On PuTTY-SC homepage is written the following information:
The agent uses the stored sessions (created when using PuTTY SC) from the registry to detect a usable key. The first key available on the smartcard is loaded into the agent key store (the current version only supports one active key). The agent can be used with some other SSH clients as well, e.g WinSCP.
Double-click on pageantsc.exe.
You should see the following dialog:

It works, the agent is able to use your smartcard / token.
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