Missing gnomAD and 1000G Allele Frequencies from VEP 90

[tonydisera]

It looks like VEP 90 is only showing gnomAD allele frequencies for exomes.

IMPORTANT:

VEP 90 isn’t matching 1000G Allele frequencies in all cases:

ubuntu@nv-dev-new:~/minion/bin$ tabix http://s3.amazonaws.com/vcf.files/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5.20130502.sites.vcf.gz 5:55224484-55224484 | ./vep.sh --af --af_1kg --af_gnomad ##fileformat=VCFv4.1 ##VEP="v90" time="2017-10-01 17:25:05" cache="/mnt/vep-cache/homo_sapiens/90_GRCh37" ensembl=90.4a44397 ensembl-variation=90.0f096c9 ensembl-funcgen=90.e775c00 ensembl-io=90.9a148ea 1000genomes="phase3" COSMIC="81" ClinVar="201706" ESP="20141103" HGMD-PUBLIC="20164" assembly="GRCh37.p13" dbSNP="150" gencode="GENCODE 19" genebuild="2011-04" gnomAD="170228" polyphen="2.2.2" regbuild="1.0" sift="sift5.2.2" ##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|DISTANCE|STRAND|FLAGS|SYMBOL_SOURCE|HGNC_ID|SIFT|PolyPhen|AF|AFR_AF|AMR_AF|EAS_AF|EUR_AF|SAS_AF|gnomAD_AF|gnomAD_AFR_AF|gnomAD_AMR_AF|gnomAD_ASJ_AF|gnomAD_EAS_AF|gnomAD_FIN_AF|gnomAD_NFE_AF|gnomAD_OTH_AF|gnomAD_SAS_AF|CLIN_SIG|SOMATIC|PHENO|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE"> #CHROM POS ID REF ALT QUAL FILTER INFO 5 55224484 rs34525804 GT G 100 PASS AC=3481;AF=0.695088;AN=5008;NS=2504;DP=16625;EAS_AF=0.7113;AMR_AF=0.755;AFR_AF=0.6755;EUR_AF=0.7048;SAS_AF=0.6524;AA=|||unknown(HR);CSQ=-|frameshift_variant|HIGH|AC008914.1|ENSG00000268280|Transcript|ENST00000595799|protein_coding|2/2||||55|55|19|T/X|Acc/cc|||-1||Clone_based_ensembl_gene||||||||||||||||||||||||| [Uploading image002.png...]

[tonydisera]

Matt asked Ensembl about this and they did confirm that this is the case.