Fanconi anemia (FA) is the most common inherited bone marrow failure syndrome with 22 FA-related genes identified to date. Fragment deletions are frequently occurring aberrances accounting for ~30% of pathogenic variants in them, especially in FANCA, most of which are the results of genomic rearrangement events mediated by the highly concentrated Alu elements interspersing in it. Owing to the capability to detect genome-wide copy number variations (CNVs) with the resolution of 400 kb or larger, cytogenomic microarray is the most widely used method in the clinic currently. However, thereis still a technical gap in the detection of CNVs ranging from hundreds of bp to hundreds of kb between microarray, Sanger sequencing, and direct targeted high-throughput sequencing (THS). Here, we report the analysis of overlapping heterozygous novel submicroscopic deletions of FANCA gene in a FA patient, and discuss the mechanism of the deletions and the formation of FANCA-VPS9D1 fusion transcripts. Our results support that both low-coverage whole-genome sequencing and bioinformatics analysis of THS data for submicroscopic CNVs surpass SNP array in efficacy and accuracy.