A method to solve the three-dimensional compressible Navier-Stokes equations on the sphere is suggested, based on a stereographic projection with a high-order mapping of the elements from the stereographic space to the sphere. The projection is slightly modified, in order to take into account the domain thickness without introducing any approximation about the aspect ratio (deep-atmosphere). In a discontinuous Galerkin framework, the elements alongside the equator are exactly represented using a nonpolynomial geometry, in order to avoid the numerical issues associated with the seam connecting the two hemispheres. This is an crucial point, necessary to avoid mass loss and spurious deviations of the velocity. The resulting model is validated on idealized three-dimensional atmospheric test cases on the sphere, demonstrating the good convergence properties of the scheme, its mass conservation, and its satisfactory behavior in terms of accuracy and low numerical dissipation. A simulation is performed on a variable resolution unstructured grid, producing accurate results despite a substantial reduction of the number of elements.