Exomiser Analysis Results for Slartibartfast

Analysis Settings

Settings used for this analysis:

ExomiserSettings{vcfFilePath=Pfeiffer.vcf, pedFilePath=null, prioritiser=exomiser-mouse, maximumFrequency=1.0, minimumQuality=0.0, geneticInterval=null, removePathFilterCutOff=false, removeDbSnp=false, removeOffTargetVariants=true, candidateGene=, modeOfInheritance=AUTOSOMAL_DOMINANT, diseaseId=OMIM:101600, hpoIds=[], seedGeneList=[], numberOfGenesToShow=0, outFileName=results/Pfeiffer-exomiser-results, outputFormat=[HTML], diseaseGeneFamilyName=, buildVersion=, buildTimestamp=}

Filtering Summary

Filter Report Passed filter Failed filter
Frequency
    Allele frequency < 1.00 %
16916 20793

Variant Type Distribution

Variant Type Slartibartfast
MISSENSE 1

Analyzed samples

//if there is a multi-sample pedigree we want to see the analysis: //HTMLTable.writePedigreeTable()

affected: red, parent of affected: light blue, unaffected: white

if (this.pedigree.isNthPersonAffected(i)) { } else if (this.pedigree.isNthPersonParentOfAffected(i)) { } else { }
Sample name: manuel
famidididfathID mothID sex disease

Prioritised Genes

FGFR2 FGFR2 FGFR2

Exomiser Score: 1.005

Phenotype Score: 1.005

Variant Score: 1.005

Phenotype matches:
Manitoba oculotrichoanal syndrome
Gene scores under compatible inheritance modes:

AUTOSOMAL_DOMINANT

Exomiser Score: 1.005

Phenotype Score: 1.005

Variant Score: 1.005

Variants contributing to score:
MISSENSE chr10:g.123256215T>G [0/1] rs141235720 (variation viewer)
ClinVar: BENIGN BENIGN_OR_LIKELY_BENIGN LIKELY_BENIGN LIKELY_PATHOGENIC PATHOGENIC_OR_LIKELY_PATHOGENIC PATHOGENIC UNCERTAIN_SIGNIFICANCE (criteria_provided,_single_submitter)
Variant score: 0.600 CONTRIBUTING VARIANT WHITELIST VARIANT
Transcripts:
FGFR2:uc001lfg.4:c.518A>C:p.E173A FGFR2:ENST00000429361.1:c.518A>C:p.E173A FGFR2:NM_000141:c.518A>C:p.E173A
Pathogenicity Data:
1.00
No pathogenicity data
Mutation Taster: 0.999 (P)
Frequency Data:
No frequency data
1000Genomes: 0.02%
Other passed variants:
MISSENSE chr10:g.123256215T>G [0/1] rs141235720 (variation viewer)
ClinVar: BENIGN BENIGN_OR_LIKELY_BENIGN LIKELY_BENIGN LIKELY_PATHOGENIC PATHOGENIC_OR_LIKELY_PATHOGENIC PATHOGENIC UNCERTAIN_SIGNIFICANCE (criteria_provided,_single_submitter)
Variant score: 0.600 WHITELIST VARIANT
Transcripts:
FGFR2:uc001lfg.4:c.518A>C:p.E173A FGFR2:ENST00000429361.1:c.518A>C:p.E173A FGFR2:NM_000141:c.518A>C:p.E173A
Pathogenicity Data:
1.00
No pathogenicity data
Mutation Taster: 0.999 (P)
Frequency Data:
No frequency data
1000Genomes: 0.02%

Unanalysed Variants

MISSENSE chr10:g.123256215T>G [0/1] rs141235720 (variation viewer)

About

The Exomizer is a Java program that functionally annotates variants from whole-exome sequencing data starting from a VCF file (version 4). The functional annotation code is based on Jannovar and uses UCSC KnownGene transcript definitions and hg19 genomic coordinates

Variants are prioritized according to user-defined criteria on variant frequency, pathogenicity, quality, inheritance pattern, and model organism phenotype data. Predicted pathogenicity data was extracted from the dbNSFP resource.

Developed by the Computational Biology and Bioinformatics group at the Institute for Medical Genetics and Human Genetics of the Charité - Universitätsmedizin Berlin, the Mouse Informatics Group at the Sanger Institute and the Smedley group at Queen Mary University of London.

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