Our third independent variant (esv2663194) tags a 32 kb deletion that affects both CYP2A6 and CYP2A7. Esv2663194 has a low minor allele frequency (MAFFINRISK = 0.03) and a prominent effect size (beta = -1.08), and accounts for 3–8% of variance in NMR in the three cohorts. The 32 kb (chr19:41355715–41387669, according to GRCh37/hg19) deletion abolishes exons 1–2 in CYP2A6 and exons 2–9 in CYP2A7 when compared to the reference sequence; both genes have multiple isoforms and the consequence of the deletion varies between the isoforms. The 32 kb deletion may produce a similar construct as CYP2A6*12, which is a hybrid allele formed by an unequal crossover between CYP2A6 and CYP2A7. CYP2A6*12 is composed of the 5′-regulatory region and exons 1–2 of CYP2A7 and exons 3–9 and the 3′-regulatory region of CYP2A6, and harbors 10 amino acid differences when compared to the wild-type CYP2A6 allele, with an allele frequency of 2.2% reported among Spaniards [51]. CYP2A6*12 is shown to have reduced enzyme activity in vivo [55, 56]; in line with this, the minor allele of esv2663194 associates with decreased clearance rate.
