You are making the transaction very confusing because you are paying the TDS yourself rather than deducting it from the value of supply and GST also needs to be paid on value of supply and since your invoice value is 100 they would refund GST on invoice value.
How are you claiming refund of such GST what services are you providing?
Why are you deducting TDS? Have you checked whether it is required or not.
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Thank you.