snpEff: gene-CHR_END annotation

Question

[ciemanek]

Hi all!

I was annotating my set of variants with snpEff and for some of the variants I got the annotation that I don't know how to understand. I am working with scaffolds as a reference and coding sequences were predicted using augustus. For some variants in intergenic regions assigned name is g221-CHR_END which I don't really understand - does it mean that my SNPs are impacting some regions in general between the gene 221 and the end of the scaffold? Is there a way to get some more specific information about possible SNP impact?

For example: ANN=T|intergenic_region|MODIFIER|g221-CHR_END|g221-CHR_END|intergenic_region|g221-CHR_END|||n.1007472G>T||||||

I'd be grateful for any hints,

Agata

Answer 1

[Pierre Lindenbaum]

this annotation is used form the very last gene on the chromosome: https://github.com/pcingola/SnpEff/blob/master/src/main/java/org/snpeff/interval/Intergenic.java#L42

does it mean that my SNPs are impacting some regions in general between the gene 221 and the end of the scaffold?

yes. But "impacting" is not well known. Something is just changed.

Is there a way to get some more specific information about possible SNP impact?

see What to do with disease-associated SNPs laying intergenic regions?

[ciemanek]

Thanks a lot Pierre!

Also if you'd be kind to verify my thinking about multiple annotated variants, like:

ANN=TC|frameshift_variant|HIGH|g97|g97|transcript|g97.t1|protein_coding|1/1|c.973dupG|p.Glu325fs|973/1026|973/1026|325/341||,TC|upstream_gene_variant|MODIFIER|g95|g95|transcript|g95.t1|protein_coding||c.-3657dupG|||||3657|,TC|upstream_gene_variant|MODIFIER|g96|g96|transcript|g96.t1|protein_coding||c.-155dupG|||||155|,TC|downstream_gene_variant|MODIFIER|g98|g98|transcript|g98.t1|protein_coding||c.*4095dupG|||||4095|

Can I conclude that this is a variant falling within a coding region (gene 97) and simultaneously impacting other genes (g95, g96, g98) bringing variants on DNA level (duplications) but no variation in protein sequence (or variation is not known)?