NMD plugin - flag not annotated as expected

[rklocke]

VEP version: Docker version 107.0 Plugin version: NMD.pm release 107 Cache: Indexed RefSeq cache 107 - homo_sapiens_refseq_vep_107_GRCh37.tar.gz

Hi there, I am using the NMD plugin and have noticed that the below variant is not being annotated with the 'NMD_escaping_variant' flag but I believe it falls in the last 50bp of the penultimate exon (9/10). Please could you help me understand why it is not being annotated?

NM_130799.2:c.1304del (11-64572551-GC-G)

I am using VEP release 107 but I have also tried annotating this variant with VEP 109 through the web tool and the NMD escape flag is also not added.

docker run -v /home/dnanexus:/opt/vep/.vep 199b8c2aa90b \
./vep -i /opt/vep/.vep/NMD_escape_variant.vcf \
-o /opt/vep/.vep/NMD_escape_variant_annotated.vcf.gz \
--vcf --cache --refseq --exclude_predicted --symbol --hgvs --hgvsg --check_existing --variant_class \
--numbers --format vcf --offline --exclude_null_alleles --assembly GRCh37 \
--plugin NMD 
--fields Allele,SYMBOL,VARIANT_CLASS,Consequence,IMPACT,EXON,INTRON,Feature,HGVSc,HGVSp,HGVS_OFFSET,Existing_variation,STRAND,NMD \
--compress_output bgzip --shift_3prime 1

Filter to only this transcript:

docker run -v /home/dnanexus:/opt/vep/.vep 199b8c2aa90b \
./filter_vep -i /opt/vep/.vep/NMD_escape_variant_annotated.vcf.gz \
-o /opt/vep/.vep/NMD_escape_variant_annotated_filtered.vcf \
--only_matched --filter 'Feature match NM_130799'

Input file and output file are attached. Thank you in advance for your help! Becky

NMD_escape_variant.vcf.gz NMD_escape_variant_annotated_filtered.vcf.gz

[olaaustine]

Hi @rklocke, Thank you for your query. We have identified the issue and it has been fixed in our upcoming release 110, which is scheduled to be available soon. Thank you for bringing this to our attention. If you have any further queries, please don't hesitate to let us know. Thank you Ola.

[olaaustine]

Hi @rklocke, VEP - release 110 is now available. Thank you very much for bringing this to our attention. I will close this ticket now, please feel free to reopen this ticket or open another, if there is any other issues. Thank you Ola.