van Tintelen et al. were unsure as to the pathogenicity of this variant. Later findings from Klauke et al. and other papers found this variant present, at a similiarly low frequency, in controls. Because of this, and because the variant is not conserved and is not predicted to be disruptive, it is classified as benign.
The findings of Klauke et al. in controls strongly contradicts a severe pathogenic effect for this variant, even for a pathogenic hypothesis that is quite generous. Assuming ARVD has a prevalence of 1 in 1000, that mutations in PKP2 account for 40% of disease, that the hypothetical pathogenic variant accounts for 20% of PKP2-attributable disease, and the variant has a penetrance of just 4% — such a variant would be predicted to have an allele frequency of .2% — 10 out of 726 randomly chosen chromosomes having the variant deviates from this frequency with a significance 3 * 10^-6.