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

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.

snp variant annotation annotation snpeff hgvs
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written by mariafirulevabio • mariafirulevabio

I guess I'm missing sth

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

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written by Ram Ram

1 answer

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.

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written by Ram Ram

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.

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written by Ram Ram

Dear RamRS,

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

Best wishes, Maria.

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written by mariafirulevabio • mariafirulevabio

Please accept the answer using the green check mark.

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written by Ram Ram

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