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Background  Leukemia is different from solid tumor by harboring genetic rearrangements that predict prognosis and guide treatment strategy.  PML-RARA ,  RUNX1-RUNX1T1 , and  KMT2A -rearrangement are common genetic rearrangements that drive the development of acute myeloid leukemia (AML). By contrast, rare genetic rearrangements may also contribute to leukemogenesis but are less summarized.    Case presentation  Here we reported rare fusion genes  ZNF717-ZNF37A ,  ZNF273-DGKA , and  ZDHHC2-TTTY15  in a 47-year-old AML-M4 patient with FLT3 internal tandem duplication (ITD) discovered by whole genome sequencing (WGS) using the patient’s healthy sibling as a sequencing control.    Conclusion  This is, to our knowledge, the first case of AML with fusion gene  ZNF717-ZNF37A ,  ZNF273-DGKA , and  ZDHHC2-TTTY15 .    Electronic supplementary material  The online version of this article (10.1186/s12885-018-4396-4) contains supplementary material, which is available to authorized users.

First case of AML with rare chromosome translocations: a case report of twins