Short/branched-chain acyl-CoA dehydrogenase deficiency, also known as 2-methylbutyrylglycinuria, is a rare autosomal recessive metabolic disorder affecting the catabolism of L-isoleucine. Early detection through newborn screening programs using tandem mass spectrometry enables timely diagnosis and intervention, potentially preventing severe clinical outcomes. In this study, we report a case identified through Iran's national newborn screening program, presenting with elevated C5-acylcarnitine levels. Whole exome sequencing revealed compound heterozygosity for two ACADSB gene variants: c.908G>C and c.1159G>A. While c.1159G>A is classified as pathogenic, c.908G>C was previously considered a variant of uncertain significance. However, the observed biochemical phenotype and in silico analysis support reclassification of c.908G>C as likely pathogenic. This case highlights the importance of integrating genotype–phenotype correlation and advanced genomic tools to refine variant interpretation and improve diagnostic accuracy in rare metabolic disorders.