What led to the problem
While I was trying to fix the Github SSL error caused by the DigiCert certificates, I deleted some of the certificates in the "Keychain Access" application. By doing this I broke my SSL certificates and now I am facing some serious problems. Initially I was not even able to connect to websites such as Facebook or Github because there was some trust issues. I fixed this issue but it seems that I am missing something.
Current problem
The problem occurs only with safari. I have tested with the Chrome browser and there was no issue. When I access the Github website (the only website I know that cause the error), I get in my error console a couple of errors similar to this one:
Failed to load resource: An SSL error has occurred and a secure connection to the server cannot be made. (https://assets-cdn.github.com/images/modules/home/gh-windows-app.png)
This error affect the style of the page, there is no CSS or any image that is loaded on the Github page.
References
Here is my console output when I try to access the Github page:
Here is the list of my DigiCert certificates:
Thank you for your help!