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Spinal muscular atrophy (SMA) is caused by bi‐allelic loss or pathogenic variants in the  SMN1  gene.  SMN2 , the highly homologous copy of  SMN1 , is considered the major phenotypic modifier of the disease. Determination of  SMN2  copy number is essential to establish robust genotype–phenotype correlations and predict disease evolution, to stratify patients for clinical trials, as well as to define those eligible for treatment. Discordant genotype–phenotype correlations are not uncommon in SMA, some of which are due to intragenic  SMN2  variants that may influence the amount of complete  SMN  transcripts and, therefore, of full‐length SMN protein. Detection of these variants is crucial to predict SMA phenotypes in the present scenario of therapeutic advances and with the perspective of SMA neonatal screening and early diagnosis to start treatments. Here, we present a novel, affordable, and versatile method for complete sequencing of the  SMN2  gene based on long‐range polymerase chain reaction and next‐generation sequencing. The method was validated by analyzing samples from 53 SMA patients who lack  SMN1 , allowing to characterize paralogous, rare variants, and single‐nucleotide polymorphisms of  SMN2  as well as  SMN2 – SMN1  hybrid genes. The method identifies partial deletions and can be adapted to determine rare pathogenic variants in patients with at least one  SMN1  copy.

Beyond copy number: A new, rapid, and versatile method for sequencing the entire SMN2 gene in SMA patients