Question: SnpEff HGVS doesn't match to fields of ref and alt alleles
gravatar for mariafirulevabio
17 months ago by
mariafirulevabio40 wrote:

Dear all,

I've read SnpEff manual and I'm confused by this example:

> 22    17071756    .   T   C   .   . ANN=C|3_prime_UTR_variant|MODIFIER|CCT8L2|ENSG00000198445|transcript|ENST00000359963|protein_coding|1/1|c.*11A>G|||||11|,C|downstream_gene_variant|MODIFIER|FABP5P11|ENSG00000240122|transcript|ENST00000430910|processed_pseudogene||n.*397A>G|||||4223|

Why HGVS of ENST00000359963 is c.*11A>G if ref allele is T and alt allele is C?

I guess I'm missing something. When I've annotated my own vcf file using SnpEff, I found the same type of confusing examples.

Hope you can help me.

ADD COMMENTlink modified 17 months ago • written 17 months ago by mariafirulevabio40

I guess I'm missing sth

Please avoid texting and similar unprofessional jargon on scientific forums. When you mean "something", write "something".

ADD REPLYlink written 17 months ago by RamRS30k
gravatar for RamRS
17 months ago by
Baylor College of Medicine, Houston, TX
RamRS30k wrote:

It's because the transcript is derived from the anti-sense strand. REF and ALT alleles are defined based on the reference genome, which represents just one strand of DNA. Transcripts can be from that strand or the other, and this one is from the other.

Hence, a change of T to C on the reference genome strand equals a change from A (complement of T) to G (complement of C) in the transcript.

ADD COMMENTlink modified 17 months ago • written 17 months ago by RamRS30k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 670 users visited in the last hour