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The Philadelphia chromosome is the hallmark of chronic myeloid leukemia. However, it may also be associated with acute lymphoblastic leukemia and acute myeloblastic leukemia. The common<jats:italic>BCR-ABL1<\/jats:italic>transcripts seen in acute lymphoblastic leukemia are e1a2, e13a2, and e14a2, while other transcripts such as e1a3, e13a3, and e6a2 occur rarely. This report describes the presentation, management, and outcome of the occurrence of B-cell acute lymphoblastic leukemia with the rare e1a3<jats:italic>BCR-ABL1<\/jats:italic>transcript in a patient with sickle cell anemia.<\/jats:p><\/jats:sec><jats:sec><jats:title>Case presentation<\/jats:title><jats:p>A 19-year-old male Nigerian, a known sickle cell anemia patient was admitted on account of severe vaso-occlusive crisis. Examination revealed fever, palor, and jaundice. Full blood count showed anemia and leukocytosis. Peripheral blood and bone marrow smears revealed numerous large and small lymphoblasts in keeping with the L2 subtype of acute lymphoblastic leukemia based on the French\u2013American\u2013British classification. Further evaluation was in keeping with a diagnosis of<jats:italic>BCR-ABL1<\/jats:italic>-positive mature B-cell acute lymphoblastic leukemia associated with the rare e1a3 transcript. He was commenced simultaneously on induction chemotherapy and Imatinib while being prepared for allogeneic stem cell transplantation. However, he died \u00a0six \u00a0months after diagnosis from meningoencephalitis.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>The occurrence of acute lymphoblastic leukemia with a rare<jats:italic>BCR-ABL1<\/jats:italic>e1a3 transcript in association with sickle cell anemia is uncommon and associated with poor prognosis.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s13256-021-03060-5","type":"journal-article","created":{"date-parts":[[2021,10,10]],"date-time":"2021-10-10T07:10:46Z","timestamp":1633849846000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Philadelphia chromosome-positive B-cell acute lymphoblastic leukemia with e1a3 BCR-ABL1 transcript in a Nigerian with sickle cell anemia: a case report"],"prefix":"10.1186","volume":"15","author":[{"given":"Ibrahim O.","family":"Ahmed","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lauretta O.","family":"Ochogwu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3977-2326","authenticated-orcid":false,"given":"Temilola O.","family":"Owojuyigbe","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Norah O.","family":"Akinola","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Muheez A.","family":"Durosinmi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2021,10,8]]},"reference":[{"key":"3060_CR1","unstructured":"World Health Organization. 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