I have a CMC that has is rated at about 1kR at 100Mhz at 3A
However my circuit uses only 1A. Do I need to derate my inductance since there is less current flowing through it ?
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If your common mode choke is passing a regular circuit current of 1 amp then that will be a differential current i.e. it flows into one terminal on one side and returns in the opposite direction through the equivalent terminal on the other winding: -
Under these circumstances the currents are in opposite directions and the fluxes cancel out hence there is no need to derate the inductance. In any case, inductance will only be reduced (usually) when the common mode current reaches a significant level: -