SnpEff sequence_feature interpretation?

Question

[alexvpickering]

I am trying to interpret the following annotation from SnpEff:

chr10   96633300        rs4919045       G       A       15277.3 PASS    ...ANN=A|sequence_feature|MODERATE|PIK3AP1|ENSG00000155629|modified-residue:Phosphotyrosine|ENST00000339364|protein_coding|8/16|c.1376-4807C>T||||||,A|upstream_gene_variant|MODIFIER|PIK3AP1|ENSG00000155629|transcript|ENST00000371109.3|protein_coding||c.-241C>T|||||59|,A|intron_variant|MODIFIER|PIK3AP1|ENSG00000155629|transcript|ENST00000339364.9|protein_coding|8/16|c.1376-4807C>T||||||,A|intron_variant|MODIFIER|PIK3AP1|ENSG00000155629|transcript|ENST00000371110.6|protein_coding|7/15|c.842-4807C>T||||||,A|intron_variant|MODIFIER|PIK3AP1|ENSG00000155629|transcript|ENST00000468783.1|processed_transcript|7/7|n.1022-4807C>T|||||| ...

In particular, I am interested in understanding the MODERATE effect annotation with the Sequence Ontology feature type of modified-residue:Phosphotyrosine as the location seems to be intronic. I assume there must be an alternatively-spliced transcript where this is not the case but cannot find it anywhere. How do I interpret/track down the origin of this annotation? Thank you!

[cpad0112]

what's the reference build you have used for annotation? For GRCh 37 and 38. VEP classifies rs4919045 as modifier for all the transcripts. I got his annotation with SNPeff.

$ java -Xmx6g -jar ~/ekg/snpEff/snpEff.jar GRCh37.87 test.vcf

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  1242658141  1364665948  1242658615
10  96633300    rs4919045   G   A   .   PASS    ANN=A|upstream_gene_variant|MODIFIER|CYP2C58P|ENSG00000235199|transcript|ENST00000436281.1|processed_pseudogene||n.-414C>T|||||414|,A|intergenic_region|MODIFIER|CYP2C58P-RP11-400G3.3|ENSG00000235199-ENSG00000225354|intergenic_region|ENSG00000235199-ENSG00000225354|||n.96633300G>A||||||  GT:DS   0|0:0.193   0|0:0.193   0|0:0.193

  snpEff version SnpEff 5.0e (build 2021-03-09 06:01)

[alexvpickering]

Here is the relevant header from the VCF:

##SnpEffVersion="4.3t (build 2017-11-24 10:18), by Pablo Cingolani"
##SnpEffCmd="SnpEff  GRCh38.86 pass_snp.gnomad.vcf.gz "

Which does reproduce the above MODERATE effect but it doesn't with GRCh38.99. What would be the/a likely rationale for this change? I am guessing the more recent GRCh should be taken as the correct annotation.

[cpad0112]

with SNPeff version SnpEff 5.0e (build 2021-03-09 06:01), for 38.13.Refseq

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  1242658141  1364665948  1242658615
10  96633300    rs4919045   G   A   .   PASS    ANN=A|intron_variant|MODIFIER|PIK3AP1|PIK3AP1|transcript|NM_152309.3|protein_coding|8/16|c.1376-4807C>T||||||,A|intron_variant|MODIFIER|PIK3AP1|PIK3AP1|transcript|XM_005269498.1|protein_coding|7/15|c.842-4807C>T||||||,A|intron_variant|MODIFIER|PIK3AP1|PIK3AP1|transcript|XM_005269499.1|protein_coding|7/15|c.842-4807C>T||||||,A|intron_variant|MODIFIER|PIK3AP1|PIK3AP1|transcript|XM_011539248.1|protein_coding|8/15|c.1376-4807C>T||||||,A|intron_variant|MODIFIER|PIK3AP1|PIK3AP1|transcript|XM_011539249.1|protein_coding|8/15|c.1376-4807C>T|||||| GT:DS   0|0:0.193   0|0:0.193   0|0:0.193

with GRCh38.99,

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  1242658141  1364665948  1242658615
10  96633300    rs4919045   G   A   .   PASS    ANN=A|upstream_gene_variant|MODIFIER|PIK3AP1|ENSG00000155629|transcript|ENST00000371109.3|protein_coding||c.-241C>T|||||59|,A|intron_variant|MODIFIER|PIK3AP1|ENSG00000155629|transcript|ENST00000339364.10|protein_coding|8/16|c.1376-4807C>T||||||,A|intron_variant|MODIFIER|PIK3AP1|ENSG00000155629|transcript|ENST00000371110.6|protein_coding|7/15|c.842-4807C>T||||||,A|intron_variant|MODIFIER|PIK3AP1|ENSG00000155629|transcript|ENST00000468783.1|processed_transcript|7/7|n.1022-4807C>T||||||    GT:DS   0|0:0.193   0|0:0.193   0|0:0.193

Seems so far all the GRCh37, and 38 (refseq and ENSEMBL), result is consistent with your understanding, however it differs with your result. Can you try using some other database of GRCh38 within SNPeff in annotating this variant? Extract just this variant with headers and re-annotate with some other GRCh38 version.

Answer 1

[Pierre Lindenbaum]

How do I interpret/track down the origin of this annotation?

https://github.com/pcingola/SnpEff/blob/master/src/main/java/org/snpeff/snpEffect/EffectType.java

[alexvpickering]

care to increase the verbosity? I see there are various effect types that map to effect impacts but it's unclear to me how the above is mapped to moderate impact.