Question: Annovar Output column "AAChange.knowngene" gives different values
gravatar for shrutidesai0208
3.1 years ago by
shrutidesai02080 wrote:

Annovar Output column "AAChange.knowngene" has different values for codon and AA change. eg: Chr chr7 Start 50467736 End 50467736 Ref C Alt G Func.knowngene exonic Gene.knowngene IKZF1 GeneDetail.knowngene 0 ExonicFunc.knowngene nonsynonymous SNV AAChange.knowngene IKZF1:uc010kyx.3:exon2:c.C191G:p.A64G,IKZF1:uc022acs.1:exon3:c.C161G:p.A54G,IKZF1:uc003tpa.4:exon4:c.C266G:p.A89G,IKZF1:uc022acr.1:exon4:c.C296G:p.A99G,IKZF1:uc022acq.1:exon5:c.C542G:p.A181G,IKZF1:uc022acy.1:exon5:c.C392G:p.A131G,IKZF1:uc022acz.1:exon5:c.C422G:p.A141G,IKZF1:uc003toz.4:exon6:c.C881G:p.A294G,IKZF1:uc022acv.1:exon6:c.C554G:p.A185G,IKZF1:uc022acw.1:exon6:c.C584G:p.A195G,IKZF1:uc022acx.1:exon6:c.C710G:p.A237G,IKZF1:uc003tox.4:exon7:c.C845G:p.A282G,IKZF1:uc003toy.4:exon7:c.C845G:p.A282G,IKZF1:uc011kck.2:exon7:c.C710G:p.A237G,IKZF1:uc022act.1:exon7:c.C680G:p.A227G,IKZF1:uc022acu.1:exon7:c.C710G:p.A237G,IKZF1:uc003tow.4:exon8:c.C971G:p.A324G cosmic70 0 clinvar_20140929 0 dbnsfp30a 0.134 SIFT_score 0.16 SIFT_pred T Polyphen2_HDIV_score 1 Polyphen2_HDIV_pred D LRT_score 0 LRT_pred D FATHMM_score 4.31 FATHMM_pred T MutationTaster_score 1 MutationTaster_pred D

Which of the transcripts and/or protien/codon change annotated is important while considering the mutation?

annovar • 1.1k views
ADD COMMENTlink modified 3.1 years ago by poisonAlien2.8k • written 3.1 years ago by shrutidesai02080
gravatar for Vivek
3.1 years ago by
Vivek2.3k wrote:

Annovar is giving you the annotation with reference to each transcript within the gene, which is the right way for an annotation program to give results. The practical way to prioritize these is to rank the amino acid change in order of severity, possibly with functional annotation scores and predictions from tools like SIFT/Polyphen/Cadd etc.

Regarding which transcript to use, that's a question that cannot be correctly answered unless you have matching RNA Seq data for the sample and know which isoform of the gene is being expressed.

ADD COMMENTlink written 3.1 years ago by Vivek2.3k
gravatar for poisonAlien
3.1 years ago by
poisonAlien2.8k wrote:

Well its often debatable on choosing a transcript. However there are ways to prioritize transcripts. Use vcf2maf which will do this for you. VEP also has PICK option which will help you to choose a tx.

ADD COMMENTlink written 3.1 years ago by poisonAlien2.8k
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