We develop a Reduced Order Model (ROM) for the Navier-Stokes equations with nonlinear filtering stabilization. Our approach, that can be interpreted as a Large Eddy Simulation model, combines a three-step algorithm called Evolve-Filter-Relax (EFR) with a computationally efficient finite volume method. The main novelty of our ROM lies in the use within the EFR algorithm of a nonlinear, deconvolution-based indicator function that identifies the regions of the domain where the flow needs regularization. The ROM we propose is a hybrid projection/data-driven strategy: a classical Proper Orthogonal Decomposition Galerkin projection approach for the reconstruction of the velocity and the pressure fields and a data-driven reduction method to approximate the indicator function used by the nonlinear differential filter. This data-driven technique is based on interpolation with Radial Basis Functions. We test the performance of our ROM approach on two benchmark problems: 2D and 3D unsteady flow past a cylinder at Reynolds number 0 ≤ Re ≤ 100. The accuracy of the ROM is assessed against results obtained with the full order model for velocity, pressure, indicator function and time evolution of the aerodynamics coefficients.