[ensembl-dev] VEP output format: two different freq given for same allele

Sat Jan 31 14:31:29 GMT 2015

Hello,

I am getting two very different allele freq returned: C:0.02, C:0.81
for the AFR_MAF field at position 19:5831713

Please see output in csv format below.

Could you please explain to me how to interpret these?

The second one appears to match the freq of the second SNP:
http://www.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=19:5831213-5832213;source=dbSNP;tl=T6pK51e9LuJlbJfH-577229;v=rs112313064;vdb=variation;vf=24908425

But I don't see any freq info about the first SNP:
http://www.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=19:5831213-5832213;tl=T6pK51e9LuJlbJfH-577229;v=rs13346240;vdb=variation;vf=9502280#11943_tablePanel

How is 0.02 estimated?

Many Thanks,

Nikolas.

"Identifier of uploaded variantUploaded variation","Location of
variant in standard coordinate format (chr:start or
chr:start-end)Location","The variant allele used to calculate the
consequenceAllele","Ensembl stable ID of affected geneGene","Ensembl
stable ID of featureFeature","Type of feature - Transcript,
RegulatoryFeature or MotifFeatureFeature type","Consequence
typeConsequence","Relative position of base pair in cDNA sequencecDNA
position","Relative position of base pair in coding sequenceCDS
position","Relative position of amino acid in proteinProtein
position","Reference and variant amino acidsAmino acids","Reference
and variant codon sequenceCodons","Identifier(s) of co-located known
variantsExisting variation","Shortest distance from variant to
transcriptDistance to transcript","Strand of the feature (1/-1)Feature
strand","Gene symbol (e.g. HGNC)Symbol","Source of gene symbolSymbol
source","Stable identifer of HGNC gene symbolHGNC ID","Biotype of
transcript or regulatory featureBiotype","Indicates if transcript is
canonical for this geneCanonical","Transcript support levelTranscript
support level","Indicates if transcript is a CCDS
transcriptCCDS","Ensembl protein identiferENSP","SIFT prediction
and/or scoreSIFT","PolyPhen prediction and/or scorePolyPhen","Exon
number(s) / totalExon","Intron number(s) / totalIntron","The source
and identifer of any overlapping protein domainsDomains","HGVS coding
sequence nameHGVSc","HGVS protein sequence nameHGVSp","Minor allele
and frequency of existing variant in 1000 Genomes Phase 1 combined
populationGMAF","Frequency of existing variant in 1000 Genomes Phase 1
combined African populationAFR MAF","Frequency of existing variant in
1000 Genomes Phase 1 combined American populationAMR MAF","Frequency
of existing variant in 1000 Genomes Phase 1 combined Asian
populationASN MAF","Frequency of existing variant in 1000 Genomes
Phase 1 combined European populationEUR MAF","Frequency of existing
variant in NHLBI-ESP African American populationAA MAF","Frequency of
existing variant in NHLBI-ESP European American populationEA
MAF","Clinical significance of variant from dbSNPClinical
significance","Somatic status of existing variantSomatic
status","Pubmed ID(s) of publications that cite existing
variantPubmed","The source and identifier of a transcription factor
binding profile (TFBP) aligned at this positionMotif name","The
relative position of the variation in the aligned TFBPMotif
position","A flag indicating if the variant falls in a high
information position of the TFBPHigh info position","The difference in
motif score of the reference and variant sequences for the TFBPMotif
score change"
".","19:5831713","C","ENSG00000156413","ENST00000528505","Transcript","downstream_gene_variant","-","-","-","-","-","rs13346240,
rs112313064, COSM3766452,
COSM3766451","764","-1","FUT6","HGNC","HGNC:4017","protein_coding","-","4","-","ENSP00000433811","-","-","-","-","-","-","-","T:0.4357","C:0.02,
C:0.81","C:0.0028, C:0.52","C:0.0017, C:0.62","C:0.02,
C:0.39","-","-","-","0, 0, 1, 1","-","-","-","-","-"
".","19:5831713","C","ENSG00000156413","ENST00000526499","Transcript","downstream_gene_variant","-","-","-","-","-","rs13346240,
rs112313064, COSM3766452,
COSM3766451","3059","-1","FUT6","HGNC","HGNC:4017","retained_intron","-","5","-","-","-","-","-","-","-","-","-","T:0.4357","C:0.02,
C:0.81","C:0.0028, C:0.52","C:0.0017, C:0.62","C:0.02,
C:0.39","-","-","-","0, 0, 1, 1","-","-","-","-","-"
".","19:5831713","C","ENSG00000156413","ENST00000286955","Transcript","synonymous_variant","1908","855","285","P","CCA/CCG","rs13346240,
rs112313064, COSM3766452,
COSM3766451","-","-1","FUT6","HGNC","HGNC:4017","protein_coding","-","1","CCDS12152.1","ENSP00000286955","-","-","2/2","-","Pfam_domain:PF00852","ENST00000286955.5:c.855A>G","ENST00000286955.5:c.855A>G(p.=)","T:0.4357","C:0.02,
C:0.81","C:0.0028, C:0.52","C:0.0017, C:0.62","C:0.02,
C:0.39","-","-","-","0, 0, 1, 1","-","-","-","-","-"
".","19:5831713","C","ENSG00000156413","ENST00000531199","Transcript","downstream_gene_variant","-","-","-","-","-","rs13346240,
rs112313064, COSM3766452,
COSM3766451","655","-1","FUT6","HGNC","HGNC:4017","protein_coding","-","5","-","ENSP00000436413","-","-","-","-","-","-","-","T:0.4357","C:0.02,
C:0.81","C:0.0028, C:0.52","C:0.0017, C:0.62","C:0.02,
C:0.39","-","-","-","0, 0, 1, 1","-","-","-","-","-"
".","19:5831713","C","ENSG00000156413","ENST00000532464","Transcript","downstream_gene_variant","-","-","-","-","-","rs13346240,
rs112313064, COSM3766452,
COSM3766451","721","-1","FUT6","HGNC","HGNC:4017","protein_coding","-","4","-","ENSP00000431880","-","-","-","-","-","-","-","T:0.4357","C:0.02,
C:0.81","C:0.0028, C:0.52","C:0.0017, C:0.62","C:0.02,
C:0.39","-","-","-","0, 0, 1, 1","-","-","-","-","-"
".","19:5831713","C","ENSG00000156413","ENST00000529165","Transcript","downstream_gene_variant","-","-","-","-","-","rs13346240,
rs112313064, COSM3766452,
COSM3766451","444","-1","FUT6","HGNC","HGNC:4017","protein_coding","-","2","-","ENSP00000436547","-","-","-","-","-","-","-","T:0.4357","C:0.02,
C:0.81","C:0.0028, C:0.52","C:0.0017, C:0.62","C:0.02,
C:0.39","-","-","-","0, 0, 1, 1","-","-","-","-","-"
".","19:5831713","C","ENSG00000156413","ENST00000527106","Transcript","synonymous_variant","1124","855","285","P","CCA/CCG","rs13346240,
rs112313064, COSM3766452,
COSM3766451","-","-1","FUT6","HGNC","HGNC:4017","protein_coding","-","1","CCDS12152.1","ENSP00000432954","-","-","4/4","-","Pfam_domain:PF00852","ENST00000527106.3:c.855A>G","ENST00000527106.3:c.855A>G(p.=)","T:0.4357","C:0.02,
C:0.81","C:0.0028, C:0.52","C:0.0017, C:0.62","C:0.02,
C:0.39","-","-","-","0, 0, 1, 1","-","-","-","-","-"
".","19:5831713","C","ENSG00000156413","ENST00000318336","Transcript","synonymous_variant","2050","855","285","P","CCA/CCG","rs13346240,
rs112313064, COSM3766452,
COSM3766451","-","-1","FUT6","HGNC","HGNC:4017","protein_coding","YES","2","CCDS12152.1","ENSP00000313398","-","-","3/3","-","Pfam_domain:PF00852","ENST00000318336.6:c.855A>G","ENST00000318336.6:c.855A>G(p.=)","T:0.4357","C:0.02,
C:0.81","C:0.0028, C:0.52","C:0.0017, C:0.62","C:0.02,
C:0.39","-","-","-","0, 0, 1, 1","-","-","-","-","-"
".","19:5831713","C","ENSG00000171119","ENST00000303212","Transcript","downstream_gene_variant","-","-","-","-","-","rs13346240,
rs112313064, COSM3766452,
COSM3766451","3389","1","NRTN","HGNC","HGNC:8007","protein_coding","YES","1","CCDS12151.1","ENSP00000302648","-","-","-","-","-","-","-","T:0.4357","C:0.02,
C:0.81","C:0.0028, C:0.52","C:0.0017, C:0.62","C:0.02,
C:0.39","-","-","-","0, 0, 1, 1","-","-","-","-","-"
".","19:5831713","C","ENSG00000156413","ENST00000524754","Transcript","synonymous_variant","1495","855","285","P","CCA/CCG","rs13346240,
rs112313064, COSM3766452,
COSM3766451","-","-1","FUT6","HGNC","HGNC:4017","protein_coding","-","1","CCDS12152.1","ENSP00000431708","-","-","3/3","-","Pfam_domain:PF00852","ENST00000524754.1:c.855A>G","ENST00000524754.1:c.855A>G(p.=)","T:0.4357","C:0.02,
C:0.81","C:0.0028, C:0.52","C:0.0017, C:0.62","C:0.02,
C:0.39","-","-","-","0, 0, 1, 1","-","-","-","-","-"
".","19:5831713","C","ENSG00000156413","ENST00000531085","Transcript","downstream_gene_variant","-","-","-","-","-","rs13346240,
rs112313064, COSM3766452,
COSM3766451","648","-1","FUT6","HGNC","HGNC:4017","protein_coding","-","5","-","ENSP00000432161","-","-","-","-","-","-","-","T:0.4357","C:0.02,
C:0.81","C:0.0028, C:0.52","C:0.0017, C:0.62","C:0.02,
C:0.39","-","-","-","0, 0, 1, 1","-","-","-","-","-"
".","19:5831713","C","ENSG00000156413","ENST00000592563","Transcript","
synonymous_variant","855","855","285","P","CCA/CCG","rs13346240,
rs112313064, COSM3766452,
COSM3766451","-","-1","FUT6","HGNC","HGNC:4017","protein_coding","-","1","-","ENSP00000466016","-","-","1/2","-","Pfam_domain:PF00852","ENST00000592563.1:c.855A>G","ENST00000592563.1:c.855A>G(p.=)","T:0.4357","C:0.02,
C:0.81","C:0.0028, C:0.52","C:0.0017, C:0.62","C:0.02,
C:0.39","-","-","-","0, 0, 1, 1","-","-","-","-","-"