If your pension is fully exempt, then you would have to answer the questions regarding your exclusion in the federal interview screens. You should not adjust the taxable amount on supporting worksheets of the return. This could be the reason for the discrepancy.
Please follow these steps and make sure all the required fields are completed:
- Open your return.
- Click on Personal Income, under the Personal tab.
- Click Edit next to the 1099-R you want to correct.
- Enter the information as shown on your 1099-R.
- Answer the questions on the next two screens.
- Make sure the correct source of your 1099-R is selected. In addition, keep the NYS distribution amount as the full pension distribution. It will be shown as deducted fully on a later screen.
- Click on From a qualified plan on the screen Was this distribution from a qualified plan?
- Answer the required minimum distribution questions on the next screen.
- Finish answering the questions about your 1099-R.
- Once you are back to your federal 1099-R summary screen, click on State Taxes tab above.
- Click on Edit for New York.
- The next screen should be your pension summary screen and will show your pension fully deducted.
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