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Read the CP2000 notice carefully ... they should have taken the withholding into consideration. This error may have triggered other things on the return like more of SS benefits being taxable and/or credits being disallowed.
If the IRS is correct you really don't have anything to contest ... you missed it so just sign the form agreeing to the error and send them what you can asap. If you fail to send in the entire amount then the IRS will send you a bill for the balance + penalty + interest. The faster you pay it off the cheaper it will be in the long run.
You can request an abatement of the penalty for this error ... say something like you thought it was already taxed (the withholding) and you didn't know it still had to go on the return... this is a common misconception that may cut you a break on the penalty only ... they still have to charge the interest as that is a law.
the additional amount due would include a late payment penalty (1/2% a month for each month or fraction thereof from 4/15/2019 till the date of the notice), then there could be a 20% substantial underpayment penalty and lastly interest
(1) Substantial. An understatement (as defined in paragraph (b)(2) of this section) is “substantial” if it exceeds the greater of -
(i) 10 percent of the tax required to be shown on the return for the taxable year (as defined in paragraph (b)(3) of this section); or
(ii) $5,000 ($10,000 in the case of a corporation other than an S corporation (as defined in section 1361(a)(1)) or a personal holding company (as defined in section 542)).
(2) Understatement. Except as provided in paragraph (c)(2) of this section (relating to special rules for carrybacks), the term “understatement” means the excess of -
(i) The amount of the tax required to be shown on the return for the taxable year (as defined in paragraph (b)(3) of this section), over
(ii) The amount of the tax imposed which is shown on the return for the taxable year (as defined in paragraph (b)(4) of this section), reduced by any rebate (as defined in paragraph (b)(5) of this section).
The definition of understatement also may be expressed as -
Understatement = X − (Y − Z)
where X = the amount of the tax required to be shown on the return; Y = the amount of the tax imposed which is shown on the return; and Z = any rebate.
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