annovar annotated, but no record in clinvar online

[asmlgkj]

thanks a lot, professor wang.
here is variant annotated by annovar, but no record in clinvar online . can you have a look?
chr5 112162803 112162803 - G 799389 not_specified MedGen:CN169374 criteria_provided,_single_submitter Pathogenic NC_000005.9:g.112162808dup

[kaichop]

What is the command line that you used? Note that ANNOVAR always perform left normalization of variants. In the case of indels, it always use an annovar-specific format that use '-' to denote null nucleotide.

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On Sat, May 21, 2022 at 5:47 AM curry_fan ***@***.***> wrote: thanks a lot, professor wang. here is variant annotated by annovar, but no record in clinvar *online* . can you have a look? chr5 112162803 112162803 - G 799389 not_specified MedGen:CN169374 criteria_provided,_single_submitter Pathogenic NC_000005.9:g.112162808dup — Reply to this email directly, view it on GitHub <#193>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OH2HVADGQF44LJGSOTVLCWJPANCNFSM5WRS3H7Q> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[asmlgkj]

thanks a lot.
here is my command.
table_annovar.pl my.vcf /annovar/humandb -buildver hg19 -out my.anno -remove -protocol refGeneWithVer,1000g2015aug_all,clinvar_20211002,avsnp150,cosmic94,dbnsfp41c -operation g,f,f,f,f,f -argument '-hgvs,-hgvs,-hgvs,-hgvs,-hgvs,-hgvs' -nastring . -vcfinput -polish

[asmlgkj]

in the vcf, it is a record as follows

chr5 112162803 . A AG

[asmlgkj]

is there any comments about this? thanks a lot