You need to change the number that you are entering on your W2 form. Then you need to attach the letter to your 1040.
You should know that this isn't how the IRS wants this to be done. If you have an exclusion from your income then it should not be reported on your W2. You should contact the employer who issued you the W2 and request that they correct the form so that it doesn't show the income that you don't think you should be pay taxes on. Altering that form and those amounts so that you don't pay taxes generally just causes the IRS to send you letters.
A housing allowance can be only partially taxable to clergy. In that instance the housing allowance is entered in box 14 and then reported only for self employment tax purposes. So clergy does not have to pay income tax on the housing allowance but they do have to pay social security and medicare on it.
@jkumpire
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