The bank did not specify how much the settlement amounted to, but said it has set aside 865 million Swiss francs ($922 million, 700 million euros) in the second quarter to meet litigation costs including the case.
'The full cost of the settlement is covered by litigation provisions established by UBS during the second quarter of 2013 and in prior periods,' Switzerland's biggest bank said.
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The agency accused the 18 firms of misleading Fannie and Freddie about the credit-worthiness of the assets.
'UBS has reached an agreement in principle with the Federal Housing Finance Agency,' UBS said.
The bank added that the deal, which still requires a final go-ahead from the different parties, would settle claims connected to the securities between 2004 and 2007.
Despite setting aside massive provisions, the bank, which is due to announce its second quarter results on July 30, said it would post a net profit of around 690 million francs for the three months ending June.
That is a jump of 62.5% from a year ago and a stark improvement over the first quarter, when net profit slid 4.5%. In the fourth quarter of 2012, UBS posted a loss of 1.9-billion francs.
The bank said its operating profit before tax would reach about 1.02 billion francs, an increase of 7.3% over the second quarter in 2012.
Analysts hailed the better-than-expected results and the settlement of the mortgage securities suit, with Panagiotis Spiliopoulos of Vontobel predicting 'juicy dividend payouts in the years to come'.
Following the announcements, the bank's stocks jumped 3.4% to 18.21 francs in midday trading, outperforming the Swiss stock exchange's main index, which gained just 0.12%.
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