Snpeff Not Annotating All Protein-Coding Transcripts??

Question

[pablo.riesgo]

Hi there,

I'm digging a little bit into SnpEff and everything works fine, but I have a doubt for which I didn't find an answer in any of the SnpEff papers/documentation. I have a variant (rs4372192 ) in the intronic region of one gene (SAMD11) and it returns the annotations for all Ensembl non protein-coding transcripts in an interval of +/-5KB from this variant. Everything fine up to here. But, not all the protein-coding transcripts for the gene (SAMD11) are matched, only one. Why is it not returning all protein-coding transcripts? Anybody knows if this is configurable? But, in any case is there any reason I should know for this working.

SnpEff output:

EFF=DOWNSTREAM(MODIFIER||||NOC2L|processed_transcript|CODING|ENST00000327044|),DOWNSTREAM(MODIFIER||||NOC2L|processed_transcript|CODING|ENST00000477976|),DOWNSTREAM(MODIFIER||||NOC2L|processed_transcript|CODING|ENST00000483767|),DOWNSTREAM(MODIFIER||||NOC2L|processed_transcript|CODING|ENST00000496938|),DOWNSTREAM(MODIFIER||||SAMD11|protein_coding|CODING|ENST00000420190|),INTRON(MODIFIER||||SAMD11|protein_coding|CODING|ENST00000342066|),TRANSCRIPT(MODIFIER||||SAMD11|protein_coding|CODING|ENST00000474461|),TRANSCRIPT(MODIFIER||||SAMD11|protein_coding|CODING|ENST00000478729|),UPSTREAM(MODIFIER||||SAMD11|protein_coding|CODING|ENST00000464948|),UPSTREAM(MODIFIER||||SAMD11|protein_coding|CODING|ENST00000466827|)

Ensembl visualization: http://www.ensembl.org/Homosapiens/Share/ada5a5b75859324951f803bddc01cce786943248"]http://www.ensembl.org/Homosapiens/Share/ada5a5b75859324951f803bddc01cce786943248

Cheers,

Pablo.

Answer 1

[pablo.riesgo]

I will answer myself :) A clue for this might be that the non-matched transcripts are marked as novel in Ensemble, instead of known. So, there are two alternatives: first, that the database SnpEff is using does not include these transcripts; or second that they are filtered out as they are less confident.