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my @where;
my $sql = 'select * from table';
...
push @where, 'column3 = "' . $var3 . '" ' if defined $var3;

$sql = $sql . ' where ' . join(' and ', @where);

my @values = (undef, $var1, $var2, $var3);
my @where;
...
}

$sql = $sql . ' where ' . join(' and ', @where);