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President Obama has appointed a new acting commissioner for the IRS. He is Danny Werfel, currently a White House budget manager. His appointment comes after the president forced the resignation of the current acting head of the IRS. And now, another senior IRS official is out. Joseph Grant oversaw the agency's division that gave extra scrutiny to conservative groups seeking nonprofit status. Well, this morning, Tea Party leaders and associated lawmakers rallied about that on Capitol Hill.

But as NPR's Peter Overby reports, other lawmakers want another kind of IRS scrutiny - to look at the activities of some existing nonprofits in the 2012 elections.

PETER OVERBY, BYLINE: Minnesota Congresswoman Michele Bachmann led the rally. She's chair of the House Tea Party Caucus. She said it was troubling that the IRS targeted conservative groups as they applied for tax-exempt status as 501(c)(4) social welfare organizations.

REPRESENTATIVE MICHELE BACHMANN: Because the axiom is, the power to tax is the power to destroy.

OVERBY: Republican consultant Karl Rove and others say the IRS scrutiny was instigated by congressional Democrats. Rove was on Fox News this week, citing letters to IRS administrators from Capitol Hill.

KARL ROVE: Maybe they were influenced by Democrats in the Congress writing them letters saying: Take on these groups or else you're going to face consequences in front of us.

OVERBY: But an inspector general's report says the extra scrutiny started with lower-level IRS employees. In fact, those letters from Democratic lawmakers did not deal with 501(c)(4) applicants. What they did advocate was a crackdown on big-budget 501(c)(4)s that were already active in the 2012 campaign - groups on both sides, including one co-founded by Karl Rove himself, Crossroads GPS.

Senator Carl Levin of Michigan wrote several letters, citing a dozen 501(c)(4) groups, liberal and conservative. He said anonymous donors were funneling in millions of dollars. Here's Levin on the Senate floor in July 2012.

SENATOR CARL LEVIN: They do so covered by a fig leaf that the nonprofit groups to which they donate are dedicated to, quote, social welfare, rather than partisan politics.

OVERBY: Meanwhile, Republican lawmakers were warning the IRS to back off. Some outside groups were calling for stronger enforcement. Fred Wertheimer, of the group Democracy 21, wrote to IRS officials more than a dozen times about conservative and liberal 501(c)(4)s. He says nothing ever happened.

FRED WERTHEIMER: They were dead wrong in going after the conservative groups. And they have been dead wrong in not taking on groups that are abusing and misusing the tax laws.

OVERBY: One basic argument here is that there's often no difference between TV ads from the transparent political committees called superPACs and ads produced by the secretive social welfare organizations. For example, these two ads attacking President Obama.

(SOUNDBITE OF TV AD)

UNIDENTIFIED WOMAN #1: He's added 4 billion in debt, every day. The economy is slowing, but our debt keeps growing.

OVERBY: That one from Crossroads GPS with its anonymous funders, and this one.

(SOUNDBITE OF TV AD)

UNIDENTIFIED WOMAN #2: And he wants more spending, just like his failed stimulus. After trillions in more debt with nothing to show for it, we can't repeat those mistakes.

OVERBY: From the c4's sidekick superPAC, American Crossroads, which discloses its donors and is not so well-financed.

An NPR analysis found that the big 501(c)(4)s spent more than a quarter-billion dollars trying to shape the 2012 elections.

Paul Streckfus edits EO Tax Journal, a newsletter covering the IRS section on exempt organizations.

PAUL STRECKFUS: The IRS response was basically: Can we sort of ignore this; the law isn't very clear, and we don't want to make anybody unhappy on the Hill over this.

OVERBY: Streckfus says the IRS probably should have made an active decision on regulating the social welfare organizations. Then, Congress could react and any unhappy 501(c)(4) groups could sue. But now it's too late for that.

Peter Overby, NPR News, Washington.

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