SingleLetterAA plugin not working as expected

[MGCarta]

Hi, I tested the plugin and I got something wrong on one variant. The variant is a deletion:

• chrom 7
• position 140778036 (GRCh38)
• REF: GTAGGTGCTGTCACAT
• ALT: G

The variant description I got at mRNA (HGVSc) and protein level (HGVSp) are respectively:

• HGVSc: _NM_004333.6:c.14571471del
• HGVSp _NP_004324.2:p.NVT486APT491delinsT.

However, I have the suspicious something is going wrong with the HGVSp description. Indeed, if I try to disable the SingleLetterAA plugin the HGVSc remains the same but the HGVSp I get:

• _NP_004324.2:p.Asn486Pro490del

seems reasonable. The HGVSp I got in the version in which the plugin is enabled not only shows several amino acids but also the position of 486_491 is shifted of 1 compared to 486_490!

Shouldn't be the HGVSp something like p.N486_P490?

Thanks a lot in advance!

[olaaustine]

HI @MGCarta, Hope this meets you well 😊 Thank you for your query. Is it possible to share the full VEP command used? Thank you Ola.

[MGCarta]

Yes, sorry! I am using vep 110.1 and the command is:

    vep --offline \
    --cache \
    --fork 4 \
    --assembly GRCh38 \
    --refseq \
    --force_overwrite \
    --symbol \
    --canonical \
    --mane \
    --numbers \
    --no_intergenic \
    --clin_sig_allele 1 \
    --af \
    --af_1kg \
    --af_gnomade \
    --af_gnomadg \
    --pubmed \
    --vcf \
    --dir $4 \
    --fasta ./vep/.vep/homo_sapiens/110_GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa.gz \
    --input_file $1 \
    --plugin dbNSFP,./vep/.vep/Plugins/dbNSFP/dbNSFP4.5a_grch38.gz,pep_match=0,SIFT_converted_rankscore,Polyphen2_HDIV_rankscore,Polyphen2_HVAR_rankscore,LRT_converted_rankscore,MutationTaster_converted_rankscore,MutationAssessor_rankscore,FATHMM_converted_rankscore,PROVEAN_converted_rankscore,MetaSVM_rankscore,M-CAP_rankscore,REVEL_rankscore,MutPred_rankscore,CADD_raw_rankscore,DANN_rankscore,fathmm-MKL_coding_rankscore,fathmm-XF_coding_rankscore,GM12878_fitCons_rankscore,GERP++_RS_rankscore,phyloP100way_vertebrate_rankscore,phyloP17way_primate_rankscore,phastCons100way_vertebrate_rankscore,phastCons17way_primate_rankscore \
    --plugin SpliceAI,snv=./vep/.vep/Plugins/spliceAI/spliceai_scores.raw.snv.hg38.vcf.gz,indel=./vep/.vep/Plugins/spliceAI/spliceai_scores.raw.indel.hg38.vcf.gz,cutoff=0.5 \
    --plugin SingleLetterAA \
    --output_file $3

[olaaustine]

Hi @MGCarta, I have not been able to replicate this issue. When i run it with the SingleLetterAA plugin, i get 7_140778037_TAGGTGCTGTCACAT/- 7:140778037-140778051 - 673 NM_004333.6 Transcript inframe_deletion 1683-1697 1457-1471 486-491 NVTAPT/T aATGTGACAGCACCTAca/aca - IMPACT=MODERATE;STRAND=-1;SYMBOL=BRAF;SYMBOL_SOURCE=EntrezGene;CANONICAL=YES;MANE_SELECT=ENST00000646891.2;GIVEN_REF=TAGGTGCTGTCACAT;USED_REF=TAGGTGCTGTCACAT;EXON=12/18;HGVSp=NP_004324.2:p.N486_P490del and when I run without the plugin and just the command--hgvs I get 7_140778037_TAGGTGCTGTCACAT/- 7:140778037-140778051 - 673 NM_004333.6 Transcript inframe_deletion 1683-1697 1457-1471 486-491 NVTAPT/T aATGTGACAGCACCTAca/aca - IMPACT=MODERATE;STRAND=-1;SYMBOL=BRAF;SYMBOL_SOURCE=EntrezGene;CANONICAL=YES;MANE_SELECT=ENST00000646891.2;GIVEN_REF=TAGGTGCTGTCACAT;USED_REF=TAGGTGCTGTCACAT;EXON=12/18;HGVSc=NM_004333.6:c.1457_1471del;HGVSp=NP_004324.2:p.Asn486_Pro490del Please can you use the command --dir_plugins to see if this issue still persists and if it does can you let us know the versions of cache, you are using. Thank you very much Ola.

[olaaustine]

Hi @MGCarta, Hope you are well? Just wanted up to follow up with this issue. Thank you Ola.

[MGCarta]

Hi @olaaustine, sorry for my late reply! I tried to set the parameter --dir_plugins ./vep/.vep/Plugins but I still get the same HGVSp:

7 | 140778036 | 7_140778037_TAGGTGCTGTCACAT/- | GTAGGTGCTGTCACAT | G | . | . | Canonical | 19 | inframe_deletion | BRAF | 12/18 |   | NM_004333.6:c.1457_1471del | NP_004324.2:p.NVT486_APT491delinsT | NP_004324.2:p.NVT486_APT491delinsT | NVTAPT/T | rs1586126439 | YES |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |

The version of the cache is 110_GRCh38

[olaaustine]

Hi @MGCarta, Thank you for your response. Please is it possible to use the latest version of VEP plugins that is release/111. This issue has been fixed for this version. Do let us know if this resolves the issue. Thank you very much Ola.

[olaaustine]

Hi @MGCarta, Hope this meets you well? I am going to close this issue now. Please do not hesitate to reopen this issue or open another ticket if you have any other query. Thank you Ola.