How do I clear the unread notifications?

The only way is by opening those submissions, you can do it in My Forms page by clicking on the form and "Inbox" option: 

You can also view your submissions via the submissions page, here is a guide that will help you with that: How-to-View-Form-Submissions

Hope this helps. 

Hi, 

I did this but the red notification is still there

I checked on your My Forms page and I see that this is no longer the case.

Can you please check again. Let us know if issue persist.

Its most probably be a browser cache issue which had resolved by itself.

Thanks.