If you have nondeductible traditional IRA contributions
Finally, if you have nondeductible contributions to a traditional IRA (this is not too common), you need to determine the portion of your account that represents those contributions. To do this, divide the amount of nontaxable contributions you've made to the account, and divide this amount by your account's current value.
To determine the pre-tax portion of the account, subtract this number from one.
Pretax portion of account = 1 - nondeductible portion
Finally, use this as a multiplier to determine the amount of your withdrawal subject to a 10% penalty.
Penalty = (pretax portion) x (withdrawal amount) x (0.1)
For example, let's say that you withdraw $5,000 from your traditional IRA early. If your account is worth $50,000 and you've made $10,000 in nondeductible contributions, you can determine that the nondeductible portion is 20%, or 0.2. Subtracting from one gives a pre-tax portion of 80%, or 0.8. Finally, the penalty can be calculated using this multiplier as described in the preceding equation.
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