Annovar Output column "AAChange.knowngene" gives different values

Question

[shrutidesai0208]

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?

Answer 1

[Vivek]

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.

Answer 2

[poisonAlien]

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.