The South Atlantic Anomaly is a region in the ionosphere where the inner Van Allen radiation belt lies close to the earth's surface, which is still several hundred miles. There is no evidence that the anomaly has any effect on surface weather, and Flight 477 had left the area of the anomaly well before it crashed.

Map showing the South Atlantic Anomaly:
http://upload.wikimedia.org/wikipedia/commons/b/bc/ROSAT_SAA.gif

Map showing the flight path of Air France 477:
http://1.bp.blogspot.com/_H44IkuSV9qQ/SiWOncyUIJI/AAAAAAAAJJM/kigB6tx3ZoA/s400/air_france_447_a.jpg

Note that the first part of the flight was through the middle of the anomaly, and the aircraft had left the anomaly completely before it ran into trouble. There is no correlation between the South Atlantic Anomaly and the Air France disaster.
Source(s):
http://en.wikipedia.org/wiki/South_Atlantic_Anomaly


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