and large CNVs) underlining an increased genomic instability in paediatric CML‐BP. The gene discussed is RUNX1; the disease is chronic myelogenous leukemia, BCR-ABL1 positive.