The predictions for the atmospheric neutrino flux at high energies strongly depend on the contribution of prompt neutrinos, which are determined by the production of charmed meson in the atmosphere at very forward rapidities. In this seminar I will present our recent estimation of the related cross sections taking into account the presence of an intrinsic charm (IC) component in the proton wave function and the QCD dynamics modified by the onset of saturation effects. The impact on the predictions for the prompt neutrino flux will be discussed assuming different values for the probability to find the IC in the nucleon. Comparison with the IceCube data wil be performed and conclusions will be drawn.