Question: SnPEff ANN[*].FEATURE and ANN[*].FEATUREID annotation
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gravatar for yasminsoareslima
4 months ago by
yasminsoareslima10 wrote:

Hello everyone,

I have a question regarding ANN[*].FEATURE and ANN[*].FEATUREID annotation from snpEff in case you know how to help me.

I have variants in my annotated .tsv which comes with the following annotation for the ANN[*].FEATURE field: structural_interaction_variant. Then, for the ANN[*].FEATUREID I have the the following structure of transcript : **1XMI:D_397-D_443**:ENST00000003084.

However, I'm not sure about how to interpret this.

First of all, I have read the SnPEff documentation, which says:

Effect (Seq. Ontology)  :  structural_interaction_variant
Effect (Classic)        :  PROTEIN_STRUCTURAL_INTERACTION_LOCUS
Note & Example          :  Within protein interaction loci (e.g. two AA that are in contact within the same protein, possibly helping structural conformation)
Impact                  :  HIGH

So, I understand that my variant has some sort of impact over the protein structure. And that probably the 1XMI:D_397-D_443 before the transcript ID means the protein PDB code and the amino acids affected. On the other hand, this variant doesn't generate any amino acid change in ANN[*].HGVS_P field.

However. I'm not sure about which biological conclusions to take from this. Especially because I had some variants being annotated both like this and missense variants at the same time. Others only being annotated only like a structural interaction variants.

I leave here a line of my tsv, tough I don know how to properly copy table lines in here.

CHROM   POS REF ALT ID  QUAL    ANN[*].ALLELE   ANN[*].EFFECT   ANN[*].IMPACT   ANN[*].GENE ANN[*].GENEID   ANN[*].FEATURE  ANN[*].FEATUREID    ANN[*].BIOTYPE  ANN[*].RANK ANN[*].HGVS_C
7   117188812   G   T   rs147422190 100 T   structural_interaction_variant  HIGH    CFTR    ENSG00000001626 interaction 1XMI:A_397-A_443:ENST00000003084    protein_coding  10  c.1327G>T

Many thanks!

ADD COMMENTlink modified 4 months ago by RamRS24k • written 4 months ago by yasminsoareslima10

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.
code_formatting

ADD REPLYlink written 4 months ago by RamRS24k

Many thanks! Next time I'll do it right

ADD REPLYlink written 4 months ago by yasminsoareslima10
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