$line=~/(\w+),(\w+),(\d+),(\d+),(\d+)/;

And what happens when the regex doesn't match? don't use $1, $2, ... withouth checking that.

An alternative appraoch:

my ($firstname, $lastname, @marks) = split m/,/, $line;
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This has the advantage that you can have an arbitrary number of marks. Of course you'll need to adjust the rest of the code a bit, for example;

$totalmarks = 0;
$totalmarks += $_ for (@marks);
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        foreach $mark(@marks){
           $status=checkpass($mark);
        }
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So $status is the status of the last mark only. Is that what you want?

You should test your script also with data of failing students.

BTW I strongly recommend to align the code better, one tab for each opening brace.