This thesis presents the case report of a phenotypically male dizygotic twin with congenital dysmorphology and developmental delay. His clinical features involve the following systems: head and neck, skeletal, limbs, skin and nails, and, possibly, central nervous system. In comparison, his twin sister had only mild motor delay and no known dysmorphology. A chromosome microarray revealed an incidental finding of either sex chromosome chimerism or mosaicism with no explanation for the proband’s phenotype. This case highlights the situation where the clinical presentation of the proband does not align with a known syndrome. In addition, the presence of two cell lines in the proband requires a customized, family-based approach to DNA sequencing to detect both lines. Therefore, a customized quartet-plus wholeexome-sequencing (WES) study was designed through the University of Arizona’s Genetics Core facility. The results of the WES revealed a variant in the SF3B4 gene in the proband consistent with a diagnosis of Nager syndrome. Chimerism due to the presence of his twin sister’s genome in both of the proband’s samples (blood and buccal swab) was also confirmed. Lastly, as the proband’s mother had reported a family history of cancer and a familial variant in BRCA1, WES revealed no clinically significant secondary findings indicating that she was negative for known pathogenic variants in this gene. The complexities of the case, including WES methodology and secondary findings are discussed. This case brings up multiple genetic counseling issues including the need for proper pre- and post-test counseling and implications of chimerism. It also highlights the importance of identifying chimerism and the need for further research in this area