use or no use shift_3prime , Inconsistency result in hgvsg and clinvar

[ArsFc]

Describe the issue

A clear and concise description of what the bug is.

Additional information

Please fill in the following sections to help us find the source of your issue as quickly as possible.

System

• VEP version: 111
• VEP Cache version: 111
• Perl version: v5.30.0
• OS: Ubuntu20.04
• tabix installed yes

Full VEP command line

vep --fork 16 --offline --cache --refseq --species homo_sapiens --assembly GRCh37  --dir_cache ensembl-vep/cache/  --dir_plugins ensembl-vep/cache/Plugins/ -id '7 80303353 3382270 A AAAAT'  --show_ref_allele --symbol --canonical --variant_class --hgvs --shift_3prime 1 --hgvsg --biotype --minimal --allele_number --total_length --numbers --domains --flag_pick_allele_gene --pick_order biotype,ccds,rank,canonical,refseq --check_existing --exclude_null_alleles --af --af_1kg --max_af  --sift s --polyphen s --no_stats --fasta  ensembl-vep/cache/Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz  --tab --output_file  b1.tsv  --force_overwrite   --custom ensembl-vep/cache/Custom/clinvar_20250415.vcf.gz,ClinVar,vcf,exact,0,CLNSIG,CLNREVSTAT,CLNSIGCONF,CLNDN

#######
part result （command line with shift_3prime）

<style> </style>

#Uploaded_variation	Location	Feature	Consequence	Existing_variation	HGVSc	HGVSp	HGVS_OFFSET	HGVSg	ClinVar	ClinVar_CLNSIG	ClinVar_CLNREVSTAT	ClinVar_CLNSIGCONF	ClinVar_CLNDN
3382270	7:80303353-80303354	NM_000072.3	frameshift_variant	-	NM_000072.3:c.1313_1316dup	NP_000063.2:p.Leu440LysfsTer70	7	-	-	-	-	-	-
3382270	7:80303353-80303354	NM_001001547.3	frameshift_variant	-	NM_001001547.3:c.1313_1316dup	NP_001001547.1:p.Leu440LysfsTer70	7	-	-	-	-	-	-
3382270	7:80303353-80303354	NM_001001548.3	frameshift_variant	-	NM_001001548.3:c.1313_1316dup	NP_001001548.1:p.Leu440LysfsTer115	7	-	-	-	-	-	-
3382270	7:80303353-80303354	NM_001127443.2	frameshift_variant	-	NM_001127443.2:c.1313_1316dup	NP_001120915.1:p.Leu440LysfsTer70	7	-	-	-	-	-	-
3382270	7:80303353-80303354	NM_001127444.2	frameshift_variant	-	NM_001127444.2:c.1313_1316dup	NP_001120916.1:p.Leu440LysfsTer70	7	-	-	-	-	-	-
3382270	7:80303353-80303354	NM_001289908.1	frameshift_variant	-	NM_001289908.1:c.1196_1199dup	NP_001276837.1:p.Leu401LysfsTer70	7	-	-	-	-	-	-
3382270	7:80303353-80303354	NM_001289909.1	frameshift_variant	-	NM_001289909.1:c.1133_1136dup	NP_001276838.1:p.Leu380LysfsTer70	7	-	-	-	-	-	-
3382270	7:80303353-80303354	NM_001289911.2	frameshift_variant	-	NM_001289911.2:c.1085_1088dup	NP_001276840.1:p.Leu364LysfsTer70	7	-	-	-	-	-	-
3382270	7:80303353-80303354	NM_001371074.1	frameshift_variant	-	NM_001371074.1:c.1313_1316dup	NP_001358003.1:p.Leu440LysfsTer70	7	-	-	-	-	-	-
3382270	7:80303353-80303354	NM_001371075.1	frameshift_variant	-	NM_001371075.1:c.1313_1316dup	NP_001358004.1:p.Leu440LysfsTer115	7	-	-	-	-	-	-
3382270	7:80303353-80303354	NM_001371077.1	frameshift_variant	-	NM_001371077.1:c.1313_1316dup	NP_001358006.1:p.Leu440LysfsTer115	7	-	-	-	-	-	-
3382270	7:80303353-80303354	NM_001371078.1	frameshift_variant	-	NM_001371078.1:c.1313_1316dup	NP_001358007.1:p.Leu440LysfsTer70	7	-	-	-	-	-	-
3382270	7:80303353-80303354	NM_001371079.1	frameshift_variant	-	NM_001371079.1:c.1211_1214dup	NP_001358008.1:p.Leu406LysfsTer70	7	-	-	-	-	-	-
3382270	7:80303353-80303354	NM_001371080.1	frameshift_variant	-	NM_001371080.1:c.848_851dup	NP_001358009.1:p.Leu285LysfsTer70	7	-	-	-	-	-	-
3382270	7:80303353-80303354	NM_001371081.1	frameshift_variant	-	NM_001371081.1:c.848_851dup	NP_001358010.1:p.Leu285LysfsTer70	7	-	-	-	-	-	-
3382270	7:80303353-80303354	NR_110501.1	non_coding_transcript_exon_variant	rs753569550	NR_110501.1:n.1304_1307dup	-	7	7:g.80303357_80303360dup	3382270	Likely_pathogenic	criteria_provided,_single_submitter	-	Malaria,_susceptibility_to|Platelet-type_bleeding_disorder_10|Coronary_heart_disease,_susceptibility_to,_7

############
part result （command line without shift_3prime）

<style> </style>

#Uploaded_variation	Location	Feature	Consequence	Existing_variation	HGVSc	HGVSp	HGVS_OFFSET	HGVSg	ClinVar	ClinVar_CLNSIG	ClinVar_CLNREVSTAT	ClinVar_CLNSIGCONF	ClinVar_CLNDN
3382270	7:80303353-80303354	NM_000072.3	frameshift_variant	rs753569550	NM_000072.3:c.1313_1316dup	NP_000063.2:p.Leu440LysfsTer70	7	7:g.80303357_80303360dup	3382270	Likely_pathogenic	criteria_provided,_single_submitter	-	Malaria,_susceptibility_to|Platelet-type_bleeding_disorder_10|Coronary_heart_disease,_susceptibility_to,_7
3382270	7:80303353-80303354	NM_001001547.3	frameshift_variant	rs753569550	NM_001001547.3:c.1313_1316dup	NP_001001547.1:p.Leu440LysfsTer70	7	7:g.80303357_80303360dup	3382270	Likely_pathogenic	criteria_provided,_single_submitter	-	Malaria,_susceptibility_to|Platelet-type_bleeding_disorder_10|Coronary_heart_disease,_susceptibility_to,_7
3382270	7:80303353-80303354	NM_001001548.3	frameshift_variant	rs753569550	NM_001001548.3:c.1313_1316dup	NP_001001548.1:p.Leu440LysfsTer115	7	7:g.80303357_80303360dup	3382270	Likely_pathogenic	criteria_provided,_single_submitter	-	Malaria,_susceptibility_to|Platelet-type_bleeding_disorder_10|Coronary_heart_disease,_susceptibility_to,_7
3382270	7:80303353-80303354	NM_001127443.2	frameshift_variant	rs753569550	NM_001127443.2:c.1313_1316dup	NP_001120915.1:p.Leu440LysfsTer70	7	7:g.80303357_80303360dup	3382270	Likely_pathogenic	criteria_provided,_single_submitter	-	Malaria,_susceptibility_to|Platelet-type_bleeding_disorder_10|Coronary_heart_disease,_susceptibility_to,_7
3382270	7:80303353-80303354	NM_001127444.2	frameshift_variant	rs753569550	NM_001127444.2:c.1313_1316dup	NP_001120916.1:p.Leu440LysfsTer70	7	7:g.80303357_80303360dup	3382270	Likely_pathogenic	criteria_provided,_single_submitter	-	Malaria,_susceptibility_to|Platelet-type_bleeding_disorder_10|Coronary_heart_disease,_susceptibility_to,_7
3382270	7:80303353-80303354	NM_001289908.1	frameshift_variant	rs753569550	NM_001289908.1:c.1196_1199dup	NP_001276837.1:p.Leu401LysfsTer70	7	7:g.80303357_80303360dup	3382270	Likely_pathogenic	criteria_provided,_single_submitter	-	Malaria,_susceptibility_to|Platelet-type_bleeding_disorder_10|Coronary_heart_disease,_susceptibility_to,_7
3382270	7:80303353-80303354	NM_001289909.1	frameshift_variant	rs753569550	NM_001289909.1:c.1133_1136dup	NP_001276838.1:p.Leu380LysfsTer70	7	7:g.80303357_80303360dup	3382270	Likely_pathogenic	criteria_provided,_single_submitter	-	Malaria,_susceptibility_to|Platelet-type_bleeding_disorder_10|Coronary_heart_disease,_susceptibility_to,_7
3382270	7:80303353-80303354	NM_001289911.2	frameshift_variant	rs753569550	NM_001289911.2:c.1085_1088dup	NP_001276840.1:p.Leu364LysfsTer70	7	7:g.80303357_80303360dup	3382270	Likely_pathogenic	criteria_provided,_single_submitter	-	Malaria,_susceptibility_to|Platelet-type_bleeding_disorder_10|Coronary_heart_disease,_susceptibility_to,_7
3382270	7:80303353-80303354	NM_001371074.1	frameshift_variant	rs753569550	NM_001371074.1:c.1313_1316dup	NP_001358003.1:p.Leu440LysfsTer70	7	7:g.80303357_80303360dup	3382270	Likely_pathogenic	criteria_provided,_single_submitter	-	Malaria,_susceptibility_to|Platelet-type_bleeding_disorder_10|Coronary_heart_disease,_susceptibility_to,_7
3382270	7:80303353-80303354	NM_001371075.1	frameshift_variant	rs753569550	NM_001371075.1:c.1313_1316dup	NP_001358004.1:p.Leu440LysfsTer115	7	7:g.80303357_80303360dup	3382270	Likely_pathogenic	criteria_provided,_single_submitter	-	Malaria,_susceptibility_to|Platelet-type_bleeding_disorder_10|Coronary_heart_disease,_susceptibility_to,_7
3382270	7:80303353-80303354	NM_001371077.1	frameshift_variant	rs753569550	NM_001371077.1:c.1313_1316dup	NP_001358006.1:p.Leu440LysfsTer115	7	7:g.80303357_80303360dup	3382270	Likely_pathogenic	criteria_provided,_single_submitter	-	Malaria,_susceptibility_to|Platelet-type_bleeding_disorder_10|Coronary_heart_disease,_susceptibility_to,_7
3382270	7:80303353-80303354	NM_001371078.1	frameshift_variant	rs753569550	NM_001371078.1:c.1313_1316dup	NP_001358007.1:p.Leu440LysfsTer70	7	7:g.80303357_80303360dup	3382270	Likely_pathogenic	criteria_provided,_single_submitter	-	Malaria,_susceptibility_to|Platelet-type_bleeding_disorder_10|Coronary_heart_disease,_susceptibility_to,_7
3382270	7:80303353-80303354	NM_001371079.1	frameshift_variant	rs753569550	NM_001371079.1:c.1211_1214dup	NP_001358008.1:p.Leu406LysfsTer70	7	7:g.80303357_80303360dup	3382270	Likely_pathogenic	criteria_provided,_single_submitter	-	Malaria,_susceptibility_to|Platelet-type_bleeding_disorder_10|Coronary_heart_disease,_susceptibility_to,_7
3382270	7:80303353-80303354	NM_001371080.1	frameshift_variant	rs753569550	NM_001371080.1:c.848_851dup	NP_001358009.1:p.Leu285LysfsTer70	7	7:g.80303357_80303360dup	3382270	Likely_pathogenic	criteria_provided,_single_submitter	-	Malaria,_susceptibility_to|Platelet-type_bleeding_disorder_10|Coronary_heart_disease,_susceptibility_to,_7
3382270	7:80303353-80303354	NM_001371081.1	frameshift_variant	rs753569550	NM_001371081.1:c.848_851dup	NP_001358010.1:p.Leu285LysfsTer70	7	7:g.80303357_80303360dup	3382270	Likely_pathogenic	criteria_provided,_single_submitter	-	Malaria,_susceptibility_to|Platelet-type_bleeding_disorder_10|Coronary_heart_disease,_susceptibility_to,_7
3382270	7:80303353-80303354	NR_110501.1	non_coding_transcript_exon_variant	rs753569550	NR_110501.1:n.1304_1307dup	-	7	7:g.80303357_80303360dup	3382270	Likely_pathogenic	criteria_provided,_single_submitter	-	Malaria,_susceptibility_to|Platelet-type_bleeding_disorder_10|Coronary_heart_disease,_susceptibility_to,_7

[nakib103]

Hi @ArsFc,

Thanks for your query.

Just to let you know I can re-produce the issue. I am still investigating the cause of this mismatch. It seems like how is allele being handled by VEP currently. Once I have more concrete understanding of the issue I will update here.

Best regards,
Nakib

[nakib103]

Hi @ArsFc ,

An update to this issue.

I have found the bug for HGVSg. I will add a fix for it and let you know once it is available.

For the custom annotation it is little bit complicated. With shift_3prime the allele gets shifted and change from AAAT to TAAA. And exact option in custom annotation will do an exact allele match. That's why we are not seeing any custom annotation when shift_3prime=1. Except for the last transcript, which is non coding transcript, and It turns out that non coding transcript does not get their allele shifted even if shift_3prime is enabled. This has been noted as known bug for now.

Best regards,
Nakib

[ArsFc]

thanks a lot for your respanse, and not only hgvsg different , also the custom clinvar annot

[nakib103]

Hi @ArsFc,

A hotfix has been published with the fix for HGVSg. You can update to the latest Ensembl VEP release and try again -

cd ensembl-vep
git pull
git checkout release/114.1
perl INSTALL.pl

Hopefully it will resolve your HGVSg issue.

Best regards,
Nakib

[ArsFc]

thanks a lot ! i will update and test netx week .

[Stikus]

@nakib103 Looks like after 114.1 release we are getting tons of warnings about updated string:

WARNING: 479 : Use of uninitialized value $allele_string in hash element at /soft/ensembl-vep-114.1/modules/Bio/EnsEMBL/VEP/OutputFactory.pm line 1318, <$fh> line 7846.
Use of uninitialized value $allele_string in hash element at /soft/ensembl-vep-114.1/modules/Bio/EnsEMBL/VEP/OutputFactory.pm line 1318, <$fh> line 7846.
Use of uninitialized value $allele_string in hash element at /soft/ensembl-vep-114.1/modules/Bio/EnsEMBL/VEP/OutputFactory.pm line 1318, <$fh> line 7846.
Use of uninitialized value $allele_string in hash element at /soft/ensembl-vep-114.1/modules/Bio/EnsEMBL/VEP/OutputFactory.pm line 1318, <$fh> line 7846.
Use of uninitialized value $allele_string in hash element at /soft/ensembl-vep-114.1/modules/Bio/EnsEMBL/VEP/OutputFactory.pm line 1318, <$fh> line 7846.
Use of uninitialized value $allele_string in hash element at /soft/ensembl-vep-114.1/modules/Bio/EnsEMBL/VEP/OutputFactory.pm line 1318, <$fh> line 7846.
Use of uninitialized value $allele_string in hash element at /soft/ensembl-vep-114.1/modules/Bio/EnsEMBL/VEP/OutputFactory.pm line 1318, <$fh> line 7846.

Our VEP command:

  Command: '/soft/ensembl-vep-114.1/vep --fork 96 --input_file /var/lib/cwl/stg2a5f448e-d17e-4b90-ab5f-fd160fdcccd8/770500050143_strelka.PASSonly.vcf.gz --format vcf --cache --dir_cache /kLHYbu/output/ref/.vep --dir_plugins /soft/ensembl-vep-114.1/Plugins --assembly GRCh38 --offline --output_file /kLHYbu/output/7705
00050143_strelka.annot-vep.vcf --vcf --force_overwrite --symbol --check_existing --terms SO --tsl --hgvs --hgvsg --transcript_version --failed 1 --af --max_af --af_1kg --af_gnomad --pubmed --sift b --polyphen b --variant_class --gene_phenotype --regulatory --numbers --domains --protein --canonical --ccds --uniprot -
-biotype --shift_hgvs 1 --xref_refseq --flag_pick_allele --no_escape --minimal --allele_number --total_length     '.

Or this is a separate issue?

[nakib103]

Hi @Stikus,

Thanks for reporting this issue. It very well could be due to that hotfix.
Are you getting HGVSg correctly? Also, can you share example variant that is causing this issue.

Best regards,
Nakib

[Stikus]

I've found problematic variant example:

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	770500050143_S8_L00
chr1	964629	.	CG	C,CGC	976	PASS	CIGAR=1M1D,2M1I;RU=G,C;REFREP=1,1;IDREP=0,2;MQ=49	GT:GQ:GQX:DPI:AD:ADF:ADR:FT:PL	1/1:67:6:25:0,22,0:0,5,0:0,17,0:PASS:999,70,0,992,67,999

Its annotation:

##VEP="v114.1" API="v114" time="2025-06-17 12:54:01" cache="/ref/.vep/homo_sapiens/114_GRCh38" ensembl=114.1117691 ensembl-compara=114.0efa758 ensembl-funcgen=114.dc9dfbc ensembl-io=114.ec3b610 ensembl-variation=114.ca00935 1000genomes="phase3" COSMIC="100" ClinVar="202409" HGMD-PUBLIC="20204" assembly="GRCh38.p14" dbSNP="156" gencode="GENCODE 48" genebuild="GENCODE48" gnomADe="v4.1" gnomADg="v4.1" polyphen="2.2.3" regbuild="1.0" sift="6.2.1"
##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|ALLELE_NUM|DISTANCE|STRAND|FLAGS|PICK|VARIANT_CLASS|MINIMISED|SYMBOL_SOURCE|HGNC_ID|CANONICAL|TSL|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|UNIPROT_ISOFORM|RefSeq|GENE_PHENO|SIFT|PolyPhen|DOMAINS|HGVS_OFFSET|HGVSg|AF|AFR_AF|AMR_AF|EAS_AF|EUR_AF|SAS_AF|gnomADe_AF|gnomADe_AFR_AF|gnomADe_AMR_AF|gnomADe_ASJ_AF|gnomADe_EAS_AF|gnomADe_FIN_AF|gnomADe_MID_AF|gnomADe_NFE_AF|gnomADe_REMAINING_AF|gnomADe_SAS_AF|MAX_AF|MAX_AF_POPS|CLIN_SIG|SOMATIC|PHENO|PUBMED|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|TRANSCRIPTION_FACTORS">
##VEP-command-line='vep --af --af_1kg --af_gnomad --allele_number --assembly GRCh38 --biotype --cache --cache_version 114 --canonical --ccds --check_existing --database 0 --dir_cache [PATH]/.vep --dir_plugins [PATH]/Plugins --domains --failed --flag_pick_allele --force_overwrite --fork 96 --format vcf --gene_phenotype --hgvs --hgvsg --input_file [PATH]/770500050143_strelka_v2.2.0.PASSonly.error.woc.vcf --max_af --minimal --no_escape --numbers --offline --output_file [PATH]/770500050143_strelka_error_woc.annot-vep.vcf --polyphen b --protein --pubmed --regulatory --shift_hgvs --sift b --symbol --total_length --transcript_version --tsl --uniprot --variant_class --vcf --xref_refseq'
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	770500050143_S8_L00
chr1	964629	.	CG	C,CGC	976	PASS	CIGAR=1M1D,2M1I;RU=G,C;REFREP=1,1;IDREP=0,2;MQ=49;CSQ=C|intron_variant|MODIFIER|KLHL17|ENSG00000187961|Transcript|ENST00000338591.8|protein_coding||11/11|ENST00000338591.8:c.1700+101dup||||||||2||1||1|deletion|1|HGNC|HGNC:24023|YES|1|CCDS30550.1|ENSP00000343930|Q6TDP4.156||UPI00001DFBF0||NM_198317.3|||||1||||||||||||||||||||||||||||,C|upstream_gene_variant|MODIFIER|PLEKHN1|ENSG00000187583|Transcript|ENST00000379407.7|protein_coding|||||||||||2|1871|1|||deletion|1|HGNC|HGNC:25284||1|CCDS53256.1|ENSP00000368717|Q494U1.140||UPI00005764FF|Q494U1-3|NM_001160184.2|||||||||||||||||||||||||||||||||,C|upstream_gene_variant|MODIFIER|PLEKHN1|ENSG00000187583|Transcript|ENST00000379409.6|protein_coding|||||||||||2|1871|1|||deletion|1|HGNC|HGNC:25284||2|CCDS90835.1|ENSP00000368719|Q494U1.140||UPI0000D61E06|Q494U1-2|NM_001410697.1|||||||||||||||||||||||||||||||||,C|upstream_gene_variant|MODIFIER|PLEKHN1|ENSG00000187583|Transcript|ENST00000379410.8|protein_coding|||||||||||2|1851|1|||deletion|1|HGNC|HGNC:25284|YES|1|CCDS4.1|ENSP00000368720|Q494U1.140||UPI00001416D8|Q494U1-1|NM_001367552.1&NM_032129.3|||||||||||||||||||||||||||||||||,C|downstream_gene_variant|MODIFIER|KLHL17|ENSG00000187961|Transcript|ENST00000463212.1|retained_intron|||||||||||2|2152|1|||deletion|1|HGNC|HGNC:24023||1||||||||||||||||||||||||||||||||||||||||,C|downstream_gene_variant|MODIFIER|KLHL17|ENSG00000187961|Transcript|ENST00000466300.1|nonsense_mediated_decay|||||||||||2|100|1|cds_start_NF||deletion|1|HGNC|HGNC:24023||3||ENSP00000463694||J3QLT4.52|UPI000268AE1E|||||||||||||||||||||||||||||||||||,C|downstream_gene_variant|MODIFIER|KLHL17|ENSG00000187961|Transcript|ENST00000481067.1|retained_intron|||||||||||2|466|1|||deletion|1|HGNC|HGNC:24023||2||||||||||||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|KLHL17|ENSG00000187961|Transcript|ENST00000338591.8|protein_coding||11/11|ENST00000338591.8:c.1700+100del|||||||rs371055706|1||1||1|deletion|1|HGNC|HGNC:24023|YES|1|CCDS30550.1|ENSP00000343930|Q6TDP4.156||UPI00001DFBF0||NM_198317.3||||||chr1:g.964630del|||||||0.05705|0.009871|0.04404|0.07842|0.01792|0.05182|0.05843|0.05938|0.05614|0.07734|0.07842|gnomADe_ASJ|||||||||,-|upstream_gene_variant|MODIFIER|PLEKHN1|ENSG00000187583|Transcript|ENST00000379407.7|protein_coding||||||||||rs371055706|1|1872|1|||deletion|1|HGNC|HGNC:25284||1|CCDS53256.1|ENSP00000368717|Q494U1.140||UPI00005764FF|Q494U1-3|NM_001160184.2||||||chr1:g.964630del|||||||0.05705|0.009871|0.04404|0.07842|0.01792|0.05182|0.05843|0.05938|0.05614|0.07734|0.07842|gnomADe_ASJ|||||||||,-|upstream_gene_variant|MODIFIER|PLEKHN1|ENSG00000187583|Transcript|ENST00000379409.6|protein_coding||||||||||rs371055706|1|1872|1|||deletion|1|HGNC|HGNC:25284||2|CCDS90835.1|ENSP00000368719|Q494U1.140||UPI0000D61E06|Q494U1-2|NM_001410697.1||||||chr1:g.964630del|||||||0.05705|0.009871|0.04404|0.07842|0.01792|0.05182|0.05843|0.05938|0.05614|0.07734|0.07842|gnomADe_ASJ|||||||||,-|upstream_gene_variant|MODIFIER|PLEKHN1|ENSG00000187583|Transcript|ENST00000379410.8|protein_coding||||||||||rs371055706|1|1852|1|||deletion|1|HGNC|HGNC:25284|YES|1|CCDS4.1|ENSP00000368720|Q494U1.140||UPI00001416D8|Q494U1-1|NM_001367552.1&NM_032129.3||||||chr1:g.964630del|||||||0.05705|0.009871|0.04404|0.07842|0.01792|0.05182|0.05843|0.05938|0.05614|0.07734|0.07842|gnomADe_ASJ|||||||||,-|downstream_gene_variant|MODIFIER|KLHL17|ENSG00000187961|Transcript|ENST00000463212.1|retained_intron||||||||||rs371055706|1|2152|1|||deletion|1|HGNC|HGNC:24023||1|||||||||||||chr1:g.964630del|||||||0.05705|0.009871|0.04404|0.07842|0.01792|0.05182|0.05843|0.05938|0.05614|0.07734|0.07842|gnomADe_ASJ|||||||||,-|downstream_gene_variant|MODIFIER|KLHL17|ENSG00000187961|Transcript|ENST00000466300.1|nonsense_mediated_decay||||||||||rs371055706|1|100|1|cds_start_NF||deletion|1|HGNC|HGNC:24023||3||ENSP00000463694||J3QLT4.52|UPI000268AE1E||||||||chr1:g.964630del|||||||0.05705|0.009871|0.04404|0.07842|0.01792|0.05182|0.05843|0.05938|0.05614|0.07734|0.07842|gnomADe_ASJ|||||||||,-|downstream_gene_variant|MODIFIER|KLHL17|ENSG00000187961|Transcript|ENST00000481067.1|retained_intron||||||||||rs371055706|1|466|1|||deletion|1|HGNC|HGNC:24023||2|||||||||||||chr1:g.964630del|||||||0.05705|0.009871|0.04404|0.07842|0.01792|0.05182|0.05843|0.05938|0.05614|0.07734|0.07842|gnomADe_ASJ|||||||||	GT:GQ:GQX:DPI:AD:ADF:ADR:FT:PL	1/1:67:6:25:0,22,0:0,5,0:0,17,0:PASS:999,70,0,992,67,999

And warnings:

WARNING: 5384 : Use of uninitialized value $allele_string in hash element at /soft/ensembl-vep-114.1/modules/Bio/EnsEMBL/VEP/OutputFactory.pm line 1318, <__ANONIO__> line 67.
Use of uninitialized value $allele_string in hash element at /soft/ensembl-vep-114.1/modules/Bio/EnsEMBL/VEP/OutputFactory.pm line 1318, <__ANONIO__> line 67.
Use of uninitialized value $allele_string in hash element at /soft/ensembl-vep-114.1/modules/Bio/EnsEMBL/VEP/OutputFactory.pm line 1318, <__ANONIO__> line 67.
Use of uninitialized value $allele_string in hash element at /soft/ensembl-vep-114.1/modules/Bio/EnsEMBL/VEP/OutputFactory.pm line 1318, <__ANONIO__> line 67.
Use of uninitialized value $allele_string in hash element at /soft/ensembl-vep-114.1/modules/Bio/EnsEMBL/VEP/OutputFactory.pm line 1318, <__ANONIO__> line 67.
Use of uninitialized value $allele_string in hash element at /soft/ensembl-vep-114.1/modules/Bio/EnsEMBL/VEP/OutputFactory.pm line 1318, <__ANONIO__> line 67.
Use of uninitialized value $allele_string in hash element at /soft/ensembl-vep-114.1/modules/Bio/EnsEMBL/VEP/OutputFactory.pm line 1318, <__ANONIO__> line 67.

[nakib103]

thanks @Stikus ,

I can re-produce the issue now. It seems I have not handled the multi allelic case quit well while solving the reported issue in this ticket. I will put in a fix and let you know.

[nakib103]

@Stikus ,
The fix has been added and released in VEP version 114.2. Can you update VEP and let us know if you face any further problems? TIA