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

Mon Feb 2 09:39:21 GMT 2015

Hi Nikolas,

It appears there's some erroneous data in the cache for rs13346240; the SNP
does not appear in the 1000 genomes phase 1 source data, but somehow some
frequency data corresponding to that rsID has appeared in the cache files.

The correct value for the AFR_AF at this locus is C:0.81

We'll look into making sure this doesn't appear in future versions of the
cache.

Regards

Will McLaren
Ensembl Variation

On 31 January 2015 at 14:31, Nikolas Pontikos <n.pontikos at ucl.ac.uk> wrote:

> 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","-","-","-","-","-"
>
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