 Genetic variance of penetrance

For a binary disease trait $Y$ with genotype $G$, the genetic variance of penetrance is the between-genotype term in the law of total variance. The averaged within-genotype term is $\mathbb{E}[q_G(1-q_G)]$. Under multiplicative diallelic penetrance, the genetic term is $p^2({\beta }^2-{\alpha }^4)$. This decomposition attributes variance to the modeled locus, not automatically to all hereditary causes.