HUD Handbook 4350.1 Chapter 7 says I need to explain all increases over 5% when I submit a Budget Based rent increase request. Does that apply to increases from last fiscal year’s audited figures to the proposed amounts or from the this year’s actuals to the proposed amounts?

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It applies to both. You should explain why the increase occurred (e.g. higher rates, new staff, etc.) and provide any back up documentation that you have (e.g. letters from utility companies, insurance providers, salary schedules, etc.)