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State tax filing
You're correct that your retirement income would be nontaxable in NY under a certain threshold. If you qualify for that exclusion, your distribution should be removed from your return. However, as @KrisD15 mentioned, the taxes that were withheld would be pooled together and applied to your tax liability on any other income you may have. If your return is currently showing a refund, it would already include the $650 tax that was paid from the retirement distribution. If your refund is less than $650, this means that you would likely have had a balance due if you hadn't had the extra $650 withheld.
We can look at your return and see exactly what you see to verify that the return is calculating your refund as it should. The return will be scrubbed and won't include any of your personal details.
If you're using TurboTax Online:
Once you're logged in to your account,
- on the left hand panel, click on Tax Tools and then choose Tools
- on the pop up window, select Share my file with Agent
- you'll see a message saying you'll give us a copy of your tax return. Your personal information will be changed so we can't see any private information.
- click okay and you'll get another message with a token
If you're using TurboTax Desktop:
- Click on Online in the top menu of TurboTax Desktop for Windows
- Select 'Send Tax File to Agent'
- Write down or send an image of your token number and state then place in this issue.
- We can then review your exact scenario for a solution
Please reply to this message with your token so that we can further assist you. Let us know all other states, if any, that are included on the return.