We investigate the low energy properties of an effective local model with flipped SU(5)times U(1)_{chi } gauge group, constructed within the framework of F-theory. Its origin is traced back to the SO(10) symmetry – associated with a geometric singularity of the compactification manifold – broken by an internal flux which is turned on along the seven-brane in the U(1)_{chi } direction. Topological properties and the choice of flux parameters determine the massless spectrum of the model to be that of the minimal flipped SU(5) supplemented with an extra right-handed electron-type state and its complex conjugate, E^c+{{bar{E}}}^c, as well as neutral singlet fields. The subsequent symmetry breaking to the SU(3)times SU(2)times U(1)_Y gauge group occurs with a Higgs pair in 10+{overline{10}} representations of SU(5). Next we proceed to the phenomenological analysis of the resulting effective model and the salient outcomes are: The E^c+{{bar{E}}}^c pair acquires a mass of few TeV and as such could solve the g_{mu }-2 discrepancy. Neutrino couplings to extra neutral singlets lead to an inverse seesaw mechanism where an extra light state could be a suitable dark matter candidate. The predictions of the model for the {0nu }beta beta decay rate could be tested in near future experiments. There are non-unitarity deviations from the lepton mixing matrix (U_{PMNS}), which could in principle explain the new precision measurement of the W-boson mass recently reported by the CDF II collaboration.