Setting a self signed certificate into list of windows certificates does not resolve SEC_E_UNTRUSTED_ROOT

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I set http.sslbackend=schannel and imported my self-signed certificate into windows 10 (Personal | Certificates) pane in MMC. Now, I'm trying to clone a repository hosted on a server configured with the self-signed certificate.

As far as I understood as long as having the certificate in windows (explained above) git should not complain about the certificate. This is not the case. whenever I try to clone I'm getting:

unable to access https://server.com/project.git : schannel: SEC_E_UNTRUSTED_ROOT (0X80090325) - THE CERTIFICATE CHAIN WAS ISSUED BY AN AUTHORITY THAT IS NOT TRUSTED.

What am I missing here?

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