  Let $M$ be an $n$-cusped hyperbolic $3$-manifold having rationally
independent cusp shapes and $X$ be its holonomy variety. We first show that
every maximal anomalous subvariety of $X$ containing the identity is its
subvariety of codimension $1$ which arises by having a cusp of $M$ complete.
Second, we prove if $X^{oa} =\emptyset$ , then $M$ has cusps which are, keeping
some other cusps of it complete, strongly geometrically isolated from the rest.
Third, we resolve the Zilber-Pink conjecture for holonomy varieties of any
$2$-cusped hyperbolic $3$-manifolds.
