Charges as in a tax due? Self-Employment taxes can apply to the housing allowance. The housing allowance is excluded from regular income tax, but not self-employment tax.
"If your congregation furnishes housing in kind as pay for your services as a minister instead of a housing allowance, you may exclude the fair market rental value of the housing from income, but you must include the fair market rental value of the housing in net earnings from self-employment for self-employment tax purposes." Clergy Housing Allowance & SE
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