Question: SnpEff HGVS doesn't match to fields of ref and alt alleles
0
gravatar for mariafirulevabio
10 days ago by
mariafirulevabio0 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 10 days ago • written 10 days ago by mariafirulevabio0

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 10 days ago by RamRS21k
3
gravatar for RamRS
10 days ago by
RamRS21k
Houston, TX
RamRS21k 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 10 days ago • written 10 days ago by RamRS21k

Hello mariafirulevabio ,

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they work.

ADD REPLYlink written 10 days ago by RamRS21k

Dear RamRS,

I appreciate your help. Thanks for it and also for correcting my question.

Best wishes, Maria.

ADD REPLYlink written 10 days ago by mariafirulevabio0

Please accept the answer using the green check mark.

ADD REPLYlink written 10 days ago by RamRS21k
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