Deletions also increased risk for kidney stones (chr16:15,120,501–16,353,166; ORdel = 5.9; 95%-CI [2.9; 11.9]; p = 7.3 × 10−7), with the CNV-GWAS signal peaking close to a missense variant (rs41278174 G > A; FrequencyA: 2.6%) in exon 23 of ABCC6 [MIM: 603234] associating with calcium and phosphate levels through SNP-GWASs (Fig. 5D). Here, ABCC6 is linked to nephrolithiasis.