The supersymmetric (SUSY) minimal SO(10) model is a well-motivated grand unified theory, where the Standard Model (SM) fermions have Yukawa couplings with only one 10-plet and one 1̅2̅6̅-plet Higgs fields and it is highly non-trivial if the realistic quark and lepton mass matrices can be reproduced in this context. It has been known that the best fit for all the SM fermion mass matrices is achieved by a vacuum expectation value of the 1̅2̅6̅-plet Higgs field being at the intermediate scale of around O(10¹³)GeV. Under the presence of the SO(10) symmetry breaking at the intermediate scale, the successful SM gauge coupling unification is at risk and likely to be spoiled. Recently, it has been shown that the low-energy fermion mass matrices, except for the down-quark mass predicted to be too low, are very well-fitted without the intermediate scale. In order to resolve the too-low down quark mass while keeping the other fittings intact, we consider SUSY threshold corrections to reproduce the right down quark mass. It turns out that this requires flavor-dependent soft parameters. Motivated by this fact, we calculate particle mass spectra at low energies with flavor-dependent sfermion masses at the grand unification scale. We present a benchmark particle mass spectrum which satisfies a variety of phenomenological constraints, in particular, the observed SM-like Higgs boson mass of around 125 GeV and the relic abundance of the neutralino dark matter as well as the experimental result of the muon anomalous magnetic moment. In the resultant mass spectrum, sleptons in the first and second generations, bino and winos are all light, and this scenario can be tested at the LHC Run-2 in the near future.