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Spinal muscular atrophy (SMA) is a severe neuromuscular disorder caused by biallelic loss or pathogenic variants in the <i>SMN1</i> gene. Copy number and modifier intragenic variants in <i>SMN2</i>, an almost identical paralog gene of <i>SMN1</i>, are known to influence the amount of complete SMN proteins. Therefore, <i>SMN2</i> is considered the main phenotypic modifier of SMA, although genotype–phenotype correlation is not absolute. We present eleven unrelated SMA patients with milder phenotypes carrying the c.859G>C-positive modifier variant in <i>SMN2</i>. All were studied by a specific NGS method to allow a deep characterization of the entire <i>SMN</i> region. Analysis of two homozygous cases for the variant allowed us to identify a specific haplotype, <i>Smn2-859C.1,</i> in association with c.859G>C. Two other cases with the c.859G>C variant in their two <i>SMN2</i> copies showed a second haplotype, <i>Smn2-859C.2,</i> in cis with <i>Smn2-859C.1</i>, assembling a more complex allele. We also identified a previously unreported variant in intron 2a exclusively linked to the <i>Smn2-859C.1</i> haplotype (c.154-1141G>A), further suggesting that this region has been ancestrally conserved. The deep molecular characterization of <i>SMN2</i> in our cohort highlights the importance of testing c.859G>C, as well as accurately assessing the <i>SMN2</i> region in SMA patients to gain insight into the complex genotype–phenotype correlations and improve prognostic outcomes.