Hello bisansamara,

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fin swimmer

if you can install transvar on your machine, it would be much easy:

$ tail -n+2 test.txt |transvar canno -l - -g 1 -m 2  --refseq | cut -f1,2,5 | awk '{gsub("[|/(]","\t")}1' |cut --complement -f3,5,7 | tail -n+2

MAN1B1  c.1897G>T   XM_006716945    chr9:g.137107663G>T p.V633L
MAN1B1  c.1897G>T   NM_016219   chr9:g.137108388G>T p.V633F
CRY1    c.272G>A    NM_004075   chr12:g.107005244C>T    p.W91*

input:

$ cat test.txt 
Gene    BaseChange  refseqID
MAN1B1  c.1897G>T   NM_016219
CRY1    c.272G>A    NM_004075

If you want only for the transcripts in the list:

$ tail -n+2 test.txt |transvar canno -l - -g 1 -m 2 -t3 --refseq | cut -f1,2,5 | awk '{gsub("[|/(]","\t")}1' |cut --complement -f3,5,7 | tail -n+2

MAN1B1  c.1897G>T   NM_016219   chr9:g.137108388G>T p.V633F
CRY1    c.272G>A    NM_004075   chr12:g.107005244C>T    p.W91*