#!/usr/bin/perl
use strict;

while (<>)
{
        $.<2 and print and next;
          my @f=split/\t/;
         #my @f=split/\s+/;
          my ($FuncIDPrefGene,$AAChangeIDPrefGene,$PopFreqMax,$GeneDetailIDPrefGene,$ClinSig,$Score)=@f[6,11,13,8,46,54];
# Check score for exonic set to 5
         $FuncIDPrefGene eq "exonic" && abs($Score) < 5 and &pj(\@f,"Likely Benign") and next; # Rule 1. Set classification to Likely benign based on score less than 5 for exons

# Check score for everything else set to 5 with GeneDetail following c. nomenclature
        $FuncIDPrefGene !~ "exonic" and abs($Score) < 5 and $GeneDetailIDPrefGene=~/\.\d+[\+\-](\d+)/; # this will capture the digits after    +/- into $1
        $1 < 10 and &pj(\@f,"Likely Benign") and next; # Rule 2. Reclassify intronic variants (with c.) less than 10 based on score

# PopFreqMax VUS
         &pj(\@f,"VUS"); # Rule 3.  If none of the above tests succeeded, and the PopFreqMax < 0.011 set the Classification field to the string VUS.
}
sub pj
{
    my $fr=shift;
       $fr->[55]=shift;
       print join("\t",@{$fr}); # add separator ,"\n"
}

VUS
Likely Benign
Likely Benign