Sanju, There's two point in your code:First, define variables that used in interrupt routines as volatile.Second, for a 50 Hz sine wave with 100 samples, your sampling rate is 5000 Hz. and in your pictures your ISR frequency is very low. And in reali...

fclock is 48 MHz and you see 2 ms because you set ARR=1, Time Period = ((PSC+1)*(ARR+1))/FClock in Second in your case ((48000+1)*(1+1))/48000000 almost equal to 2 Ms.