BRINGING NEW MEANING TO THE PHRASE “THE WEAPONIZED IRS:”

An Internal Revenue Service agent got a 21-year-old intern drunk last July and then allegedly handcuffed her in his government-issued car in Boston before shoving “his service weapon deep into her mouth” and raping her, a Suffolk prosecutor said Thursday.

The allegations were made during the arraignment of James R. Clarke, 44, in Suffolk Superior Court. He pleaded not guilty to charges including aggravated rape, assault and battery with a dangerous weapon, and indecent assault and battery.

Clarke — who was assigned to the IRS criminal investigations office in Boston at the time of the incident — was released on personal recognizance after a magistrate rejected a prosecution request that bail be set at $10,000 cash.

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The IRS declined to discuss his employment status after his indictment last month and said Thursday that the agency can’t discuss individual personnel matters.

“The IRS cannot comment on specifics involving these serious and disturbing allegations,” the agency said in a statement. “The IRS holds our employees to high standards, and we do not tolerate inappropriate behavior.”

Regarding that last quote, Lois Lerner and John Koskinen could not be reached for comment.