I am system Integrator dealing with an IT related products and services. I have Purchased few Items on 18% from the company but I have supplied that same item in 5% GST rate. The matter is like I have supplied that item to one research institutes where they are only paying 5% GST as they have certificate from GST council that they can purchase the item in 5% rate as concessional GST rate.
https://www.indiafilings.com/learn/concessional-gst-rate-research-institutions/
http://stores.vnit.ac.in/images/store/2017/Circular_reg_GST_Rates.pdf
in this case how can I get the GST extra I have paid as GST input?
It does not matter what rate you are charging for your outward supplies.
If you have paid GST on purchase then you will get input tax credit.
In your case you will get 100% input credit of amount you paid on purchase of IT systems.
You can claim full Input Tax Credit.
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