@Brian7771
You are thinking about this wrong.
1) Your tax return takes ALL your income from everywhere, including that 1099-R, and calculates a tax on ALL of it at whatever rates are appropriate for everything together , includes the penalty, and puts that amount on line 16 of the 1040.
2) Then it takes ALL your withholding...from every source, (including box 4 on your 1099-R) and puts all your withholding on line 17 of the form 1040...adds in a few other possible credits to get line 19....which includes ALL your credits.
3) The difference between these two is your refund...or balance due . So you ARE getting credit for having prepaid some of your taxes paid with that 1099-R because the $$ in box 4 of your 1099-R are included in line 19's value on the 1040.
Your tax return is the final Full-Year tax accounting for Everything..,.not just one form.
____________*Answers are correct to the best of my knowledge when posted, but should not be considered to be legal or official tax advice.*
