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4.9 years ago
hns
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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.
Anyone able to help with this request?
How does the read pileup appear in IGV?
Hi Kevin, Thanks for your reply. Unfortunately, I dont have the bam file and just have the vcf file.
Hey, can you show me the full line from the VCF? If there is low depth of coverage over the region, then the call is not reliable. The fact that there already exists a discrepancy is worrying.
Sure, here is the actual line
7 55248980 . C CTCCAGGAAGCCT 2316 PASS DP=397;AF=0.198992;SB=2;DP4=171,147,46,33;INDEL;HRUN=1
We ran the same line through VEP and annovar, VEP correctly calls it as it is in Cosmic but annovar calls it intronic.
Did you check all of the transcript IDs? EGFR has many splice isoforms - it could be that ANNOVAR has just chosen one that has an intron at that position. It would also be very helpful to obtain the BAM file, but , alas!, you do not have this.
By the way: its presence in COSMIC is not confirmation that the variant is real - it may still be false-positive.
Hi Kevin, we have confirmed the variant via orthogonal assay. The questions is more about the left shifting/normalization vs right and how does annovar handle it
That is a question for the developer of ANNOVAR, Kai Wang. I suggest that you enter in contact with him: http://annovar.openbioinformatics.org/en/latest/misc/contributing/