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using app_timer_cnt_get() inside uart_fifo interrupt?

I developing applciation based on nrf51822, sdk11. I have read several posts about using app_timer_cnt_get() and get only 0 value. As far as I understand, this is because the RTC1 has LOW_APP priority therefore it can not use inside other interrupt which has higher priority. How to fix this problem since I really need to measure time that the fifo_uart interrupt used? 

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