After you file

On Form 1040-X,

Line 8 "Tax" will not change

Penalty i.e. Form 5329 goes on line 10.

Therefore Line 11 "Total Tax" will increase.

 

Amount you owe Line 20 depends on Line 11.

Form 1040-X becomes your new tax return.

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I can only refer you to the INSTRUCTIONS:

When and Where To File
File Form 5329 with your 2023 Form 1040, 1040-SR,1040-NR,
or 1041 by the due date, including extensions, of your tax return.
If you don’t have to file a 2023 income tax return, complete
and file Form 5329 by itself at the time and place you would be
required to file Form 1040, 1040-SR, or 1040-NR. If you file Form
5329 by itself, then it can’t be filed electronically. Be sure to
include your address on page 1 of the form and your signature
and the date on page 2 of the form. Enclose, but don’t attach, a
check or money order payable to “United States Treasury” for
any taxes due. Write your social security number and “2023
Form 5329” on the check. For information on other payment
options, including credit or debit card payments, see the
Instructions for Form 1040 or the Instructions for Form 1040-NR,
or go to IRS.gov.
Prior tax years. If you are filing Form 5329 for a prior year, you
must use the prior year's version of the form. If you don’t have
any other changes and haven’t previously filed a federal income
tax return for the prior year, file the prior year's version of Form
5329 by itself (discussed earlier).

@msv1