SnpEff HGVS doesn't match to fields of ref and alt alleles

Question

[mariafirulevabio]

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.

[Ram]

I guess I'm missing sth

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

Answer 1

[Ram]

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.