$ 
$ cat -n process_files.pl
     1    #!perl
     2    
     3    $file = $ARGV[0];
     4    open(FH, '<', $file) or die "Can't open $file: $!";
     5    while (<FH>) {
     6        next if $. == 1;
     7        chomp;
     8        @x = split /\s+/;
     9        $FuncrefGene = $x[6];
    10        $GeneDetailrefGene = $x[8];
    11        printf("Row no. = [%d]\n", $.);
    12        printf("FuncrefGene = [%s]\n", $FuncrefGene);
    13        printf("GeneDetailrefGene = [%s]\n", $GeneDetailrefGene);
    14        if ($FuncrefGene !~ /exonic/i && $GeneDetailrefGene=~/(\D\d+)/) {
    15            printf("In IF branch:\n");
    16            printf("==> \$1 = [%s]\n", $1);
    17            if ($1 > 11) {
    18                printf("==> Inside \$1 > 11\n");
    19                $1 //= 0;
    20                $classification = 'Likely Benign';
    21            }
    22            printf("==> Last line in IF branch: classification = [%s]\n", $classification);
    23        } else {
    24            printf("In ELSE branch:\n");
    25            if ($FuncrefGene !~ /exonic/i) {
    26                my ($transcript) = ($GeneDetailrefGene) =~ /(?:\.\d+[+*-])(\d+)/;
    27                printf("==> transcript = [%s]\n", $transcript);
    28                $transcript //= 0;
    29                $classification = 'Likely Benign' if $transcript > 11;
    30            }
    31            printf("==> Last line in ELSE branch: classification = [%s]\n", $classification);
    32        }
    33        printf("%s\n\n", "="x60);
    34    }
    35    close(FH) or die "Can't close $file: $!";
    36    
$ 
$ perl process_files.pl data.txt
Row no. = [2]
FuncrefGene = [splicing]
GeneDetailrefGene = [NM_018328:exon12:c.3055-9T>C]
In IF branch:
==> $1 = [_018328]
==> Last line in IF branch: classification = []
============================================================

Row no. = [3]
FuncrefGene = [upstream]
GeneDetailrefGene = [27]
In ELSE branch:
==> transcript = []
==> Last line in ELSE branch: classification = []
============================================================

Row no. = [4]
FuncrefGene = [upstream]
GeneDetailrefGene = [35]
In ELSE branch:
==> transcript = []
==> Last line in ELSE branch: classification = []
============================================================

Row no. = [5]
FuncrefGene = [splicing]
GeneDetailrefGene = [>50]
In IF branch:
==> $1 = [>50]
==> Last line in IF branch: classification = []
============================================================

Row no. = [6]
FuncrefGene = [UTR3]
GeneDetailrefGene = [NM_003042:c.*234C>A]
In IF branch:
==> $1 = [_003042]
==> Last line in IF branch: classification = []
============================================================

$ 
$