The study shows that certain DNA changes inside the SMN1 gene can trick standard genetic tests into wrongly saying a person has two missing copies of the gene, which could lead to a misdiagnosis of spinal muscular atrophy. Using a different test (MLPA‑P021) or sequencing avoids this error.

Accurate genetic diagnosis is necessary for guiding the treatment of spinal muscular atrophy (SMA). An updated consensus for the diagnosis and management of SMA was published in 2018. However, clinicians should remain alert to some pitfalls of genetic testing that can occur when following a routine diagnosis. In this study, we report the diagnosis of three unrelated individuals who were initially misdiagnosed as carrying a homozygous deletion of <i>SMN1</i> exon 7. MLPA (P060 and P021) and qPCR were used to detect the copy number of <i>SMN</i>. <i>SMN1</i> variants were identified by <i>SMN1</i> clone and next-generation sequencing (NGS). Transcription of <i>SMN1</i> variants was detected using qRT-PCR and ex vivo splicing analysis. Among the three individuals, one was identified as a patient with SMA carrying a heterozygous deletion and a pathogenic variant (c.835-17_835-14delCTTT) of <i>SMN1</i>, one was a healthy carrier only carrying a heterozygous deletion of <i>SMN1</i> exon 7, and the third was a patient with nemaline myopathy 2 carrying a heterozygous deletion of <i>SMN1</i> exon 7. The misdiagnosis of these individuals was attributed to the presence of the c.835-17_835-14delCTTT or c.835-17C&#xa0;&gt;&#xa0;G variants in <i>SMN1</i> intron 6, which affect the amplification of <i>SMN1</i> exon 7 during MLPA-P060 and qPCR testing. However, MLPA-P021 and NGS analyses were unaffected by these variants. These results support that additional detection methods should be employed in cases where the <i>SMN1</i> copy number is ambiguous to minimize the misdiagnosis of SMA.