Hi,
I have run exomiser v15.0.0 with the dataset 2512.
Our variant is 1-42930685-G-A on SLC2A1 gene.
It shows GLUT1 and alternating hemiplegia of childhood on the html output:
However, it just shows alternating hemiplegia of childhood on the tsv output. It would be better to show GLUT1 instead of alternating hemiplegia of childhood.
sed 1q exomiser_results20260404/E17-51.vep.tagged.vcf/E17-51.vep.tagged.vcf.variants.tsv; grep SLC2A1 exomiser_results20260404/E17
-51.vep.tagged.vcf/E17-51.vep.tagged.vcf.variants.tsv
#RANK ID GENE_SYMBOL ENTREZ_GENE_ID MOI P-VALUE EXOMISER_GENE_COMBINED_SCORE EXOMISER_GENE_PHENO_SCORE EXOMISER_GENE_VARIANT_SCORE EXOMISER_VARIANT_SCORE CONTRIBUTING_VARIANT WHITELIST_VARIANT VCF_ID RS_ID CONTIG START ENDREF ALT CHANGE_LENGTH QUAL FILTER GENOTYPE FUNCTIONAL_CLASS HGVS EXOMISER_ACMG_CLASSIFICATION EXOMISER_ACMG_EVIDENCE EXOMISER_ACMG_DISEASE_ID EXOMISER_ACMG_DISEASE_NAME CLINVAR_VARIATION_ID CLINVAR_PRIMARY_INTERPRETATION CLINVAR_STAR_RATING GENE_CONSTRAINT_LOEUF GENE_CONSTRAINT_LOEUF_LOWER GENE_CONSTRAINT_LOEUF_UPPER MAX_FREQ_SOURCE MAX_FREQ ALL_FREQ MAX_PATH_SOURCE MAX_PATH ALL_PATH
1 1-42930685-G-A_ANY SLC2A1 6513 ANY 0.0001 0.9228 0.7807 1.0000 1.0000 1 1 rs16434794611 42930685 42930685 G A 0 39.2000 PASS 0/1 missense_variant SLC2A1:ENST00000426263.10:c.457C>T:p.(Arg153Cys) PATHOGENIC PM1_Supporting,PM2_Supporting,PM5_Supporting,PP3_Moderate,PP4_Moderate,PP5_Strong ORPHA:2131 Alternating hemiplegia of childhood 1076377 PATHOGENIC 2 0.04404 0.017 0.139 MVP 0.97614944 REVEL=0.884,MVP=0.97614944,ALPHA_MISSENSE=0.9699
yaml file:
---
sample:
genomeAssembly: "hg38"
vcf: "input/sample.vcf"
hpoIds:
- "HP:0001250"
- "HP:0020219"
- "HP:0002197"
- "HP:0032677"
- "HP:0011146"
- "HP:0011097"
- "HP:0002069"
- "HP:0012469"
- "HP:0033259"
- "HP:0007359"
- "HP:0032794"
- "HP:0002123"
- "HP:0002121"
- "HP:0032792"
- "HP:0010818"
- "HP:0010819"
- "HP:0002384"
- "HP:0025190"
- "HP:0007270"
- "HP:0002133"
- "HP:0011153"
- "HP:0032892"
- "HP:0032894"
- "HP:0002373"
- "HP:0020221"
- "HP:0007334"
- "HP:0011147"
- "HP:0002266"
- "HP:0011170"
- "HP:0032679"
- "HP:0011175"
- "HP:0002349"
pedigree: {}
age: {}
analysis:
frequencySources:
- "THOUSAND_GENOMES"
- "TOPMED"
- "UK10K"
- "ESP_AA"
- "ESP_EA"
- "ESP_ALL"
- "EXAC_AFRICAN_INC_AFRICAN_AMERICAN"
- "EXAC_AMERICAN"
- "EXAC_EAST_ASIAN"
- "EXAC_NON_FINNISH_EUROPEAN"
- "EXAC_SOUTH_ASIAN"
- "GNOMAD_E_AFR"
- "GNOMAD_E_AMR"
- "GNOMAD_E_EAS"
- "GNOMAD_E_NFE"
- "GNOMAD_E_SAS"
- "GNOMAD_G_AFR"
- "GNOMAD_G_AMR"
- "GNOMAD_G_EAS"
- "GNOMAD_G_NFE"
- "GNOMAD_G_SAS"
pathogenicitySources:
- "REVEL"
- "MVP"
- "SPLICE_AI"
- "ALPHA_MISSENSE"
steps:
- frequencyFilter:
maxFrequency: 0.1
- pathogenicityFilter:
keepNonPathogenic: true
- omimPrioritiser: {}
- hiPhivePrioritiser:
runParams: "human, mouse, fish, ppi"
outputOptions:
outputFormats:
- "HTML"
- "VCF"
- "TSV_GENE"
- "TSV_VARIANT"
- "JSON"
outputFileName: "sample.vcf"
outputDirectory: "results/sample"
Hi,
I have run exomiser v15.0.0 with the dataset 2512.
Our variant is 1-42930685-G-A on SLC2A1 gene.
It shows GLUT1 and alternating hemiplegia of childhood on the html output:
However, it just shows alternating hemiplegia of childhood on the tsv output. It would be better to show GLUT1 instead of alternating hemiplegia of childhood.
yaml file: