Fannie Mae was affected by the same derivatives accounting mismatch that led to Freddie Mac's first quarterly loss in four years. But its bulk and balance sheet provided enough cushion for the larger of the two government-sponsored enterprises to post a profit for the third quarter.

Fannie's third-quarter net income of $2 billion was roughly half of the $3.9 billion it earned a year ago and the $4.6 billion in net income earned during the second quarter of 2015. But while the hedging instrument accounting issues create "significant volatility" to Fannie's quarterly and annual reporting CEO Timothy Mayopoulos expects the company to remain profitable on an annual basis.

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