If you are merely using commas for readability, you can use underscores instead. But you can only use them in unquoted numbers, not strings.

print  1_000_000  + 1000;  # 1001000
print '1_000_000' + 1000;  # Warning!
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BTW, Perl will completely ignore the underscores, so if you accidentally mistype 1_000_00_000, you'll get 100 million instead of 1 billion -- and no warning.