Annotation of exon-intron junction variant

[Bin-Guan]

We used annovar/2020-06-08 for the hg19 variant 6-64574078-CC-TA, which resulted in EYS; exonic,splicing; nonsynonymous SNV; EYS:NM_001142800.2:exon36:c.7228G>T:p.A2410S. Because the variant is at the exon-intron junction, so a proper annotation could be "splicing" instead of "nonsynonymous SNV" & c.7228_7228+1delinsTA. Possible to change the behavior here?

Thanks.

[kaichop]

The annotation seems to be exonic,splicing already, which means it disrupts exon region but also splice site. ANNOVAR does not give HGVS notation to splice variants that disrupt multiple nucleotide though, so it shows as p.A2410S. I hope this helps.

…

On Tue, Jan 10, 2023 at 10:55 PM Bin-Guan ***@***.***> wrote: We used annovar/2020-06-08 for the hg19 variant 6-64574078-CC-TA, which resulted in EYS; exonic,splicing; nonsynonymous SNV; EYS:NM_001142800.2:exon36:c.7228G>T:p.A2410S. Because the variant is at the exon-intron junction, so a proper annotation could be "splicing" instead of "nonsynonymous SNV" & c.7228_7228+1delinsTA. Possible to change the behavior here? Thanks. — Reply to this email directly, view it on GitHub <#207>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OA77OPOBTNMW7UBRC3WRYVJ5ANCNFSM6AAAAAATXRWYGE> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[Bin-Guan]

Thanks!