TDS deduction

I assume you have deducted the TDS under GST and have not paid the amount or disclosed it in your GSTR 7.

In my opinion the possible solution is ,

Deposit the amount and disclose the amount in the next GSTR 7 , by paying Interest 18% as per section 50(1) and pay interest from  10th (Due date of return filing) to the date of actual payment. Ensure you generate the TDS certificate with 5 days of payment to government to avoid additional penalty of Rs. 100 ( CGST) Rs. 100 SGST or Rs. 200 IGST per day of delay. 

Additional Tip: Pay this non deposited amount only with the next months TDS liability and not separately.