The 5498 shows info for money coming into a IRA, etc. Like from a transfer, rollover or new contribution. You only enter the 1099R for money going out like a distribution or to another account.
The 1099R will have a code in box 7 that tells what kind of transaction it is for. And Turbo Tax will ask what you did with it when you enter the 1099R. There will be several follow up questions if it needs to determine if it is taxable and how much.
If you got a 1099R what code is in box 7? Why did you get a 1099R?
