We consider the problem of sparse phase retrieval from Fourier transform magnitudes to recover the k-sparse signal vector and its support T. We exploit extended support estimate epsilon with size larger than k satisfying epsilon superset of T and obtained by a trained deep neural network (DNN). To make the DNN learnable, it provides epsilon as the union of equivalent solutions of T by utilizing modulo Fourier invariances. Set epsilon can be estimated with short running time via the DNN, and support T can he determined from the DNN output rather than from the full index set by applying hard thresholding to epsilon. Thus, the DNN-based extended support estimation improves the reconstruction performance of the signal with a low complexity burden dependent on k. Numerical results verify that the proposed scheme has a superior performance with lower complexity compared to local search-based greedy sparse phase retrieval and a state-of-the-art variant of the Fienup method.