Honestly, your CA did the right thing using 40%. Let me explain why.
The HRA exemption rule under Section 10(13A) has only two slabs — 50% of basic salary for Mumbai, Delhi, Chennai, and Kolkata. Every other city in India, including Coimbatore, Pune, Hyderabad, Bengaluru — yes even Bengaluru — gets 40%. Doesn't matter how big or expensive the city is. This rule hasn't been updated in decades and it's frankly outdated, but that's what the law says right now.
So for you the exemption is calculated as the minimum of these three:
- Actual HRA received: ₹8,000/month = ₹96,000/year
- Rent paid minus 10% of basic: ₹12,000 - ₹2,800 = ₹9,200/month = ₹1,10,400/year
- 40% of basic salary: 40% of ₹28,000 = ₹11,200/month = ₹1,34,400/year
The minimum is ₹96,000 — so your full HRA of ₹96,000 is exempt. You're actually in a good position because your rent paid easily covers it.
Now about paying rent to your father — this is completely legal and thousands of people do it. IT department won't flag it automatically. What matters is that the rent agreement is proper, you're actually transferring money (keep bank transfer records, don't pay cash), and your father is declaring it as income in his ITR. If all three are in order, you're fine. In fact the Supreme Court has upheld this in multiple cases.
One thing most people get wrong — they forget that if annual rent exceeds ₹1 lakh, you must submit your landlord's PAN to your employer. Since you're paying ₹1,44,000 per year to your father, get his PAN submitted. If you've already left that employer or they didn't collect it, you still need to mention it when filing ITR.
For ITR-1 filing, use the income tax e-filing portal directly. It's actually straightforward now. Have Form 16 from employer ready, your rent receipts, and the rent agreement.
My recommendation — go ahead and claim the full ₹96,000 HRA exemption, submit father's PAN, keep all bank transfer records safely, and file confidently. You're not doing anything wrong here.