Judge Hassan Fareed, presiding over a court in the Nile Delta town of Banha, referred the sentence to the Grand Mufti, the highest Islamic authority in Egypt, a legal requirement usually considered a formality.
The remaining 38 on trial in the case will be sentenced at the next hearing on July 5.
Among them are Brotherhood Supreme Guide Mohammed Badie, former Brotherhood lawmaker Mohammed el-Beltagy, Salafi preacher Safwat Hegazy and Bassem Auda, the supplies minister under Morsi, who was overthrown by the military last July following massive protests against his yearlong rule.
The trials are part of a fierce government crackdown in the months following Morsi's overthrow, during which the group was outlawed and then declared a terrorist movement. Hundreds of Morsi supporters have been killed in clashes with police, at least 16,000 have been detained by the military-backed government and hundreds referred to trial.
Meanwhile, an appeals court today overturned the sentences given to four police officers over the deaths of 37 detainees, most of them Morsi supporters, Egypt's state news agency MENA reported.
The court had handed a 10-year prison term to one officer and one-year suspended sentences to three in March, a verdict that outraged lawyers and families of the victims.
The court said the case will be referred back to prosecutors and a retrial will be held after an appeal by the convicted police officers. It was the first trial and conviction of police officers in connection to a crackdown on Islamists since Morsi's ouster.
The sentences come on the eve of the inauguration of Egypt's new president, retired Field Marshal Abdel-Fattah El-Sissi, who led the overthrow of Morsi.
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