Shockwaves were felt in New Delhi in northern India and across northern Pakistan, where hundreds of people ran out of buildings as the ground rolled beneath them.
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The U.S. Geological Survey said the quake had a preliminary magnitude of 7.5 and occurred at a depth of 212 kilometers (130 miles).
The quake was also felt in the Indian capital New Delhi, though no damages were reported.
In 2005, a magnitude 7.6 quake in Pakistan-administered Kashmir killed more than 75,000 people.
In the Pakistan-controlled region of Kashmir, Zaheeruddin Qureshi, a senior rescue official, said at least one person was killed and another was injured when a wall of a home collapsed in Mirpur.
In Badakhshan itself, “there are reports of casualties and destruction” in a few remote districts near the epicentre, said the provincial director of the Afghan National Disaster Management Authority, Abdullah Humayoon Dehqan.
In Pakistan, 38 deaths were reported by early evening, most in northern and northwestern regions bordering Afghanistan, officials told Reuters.
Active faults and their resultant earthquakes in northern Pakistan and adjacent parts of India and Afghanistan are the direct result of the convergence between the India and Eurasia plates.
At least 12 schoolgirls were killed in Afghanistan and at least 38 people died in Pakistan, sources told Al Jazeera.
Patients who were shifted outdoors at the government medical college hospital after a strong tremor was felt in Jammu, India.
26 December 2004: A massive undersea natural disaster off the coast of Sumatra island triggers a tsunami which kills 220,000 in countries around the Indian Ocean, including 168,000 in Indonesia.
According to Pakistani officials, four people have died in the Swat region and Charsadda districts of Khyber Pakhtunktwa.
The death toll could climb because communications were down in much of the rugged Hindu Kush mountain range area where the quake was centered.
August 11, 2012: Twin earthquakes with a magnitude 6.3 and 6.4 leave 306 dead and more than 3,000 injured near the Iranian city of Tabriz. Mild tremors were also felt for several minutes in Delhi, where Metro services were reportedly halted.
USGS reported the epicenter was 28 miles south-southwest of Jarm, Afghanistan, near the Afghanistan-Pakistan border.
In J&K capital Srinagar, residents said they saw the buildings “swinging” in a scary reminder of the devastating quake of 2005.
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25 April 2015: A 7.8 magnitude quake in Nepal kills nearly 8,900 people and destroys about half a million homes.
