Salesforce Permissions assigned to an user are stored in Permission Sets and Profiles. Profile and Permission Ses assigned to an user are stored in PermissionSetAssignment object/entity. So, by querying these two objects, we can figure out if an user have a specific Salesforce Permission.

Sample Permission:

Remote Media for Virtual Desktop

Sample SOQL for Profile:

SELECT Id, Name, PermissionsRemoteMediaVirtualDesktop
FROM Profile
WHERE Id IN (
    SELECT ProfileId 
    FROM User
    WHERE Id = '0053t00000AG695AAD'
)

Sample SOQL:

SELECT Id, Name, PermissionsRemoteMediaVirtualDesktop
FROM PermissionSet
WHERE Id IN (
    SELECT PermissionSetId
    FROM PermissionSetAssignment
    WHERE AssigneeId = '005Hs00000CaRBfIAN'
)
AND PermissionsRemoteMediaVirtualDesktop = true

In the above example, I am trying to find whether the user have “Remote Media for Virtual Desktop” permission assigned to them.