GPU in second PCI E on Sabertooth X58

The manual says this isn't recommended. Can this board run a single GPU the second slot at x16?

In the first slot it covers the regular PCI port, which I need.

Is there any real downside?

Thanks.
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  1. It will run at x16.
    It's generally recommended to use one card in the first PCI-E slot but if you use it in the second slot,it will run at x16.
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