We present an approach for the calculation of the Z2 topological invariant in non-crystalline two-dimensional quantum spin Hall insulators. While topological invariants were originally mathematically introduced for crystalline periodic systems, and crucially hinge on tracking the evolution of occupied states through the Brillouin zone, the introduction of disorder or dynamical effects can break the translational symmetry and imply the use of larger simulation cells, where the k-point sampling is typically reduced to the single Γ-point. Here, we introduce a single-point formula for the spin Chern number that enables to adopt the supercell framework, where a single Hamiltonian diagonalisation is performed. Inspired by the work of E. Prodan [Phys. Rev. B, 80, 12 (2009)], our single-point approach allows to calculate the spin Chern number even when the spin operator sz does not commute with the Hamiltonian, as in the presence of Rashba spin-orbit coupling. We validate our method on the Kane-Mele model, both pristine and in the presence of Anderson disorder. Finally, we investigate the disorder-driven transition from the trivial phase to the topological state known as topological Anderson insulator. Beyond disordered systems, our approach is particularly useful to investigate the role of defects, to study topological alloys and in the context of ab-initio molecular dynamics simulations at finite temperature.