@Veera Ragavan,Thanks for posting in Q&A.
From your description, I know that you want to deploy custom apps via Intune.
Based on my researching, I found that you can upload custom apps to Intune by converting it to Win32 app, and then you can deploy it via Intune.
You can follow the steps below to check whether the app support silently install, then you can refer the link below to prepare Win32 app and deploy it.
https://video2.skills-academy.com/en-us/mem/intune/apps/apps-win32-prepare
1.Run CMD as admin on device.
2.CD to PSTools directory. https://video2.skills-academy.com/en-us/sysinternals/downloads/psexec
3.Enter psexec -i -d -s cmd.exe
4.Enter whoami check running context.
5.Enter Silently install command.
Hope this information can be helpful. If there is any update, feel free to contact me.
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