ExAC plugin returning only ExAC_AF, not population-specific AF

[seandavi]

I need to dig through the source, but I am seeing empty columns for everything except ExAC_AF. The source ExAC VCF is directly from the ExAC download page.

[willmclaren]

I can't recreate this error:

perl variant_effect_predictor.pl -i example_GRCh37.vcf -force -cache -plugin ExAC,/lustre/scratch110/ensembl/wm2/Ex/ExAC.r0.3.sites.vep.vcf.gz -o stdout -fork 4 | grep -v # | head -n 3
rs116645811 21:26960070 A ENSG00000154736 ENST00000284987 Transcript intron_variant - - - - - -
ExAC_AF_FIN=0;IMPACT=MODIFIER;ExAC_AF_OTH=0;ExAC_AF=0.000437;ExAC_AF_AMR=0;ExAC_AF_AFR=0.000292;ExAC_AF_EAS=0;ExAC_AF_NFE=4.51e-05;ExAC_AF_SAS=0.00288;STRAND=-1
rs1135638 21:26965148 A ENSG00000154736 ENST00000284987 Transcript intron_variant - - - - - -
ExAC_AF_FIN=0.788;IMPACT=MODIFIER;ExAC_AF_OTH=0.776;ExAC_AF=0.773;ExAC_AF_AMR=0.714;ExAC_AF_AFR=0.751;ExAC_AF_EAS=0.726;ExAC_AF_NFE=0.818;ExAC_AF_SAS=0.662;STRAND=-1
rs10576 21:26965172 C ENSG00000154736 ENST00000284987 Transcript intron_variant - - - - - - ExAC_AF_FIN=0;IMPACT=MODIFIER;ExAC_AF_OTH=0.00441;ExAC_AF=0.00287;ExAC_AF_AMR=0.00121;ExAC_AF_AFR=0.0312;ExAC_AF_EAS=0;ExAC_AF_NFE=7.49e-05;ExAC_AF_SAS=0;STRAND=-1

[apastore]

I have the same Issues using VEP 81. I have seen that the problem occurs if the --vcf VEP option is chosen.

perl ~/vep/variant_effect_predictor.pl \

-plugin ExAC,/Users/alessandro/.vep/homo_sapiens/ExAC/ExAC.r0.3.sites.vep.vcf.gz
--offline --gencode_basic --everything
--total_length --allele_number --no_escape --check_existing --xref_refseq
--shift_hgvs 1 --check_alleles --quiet --no_stats --assembly GRCh37
--dir $VEP_DATA --fasta $VEP_DATA/homo_sapiens/81_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa
--input_file s_IM_pcnsl_011_T_vs_s_Normal_Pooled_FFPE_1.vcf --output_file test.vep.vcp --vcf

X 1544525 . G A . . CSQ=A|missense_variant|MODERATE|ASMTL|ENSG00000169093|Transcript|ENST00000381317|protein_coding|8/13||ENST00000381317.3:c.953C>T|ENSP00000370718.3:p.Pro318Leu|986/2027|953/1866|318/621|P/L|cCc/cTc||1||-1|SNV|HGNC|751|YES||CCDS43917.1|ENSP00000370718|ASML_HUMAN||UPI0000141AF9|NM_004192.3|tolerated(0.05)|benign(0.212)|PROSITE_profiles:PS51683&hmmpanther:PTHR11746&hmmpanther:PTHR11746:SF69&Gene3D:1.10.10.10&Superfamily_domains:SSF46785||||||||||||||||||||||0.000712||||,A|missense_variant|MODERATE|ASMTL|ENSG00000169093|Transcript|ENST00000381333|protein_coding|7/12||ENST00000381333.4:c.905C>T|ENSP00000370734.4:p.Pro302Leu|994/2035|905/1818|302/605|P/L|cCc/cTc||1||-1|SNV|HGNC|751|||CCDS55363.1|ENSP00000370734|ASML_HUMAN||UPI0000071671|NM_001173474.1|tolerated(0.06)|possibly_damaging(0.844)|PROSITE_profiles:PS51683&hmmpanther:PTHR11746&hmmpanther:PTHR11746:SF69&Gene3D:1.10.10.10&Superfamily_domains:SSF46785||||||||||||||||||||||0.000712||||,A|missense_variant|MODERATE|ASMTL|ENSG00000169093|Transcript|ENST00000534940|protein_coding|8/13||ENST00000534940.1:c.779C>T|ENSP00000446410.1:p.Pro260Leu|1005/2048|779/1692|260/563|P/L|cCc/cTc||1||-1|SNV|HGNC|751|||CCDS55362.1|ENSP00000446410|ASML_HUMAN||UPI0001CA7E5F|NM_001173473.1|tolerated(0.17)|benign(0.212)|Superfamily_domains:SSF46785&Gene3D:1.10.10.10&hmmpanther:PTHR11746:SF69&hmmpanther:PTHR11746&PROSITE_profiles:PS51683||||||||||||||||||||||0.000712||||,A|missense_variant|MODERATE|ASMTL|ENSG00000169093|Transcript|ENST00000416733|protein_coding|7/12||ENST00000416733.2:c.725C>T|ENSP00000410578.2:p.Pro242Leu|923/1966|725/1638|242/545|P/L|cCc/cTc||1||-1|SNV|HGNC|751||||ENSP00000410578||E7ER97_HUMAN|UPI0001AE6F52|||benign(0.15)|PROSITE_profiles:PS51683&hmmpanther:PTHR11746&hmmpanther:PTHR11746:SF69&Gene3D:1.10.10.10&Superfamily_domains:SSF46785||||||||||||||||||||||0.000712|||| GT:AD:DP 0/1:116,89:. 0/0:2654,7:.

perl ~/vep/variant_effect_predictor.pl -plugin ExAC,/Users/alessandro/.vep/homo_sapiens/ExAC/ExAC.r0.3.sites.vep.vcf.gz --offline --gencode_basic --everything --total_length --allele_number --no_escape --check_existing --xref_refseq --shift_hgvs 1 --check_alleles --quiet --no_stats --assembly GRCh37 --dir $VEP_DATA --fasta $VEP_DATA/homo_sapiens/81_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa --input_file s_IM_pcnsl_011_T_vs_s_Normal_Pooled_FFPE_1.vcf --output_file test.vep.vcp

X_1544525_G/A X:1544525 A ENSG00000169093 ENST00000381317 Transcript missense_variant 986/2027 953/1866 318/621 P/L cCc/cTc - ExAC_AF=0.000712;ExAC_AF_AMR=8.75e-05;ExAC_AF_OTH=0.00114;ExAC_AF_SAS=6.14e-05;ExAC_AF_FIN=0.000152;ExAC_AF_NFE=0.00124;ALLELE_NUM=1;ExAC_AF_AFR=0;ExAC_AF_EAS=0;IMPACT=MODERATE;STRAND=-1;VARIANT_CLASS=SNV;SYMBOL=ASMTL;SYMBOL_SOURCE=HGNC;HGNC_ID=751;BIOTYPE=protein_coding;CANONICAL=YES;CCDS=CCDS43917.1;ENSP=ENSP00000370718;SWISSPROT=ASML_HUMAN;UNIPARC=UPI0000141AF9;RefSeq=NM_004192.3;SIFT=tolerated(0.05);PolyPhen=benign(0.212);EXON=8/13;DOMAINS=PROSITE_profiles:PS51683,hmmpanther:PTHR11746,hmmpanther:PTHR11746:SF69,Gene3D:1.10.10.10,Superfamily_domains:SSF46785;HGVSc=ENST00000381317.3:c.953C>T;HGVSp=ENSP00000370718.3:p.Pro318Leu

[willmclaren]

Thanks @apastore , the key was using VCF output. There's an underlying issue above in the VEP script itself, but I've patched a fix to the plugin that resolves it here 3df1a73

[apastore]

Hi Will

I have update my ExAC.pm plugin, I unfortunately still have the same issues.

This is my veep run output with and without the --vcf parameter.

perl variant_effect_predictor.pl --plugin ExAC,/Users/alessandro/.vep/homo_sapiens/ExAC/ExAC.r0.3.sites.vep.vcf.gz --quiet --offline --no_stats --everything --shift_hgvs 1 --check_existing --check_alleles --total_length --allele_number --no_escape --xref_refseq --assembly GRCh37 --fasta /Users/alessandro/.vep/homo_sapiens/81_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa --dir /Users/alessandro/.vep/ --input_file example_GRCh37.vcf --output_file example_GRCh37.vep.vcf --vcf
alexbook:vep alessandro$ vim example_GRCh37.vep.vcf
alexbook:vep alessandro$ grep 'rs115683257' example_GRCh37.vep.vcf
21 34022588 rs115683257 C A . . CSQ=A|upstream_gene_variant|MODIFIER|SYNJ1|ENSG00000159082|Transcript|ENST00000438952|protein_coding|||||-/3604|-/564|-/187|||rs115683257|1|4568|-1|SNV|HGNC|11503||||ENSP00000388869|||UPI000198C84A||||||A:0.0022|A:0.0068|A:0.0029||A:0|A:0|A:0|A:0.007|A:0|||||||||||||0.000717|||,A|missense_variant|MODERATE|SYNJ1|ENSG00000159082|Transcript|ENST00000357345|protein_coding|23/32||ENST00000357345.3:c.2943G>T|ENSP00000349903.3:p.Met981Ile|3068/7059|2943/3888|981/1295|M/I|atG/atT|rs115683257|1||-1|SNV|HGNC|11503|||CCDS54483.1|ENSP00000349903|SYNJ1_HUMAN|C9J1Z6_HUMAN&B4DIP0_HUMAN|UPI000034ECCC|NM_001160302.1|tolerated(1)|benign(0.001)|Pfam_domain:PF08952&hmmpanther:PTHR11200:SF126&hmmpanther:PTHR11200||A:0.0022|A:0.0068|A:0.0029||A:0|A:0|A:0|A:0.007|A:0|||||||||||||0.000717|||,A|missense_variant|MODERATE|SYNJ1|ENSG00000159082|Transcript|ENST00000382491|protein_coding|22/28||ENST00000382491.3:c.2928G>T|ENSP00000371931.3:p.Met976Ile|3053/6942|2928/4581|976/1526|M/I|atG/atT|rs115683257|1||-1|SNV|HGNC|11503|||CCDS54484.1|ENSP00000371931||Q1ZYQ4_HUMAN&J3KPK1_HUMAN&C9JW66_HUMAN&C9J1Z6_HUMAN|UPI0001A47574|NM_001160306.1||benign(0.023)|hmmpanther:PTHR11200:SF126&hmmpanther:PTHR11200&Pfam_domain:PF08952||A:0.0022|A:0.0068|A:0.0029||A:0|A:0|A:0|A:0.007|A:0|||||||||||||0.000717|||,A|upstream_gene_variant|MODIFIER|SYNJ1|ENSG00000159082|Transcript|ENST00000416083|protein_coding|||||-/366|-/368|-/122|||rs115683257|1|4559|-1|SNV|HGNC|11503||||ENSP00000413480|||UPI000066D9AF||||||A:0.0022|A:0.0068|A:0.0029||A:0|A:0|A:0|A:0.007|A:0|||||||||||||0.000717|||,A|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|SYNJ1|ENSG00000159082|Transcript|ENST00000467445|retained_intron|2/2||ENST00000467445.1:n.883G>T||883/977|||||rs115683257|1||-1|SNV|HGNC|11503|||||||||||||A:0.0022|A:0.0068|A:0.0029||A:0|A:0|A:0|A:0.007|A:0|||||||||||||0.000717|||,A|missense_variant|MODERATE|SYNJ1|ENSG00000159082|Transcript|ENST00000322229|protein_coding|22/31||ENST00000322229.7:c.2943G>T|ENSP00000322234.7:p.Met981Ile|2943/4722|2943/4722|981/1573|M/I|atG/atT|rs115683257|1||-1|SNV|HGNC|11503||||ENSP00000322234|SYNJ1_HUMAN|C9J1Z6_HUMAN|UPI0000206D91|||benign(0.029)|hmmpanther:PTHR11200:SF126&hmmpanther:PTHR11200&Pfam_domain:PF08952||A:0.0022|A:0.0068|A:0.0029||A:0|A:0|A:0|A:0.007|A:0|||||||||||||0.000717|||,A|missense_variant|MODERATE|SYNJ1|ENSG00000159082|Transcript|ENST00000433931|protein_coding|23/32||ENST00000433931.2:c.3060G>T|ENSP00000409667.2:p.Met1020Ile|3068/4852|3060/4839|1020/1612|M/I|atG/atT|rs115683257|1||-1|SNV|HGNC|11503|YES||CCDS33539.2|ENSP00000409667||J3KQV8_HUMAN&C9J1Z6_HUMAN|UPI0001A47572|NM_003895.3|tolerated(0.73)|benign(0.026)|Pfam_domain:PF08952&hmmpanther:PTHR11200:SF126&hmmpanther:PTHR11200||A:0.0022|A:0.0068|A:0.0029||A:0|A:0|A:0|A:0.007|A:0|||||||||||||0.000717|||,A|missense_variant|MODERATE|SYNJ1|ENSG00000159082|Transcript|ENST00000382499|protein_coding|23/33||ENST00000382499.2:c.3060G>T|ENSP00000371939.2:p.Met1020Ile|3060/7094|3060/4053|1020/1350|M/I|atG/atT|rs115683257|1||-1|SNV|HGNC|11503|||CCDS33540.2|ENSP00000371939||C9JFZ1_HUMAN&C9J1Z6_HUMAN|UPI000198C848|NM_203446.2|tolerated(1)|benign(0.009)|hmmpanther:PTHR11200&hmmpanther:PTHR11200:SF126&Pfam_domain:PF08952||A:0.0022|A:0.0068|A:0.0029||A:0|A:0|A:0|A:0.007|A:0|||||||||||||0.000717|||
alexbook:vep alessandro$ rm example_GRCh37.vep.vcf*
alexbook:vep alessandro$ perl variant_effect_predictor.pl --plugin ExAC,/Users/alessandro/.vep/homo_sapiens/ExAC/ExAC.r0.3.sites.vep.vcf.gz --quiet --offline --no_stats --everything --shift_hgvs 1 --check_existing --check_alleles --total_length --allele_number --no_escape --xref_refseq --assembly GRCh37 --fasta /Users/alessandro/.vep/homo_sapiens/81_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa --dir /Users/alessandro/.vep/ --input_file example_GRCh37.vcf --output_file example_GRCh37.vep.vcf
alexbook:vep alessandro$ grep 'rs115683257' example_GRCh37.vep.vcf
rs115683257 21:34022588 A ENSG00000159082 ENST00000438952 Transcript upstream_gene_variant -/3604 -/564 -/187 - - rs115683257 ExAC_AF_OTH=0;ExAC_AF_EAS=0;ExAC_AF_SAS=0;ExAC_AF_AFR=0.0076;ExAC_AF_AMR=0.000345;ExAC_AF_FIN=0;ALLELE_NUM=1;ExAC_AF_NFE=6e-05;ExAC_AF=0.000717;IMPACT=MODIFIER;DISTANCE=4568;STRAND=-1;VARIANT_CLASS=SNV;SYMBOL=SYNJ1;SYMBOL_SOURCE=HGNC;HGNC_ID=11503;BIOTYPE=protein_coding;ENSP=ENSP00000388869;UNIPARC=UPI000198C84A;GMAF=A:0.0022;AFR_MAF=A:0.0068;AMR_MAF=A:0.0029;EAS_MAF=A:0;EUR_MAF=A:0;SAS_MAF=A:0;AA_MAF=A:0.007;EA_MAF=A:0
rs115683257 21:34022588 A ENSG00000159082 ENST00000382491 Transcript missense_variant 3053/6942 2928/4581 976/1526 M/I atG/atT rs115683257 ExAC_AF_SAS=0;ExAC_AF_OTH=0;ALLELE_NUM=1;ExAC_AF_NFE=6e-05;ExAC_AF_AFR=0.0076;ExAC_AF_FIN=0;ExAC_AF_AMR=0.000345;ExAC_AF_EAS=0;ExAC_AF=0.000717;IMPACT=MODERATE;STRAND=-1;VARIANT_CLASS=SNV;SYMBOL=SYNJ1;SYMBOL_SOURCE=HGNC;HGNC_ID=11503;BIOTYPE=protein_coding;CCDS=CCDS54484.1;ENSP=ENSP00000371931;TREMBL=Q1ZYQ4_HUMAN,J3KPK1_HUMAN,C9JW66_HUMAN,C9J1Z6_HUMAN;UNIPARC=UPI0001A47574;RefSeq=NM_001160306.1;PolyPhen=benign(0.023);EXON=22/28;DOMAINS=hmmpanther:PTHR11200:SF126,hmmpanther:PTHR11200,Pfam_domain:PF08952;HGVSc=ENST00000382491.3:c.2928G>T;HGVSp=ENSP00000371931.3:p.Met976Ile;GMAF=A:0.0022;AFR_MAF=A:0.0068;AMR_MAF=A:0.0029;EAS_MAF=A:0;EUR_MAF=A:0;SAS_MAF=A:0;AA_MAF=A:0.007;EA_MAF=A:0
rs115683257 21:34022588 A ENSG00000159082 ENST00000467445 Transcript non_coding_transcript_exon_variant,non_coding_transcript_variant 883/977 - - - - rs115683257 ExAC_AF_SAS=0;ExAC_AF_OTH=0;ExAC_AF_EAS=0;ExAC_AF_NFE=6e-05;ALLELE_NUM=1;ExAC_AF=0.000717;ExAC_AF_AMR=0.000345;ExAC_AF_FIN=0;ExAC_AF_AFR=0.0076;IMPACT=MODIFIER;STRAND=-1;VARIANT_CLASS=SNV;SYMBOL=SYNJ1;SYMBOL_SOURCE=HGNC;HGNC_ID=11503;BIOTYPE=retained_intron;EXON=2/2;HGVSc=ENST00000467445.1:n.883G>T;GMAF=A:0.0022;AFR_MAF=A:0.0068;AMR_MAF=A:0.0029;EAS_MAF=A:0;EUR_MAF=A:0;SAS_MAF=A:0;AA_MAF=A:0.007;EA_MAF=A:0
rs115683257 21:34022588 A ENSG00000159082 ENST00000416083 Transcript upstream_gene_variant -/366 -/368 -/122 - - rs115683257 ExAC_AF_AFR=0.0076;ExAC_AF_AMR=0.000345;ExAC_AF_FIN=0;ExAC_AF=0.000717;ALLELE_NUM=1;ExAC_AF_NFE=6e-05;ExAC_AF_EAS=0;ExAC_AF_OTH=0;ExAC_AF_SAS=0;IMPACT=MODIFIER;DISTANCE=4559;STRAND=-1;VARIANT_CLASS=SNV;SYMBOL=SYNJ1;SYMBOL_SOURCE=HGNC;HGNC_ID=11503;BIOTYPE=protein_coding;ENSP=ENSP00000413480;UNIPARC=UPI000066D9AF;GMAF=A:0.0022;AFR_MAF=A:0.0068;AMR_MAF=A:0.0029;EAS_MAF=A:0;EUR_MAF=A:0;SAS_MAF=A:0;AA_MAF=A:0.007;EA_MAF=A:0
rs115683257 21:34022588 A ENSG00000159082 ENST00000357345 Transcript missense_variant 3068/7059 2943/3888 981/1295 M/I atG/atT rs115683257 ExAC_AF_SAS=0;ExAC_AF_OTH=0;ExAC_AF_NFE=6e-05;ALLELE_NUM=1;ExAC_AF_FIN=0;ExAC_AF_AMR=0.000345;ExAC_AF_AFR=0.0076;ExAC_AF_EAS=0;ExAC_AF=0.000717;IMPACT=MODERATE;STRAND=-1;VARIANT_CLASS=SNV;SYMBOL=SYNJ1;SYMBOL_SOURCE=HGNC;HGNC_ID=11503;BIOTYPE=protein_coding;CCDS=CCDS54483.1;ENSP=ENSP00000349903;SWISSPROT=SYNJ1_HUMAN;TREMBL=C9J1Z6_HUMAN,B4DIP0_HUMAN;UNIPARC=UPI000034ECCC;RefSeq=NM_001160302.1;SIFT=tolerated(1);PolyPhen=benign(0.001);EXON=23/32;DOMAINS=Pfam_domain:PF08952,hmmpanther:PTHR11200:SF126,hmmpanther:PTHR11200;HGVSc=ENST00000357345.3:c.2943G>T;HGVSp=ENSP00000349903.3:p.Met981Ile;GMAF=A:0.0022;AFR_MAF=A:0.0068;AMR_MAF=A:0.0029;EAS_MAF=A:0;EUR_MAF=A:0;SAS_MAF=A:0;AA_MAF=A:0.007;EA_MAF=A:0
rs115683257 21:34022588 A ENSG00000159082 ENST00000382499 Transcript missense_variant 3060/7094 3060/4053 1020/1350 M/I atG/atT rs115683257 ALLELE_NUM=1;ExAC_AF_NFE=6e-05;ExAC_AF_AFR=0.0076;ExAC_AF_AMR=0.000345;ExAC_AF_FIN=0;ExAC_AF_SAS=0;ExAC_AF_OTH=0;ExAC_AF=0.000717;ExAC_AF_EAS=0;IMPACT=MODERATE;STRAND=-1;VARIANT_CLASS=SNV;SYMBOL=SYNJ1;SYMBOL_SOURCE=HGNC;HGNC_ID=11503;BIOTYPE=protein_coding;CCDS=CCDS33540.2;ENSP=ENSP00000371939;TREMBL=C9JFZ1_HUMAN,C9J1Z6_HUMAN;UNIPARC=UPI000198C848;RefSeq=NM_203446.2;SIFT=tolerated(1);PolyPhen=benign(0.009);EXON=23/33;DOMAINS=hmmpanther:PTHR11200,hmmpanther:PTHR11200:SF126,Pfam_domain:PF08952;HGVSc=ENST00000382499.2:c.3060G>T;HGVSp=ENSP00000371939.2:p.Met1020Ile;GMAF=A:0.0022;AFR_MAF=A:0.0068;AMR_MAF=A:0.0029;EAS_MAF=A:0;EUR_MAF=A:0;SAS_MAF=A:0;AA_MAF=A:0.007;EA_MAF=A:0
rs115683257 21:34022588 A ENSG00000159082 ENST00000322229 Transcript missense_variant 2943/4722 2943/4722 981/1573 M/I atG/atT rs115683257 ExAC_AF_AFR=0.0076;ExAC_AF_FIN=0;ExAC_AF_AMR=0.000345;ALLELE_NUM=1;ExAC_AF_NFE=6e-05;ExAC_AF_OTH=0;ExAC_AF_SAS=0;ExAC_AF=0.000717;ExAC_AF_EAS=0;IMPACT=MODERATE;STRAND=-1;VARIANT_CLASS=SNV;SYMBOL=SYNJ1;SYMBOL_SOURCE=HGNC;HGNC_ID=11503;BIOTYPE=protein_coding;ENSP=ENSP00000322234;SWISSPROT=SYNJ1_HUMAN;TREMBL=C9J1Z6_HUMAN;UNIPARC=UPI0000206D91;PolyPhen=benign(0.029);EXON=22/31;DOMAINS=hmmpanther:PTHR11200:SF126,hmmpanther:PTHR11200,Pfam_domain:PF08952;HGVSc=ENST00000322229.7:c.2943G>T;HGVSp=ENSP00000322234.7:p.Met981Ile;GMAF=A:0.0022;AFR_MAF=A:0.0068;AMR_MAF=A:0.0029;EAS_MAF=A:0;EUR_MAF=A:0;SAS_MAF=A:0;AA_MAF=A:0.007;EA_MAF=A:0
rs115683257 21:34022588 A ENSG00000159082 ENST00000433931 Transcript missense_variant 3068/4852 3060/4839 1020/1612 M/I atG/atT rs115683257 ExAC_AF_AMR=0.000345;ExAC_AF_FIN=0;ExAC_AF_AFR=0.0076;ExAC_AF_NFE=6e-05;ALLELE_NUM=1;ExAC_AF_OTH=0;ExAC_AF_SAS=0;ExAC_AF=0.000717;ExAC_AF_EAS=0;IMPACT=MODERATE;STRAND=-1;VARIANT_CLASS=SNV;SYMBOL=SYNJ1;SYMBOL_SOURCE=HGNC;HGNC_ID=11503;BIOTYPE=protein_coding;CANONICAL=YES;CCDS=CCDS33539.2;ENSP=ENSP00000409667;TREMBL=J3KQV8_HUMAN,C9J1Z6_HUMAN;UNIPARC=UPI0001A47572;RefSeq=NM_003895.3;SIFT=tolerated(0.73);PolyPhen=benign(0.026);EXON=23/32;DOMAINS=Pfam_domain:PF08952,hmmpanther:PTHR11200:SF126,hmmpanther:PTHR11200;HGVSc=ENST00000433931.2:c.3060G>T;HGVSp=ENSP00000409667.2:p.Met1020Ile;GMAF=A:0.0022;AFR_MAF=A:0.0068;AMR_MAF=A:0.0029;EAS_MAF=A:0;EUR_MAF=A:0;SAS_MAF=A:0;AA_MAF=A:0.007;EA_MAF=A:0

[willmclaren]

Thanks for the report, c295b79 should fix it.

You may also need to update your ensembl-tools folder (just re-download, or run "perl INSTALL.pl --UPDATE")