If you faced a surprise penalty for coming up short on your 2018 taxes, the IRS might be giving you some relief.

On Wednesday, the IRS said it would automatically waive the tax underpayment penalty for more than 400,000 taxpayers who have already submitted their 2018 federal income tax return and failed to claim a special penalty waiver this spring.

The waiver is only of the penalty; if you owed taxes, you must pay them.

Normally, you must pay at least 90% of the income taxes you owe for a given year, or 100% of the tax liability from the prior year before you actually file, to avoid an underpayment penalty on your tax return. The threshold is 110% if your adjusted gross income on that year's return exceeded $150,000.

More from Personal Finance:

Why women are less prepared for retirement than men

Consider this investment if you're worried about losing money

These wealthy investors are trimming their stock holdings

The Tax Cuts and Jobs Act overhauled the tax code, slashing individual income tax rates, eliminating personal exemptions and roughly doubling the standard deduction. As a result, not all taxpayers were properly withheld for 2018.

To help taxpayers contend with these changes amid the 2018 filing season, the IRS lowered its 90% threshold to 85% in January and to 80% in March.

This change was only applicable for the 2018 tax year.