I have a special case which is a duplication, when we use the following two different kinds of coordinate representation, the annotation is different. It is actually a insertion of TCCAGGAAGCCT, but if we take it as an exonic insertion, it is an exon20 insertion and can have clinical significance. But if we annotate it as intronic variant, the variant will not be associated with therapies.
7 55248992 COSM26720 T TTCCAGGAAGCCT . . GENE=EGFR;STRAND=+;CDS=c.2290_2291ins12;AA=p.A763_Y764insFQEA;CNT=6;ANNOVAR_DATE=2018-04-16;Func.refGene=exonic;Gene.refGene=EGFR;GeneDetail.refGene=.;ExonicFunc.refGene=nonframeshift_insertion;AAChange.refGene=EGFR:NM_001346941:exon14:c.1489_1490insTCCAGGAAGCCT:p.A496_Y497insFQEA,EGFR:NM_001346897:exon19:c.2155_2156insTCCAGGAAGCCT:p.A718_Y719insFQEA,EGFR:NM_001346899:exon19:c.2155_2156insTCCAGGAAGCCT:p.A718_Y719insFQEA,EGFR:NM_001346898:exon20:c.2290_2291insTCCAGGAAGCCT:p.A763_Y764insFQEA,EGFR:NM_001346900:exon20:c.2131_2132insTCCAGGAAGCCT:p.A710_Y711insFQEA,EGFR:NM_005228:exon20:c.2290_2291insTCCAGGAAGCCT:p.A763_Y764insFQEA;ALLELE_END 7 55248980 . C CTCCAGGAAGCCT 2316 PASS DP=397;AF=0.198992;SB=2;DP4=171,147,46,33;INDEL;HRUN=1;ANNOVAR_DATE=2018-04-16;Func.refGene=intronic;Gene.refGene=EGFR;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;ALLELE_END
I found VEP annotation also has it as exonic insertion for
7 55248980 C>CTCCAGGAAGCCT.
Is there anyway that annovar can interpret that the second mutation is the same as the first and call it as an exonic mutation.
Thank you so much for all your help in advance.