Why the deductible IRA contribution was changed after my return was e filed. Before I clicked last button to e-file, everything looked good.

To clarify, when you filed the return it shows that you had the IRA contribution deducted on line 20 of Schedule 1 but after you filed the download doesn't have an entry on line 20 of Schedule 1? Did you accidentally select to amend the return (refund would start at $0)?

Thank you for your reply.
Yes, I had the deducted IRA contributions on line 20 of Schedule 1, but now I see only a partial amount of the contribution. The return is not amended, it is accepted.

It would be helpful to have a TurboTax ".tax2022" file that is experiencing this issue. You can send us a “diagnostic” file that has your “numbers” but not your personal information. If you would like to do this, here are the instructions for TurboTax Online: 

1. From the left menu select Tax Tools. 
2. Then select Tools below Tax Tools. 
3. A window will pop up which says Tools Center.  
4. On this screen, select Share my file with Agent. 
5. You will see a message explaining what the diagnostic copy is. Click okay through this screen and then you will get a Token number. 
6. Reply to this thread with your Token number. This will allow us to open a copy of your return without seeing any personal information.  

We will then be able to see exactly what you are seeing and we can determine what exactly is going on in your return and provide you with a resolution.

For now, I would wait and see if the refund from the IRS matches the original return (with the full IRA deduction), and if not then you can amend your return.

@tatsialiv 

The return has been accepted, so there is no option to select Tax Tool from the menu.

Thank you.

You can open the return back up with these steps if you want us to review the issue:

1. Select Tax Home in the left menu.
2. Scroll down to Your tax returns & documents.
3. Select Add a State (you're not actually adding a state, this opens the return back up)
4. Select Tax Tools
5. Then select Tools below Tax Tools. 
6. A window will pop up which says Tools Center.  
7. On this screen, select Share my file with Agent. 
8. You will see a message explaining what the diagnostic copy is. Click okay through this screen and then you will get a Token number. 
9. Reply to this thread with your Token number. This will allow us to open a copy of your return without seeing any personal information. 

@tatsialiv 

The token number is 1094873

Thank you for your help.

Thank you for the token. I reviewed your return and noticed your wife made SEP contributions this is considered a retirement plan at work and therefore limited her traditional IRA deduction. 

To confirm, did you make any changes after saving your return the first time that included the full IRA deduction?

Please save a copy of this changed return with the limited IRA deduction. 

@tatsialiv 

First, I entered the full amount of Traditional IRA contributions, and after I entered the amount to maximize SEP contributions. I had revisited the Traditional IRA deduction before I was ready to finish the tax return.

Contributions to the SEP-IRA exceeded the maximum limits and we wanted to distribute the excess amount.

So, If she is self-employed, and does her SEP IRA deduction is 25% of net self-employment income deduct her traditional IRA contributions? Will we have to withdraw the excess contributions of the traditional IRA?

Your SEP IRA limits and your traditional IRA limits are generally independent of each other.  However, your SEP IRA contribution can reduce the income available to qualify for a traditional IRA contribution so you need to watch out for that.

Here is a really good thread on the two.

@tatsialiv