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When using transceivers with Cyclone IV GX, are there any differences in pin assignments for different transfer rates?

On the Cyclone IV GX, when the transceiver transfer rate is set to 2.97Gbps or higher, the I/O pin is used as the GND pin for the ref clk pin. The display will also change on the Pin Planner.

The GND pins added for each package are predetermined and assigned automatically by the tool, but user logic cannot be connected to those pins.

For details, please refer to page 10 of the document linked below.
  https://www.altera.com/en_US/pdfs/literature/dp/cyclone-iv/pcg-01008.pdf

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