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A phase-variant frequency is a specific shield modulation which could be utilized to prevent certain kinds of signals from penetrating the shields.
Captain Janeway, of the USS Voyager, ordered ship's shields remodulated to a phase-variant frequency in 2375, in order to deny Kurros, member of the Delta Quadrant group known as the "Think Tank," from utilizing a form of isomorphic projection from communicating with the crew. (VOY: "Think Tank")