Palestinian teen killed by Israel army in West Bank
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The ministry identified the youngster as Ghaith Yamin, 16, who died of a head wound "after being shot by Israeli forces" during clashes near Joseph's Tomb, outside the northern city of Nablus.
The Israeli army, which provides security for monthly pilgrimages to the site, said: "Hundreds of Palestinians took part in a violent riot as Jewish worshippers entered Joseph's Tomb, throwing stones and firebombs at the forces.
"Soldiers responded with fire at a suspect throwing a firebomb. A hit was identified," it said in a statement. "In addition, gunshots were heard in the area."
The Islamic Jihad militant group issued a statement praising the "ambush" its fighters prepared for Israeli forces securing the pilgrimage, saying there was an exchange of fire between the two sides.
The Palestinian Red Crescent said its medics treated four people wounded by rubber bullets and 36 who inhaled tear gas, as well as one person who fell during the clashes.
Tensions have been high in the West Bank for the past three months amid a wave of attacks on Israelis that led to arrests and clashes.
Three Israeli Arab attackers and a police commando have died.