The boy walked away from a middle school on Church Street yesterday morning.
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Police were urgently trying to find him because of his age and a medical condition.
Wednesday morning, BART community service officers spotted him riding a train.
ABC7 was at the 16th Street BART station as the boy was reunited with his family.
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They recently moved from San Francisco from the East Coast.
The San Francisco Police Department tweeted a photo of the child Tuesday night, saying he was last seen near 450 Church Street in San Francisco. He had last been seen in a dark hoodie and dark pants and was also carrying a backpack.