Variant table columns
Variant table columns:
Allele Bias - indicates the percentage of reads that include an alternate allele out of all reads. Available only for SNVs.
Allele Freq - indicates variant frequency category according to the highest allele frequency in public population frequency databases:
Private: 0;
Rare: <0.01;
Low Frequency: 0.01-0.05;
Polymorphism: >0.05.
🔻 Allows alphabetical sorting
Alternate Read - number of alternate reads.
Available only for SNVs.
🔻 Allows numerical sorting
Coding Change - variant's coding sequence change (transcript-specific).
Conservation - summarized nucleotide conservation score. Tip: you can glance at the underlying scores in the pop-up tooltip
Depth (in proband):
SNV/Indel - sequencing depth of coverage at the variant position;
CNV - depth of coverage across the CNV region.
🔻 Allows numerical sorting
Emedgene DB Frequency - variant frequency in Emedgene's internal control database.
Father Depth:
SNV/Indel - sequencing depth of coverage at the variant position;
CNV - depth of coverage across the CNV region.
🔻 Allows numerical sorting
Father Quality - overall variant quality score in father:
SNV/Indel - based on Base Quality, Depth, Mapping Quality, and Genotype Quality;
CNV - based on CNV Quality, Size, and Bin Count.
🔻 Allows alphabetical sorting
Father Zygosity - variant zygosity in father. 🔻 Allows alphabetical sorting
Gene:
SNV/Indel/single-gene CNV - an HGNC-approved gene symbol;
Multi-gene CNVs - a list of HGNC-approved gene symbols and number of genes included if only part of the list is shown. Tip: if only the beginning of the list is displayed in the table, you can see the full gene list in the pop-up tooltip.
gnomAD All AF - overall alternative allele frequency across gnomAD populations (also called Total AF in the Summary section). 🔻 Allows numerical sorting
gnomAD Het Count - number of gnomAD subjects who are heterozygous for this variant.
gnomAD Hom / Hemi - number of gnomAD subjects who are homozygous (autosomal or X-linked variant in a female) or hemizygous (X-linked variant in a male) for this variant.
Historic AF - variant frequency in the organization's pre-loaded Historic DB.
Known Variants - displays the variant's classification(s) in ClinVar and your own curated variant database.
Main Effect - predicted effect(s) of the variant on protein structure and function (transcript-specific). By default the most severe effect is presented. 🔻 Allows alphabetical sorting
Manual Classification - displays the user-assigned Pathogenicities from your previous cases. The color of each element indicates the variant's Pathogenicity, while a number corresponds to a number of the previous classifications. Tip: hover over the badge to see the Pathogenicity.
Max AF - the highest alternative allele frequency among all public population databases. Note: not to be confused with Max AF in Summary section that only considers gnomAD statistics. 🔻 Allows numerical sorting
Mother Depth:
SNV/Indel - sequencing depth of coverage at the variant position;
CNV - depth of coverage across the CNV region.
🔻 Allows numerical sorting
Mother Quality - overall variant quality score in mother:
SNV/Indel - based on Base Quality, Depth, Mapping Quality, and Genotype Quality;
CNV - based on CNV Quality, Size, and Bin Count.
🔻 Allows alphabetical sorting
Mother Zygosity - variant zygosity in mother. 🔻 Allows alphabetical sorting
Networks Classification - displays the Pathogenicities assigned by partnering organizations in your network. The color of each element indicates the variant's Pathogenicity, while a number corresponds to a number of the previous classifications. Tip: hover over the badge to see the Pathogenicity.
Pathogenicity - variant pathogenicity that has been manually assigned in the Evidence section.
Phenomatch score - a score reflective of the phenotypic match between a patient's phenotypes and clinical presentation of one of the gene-related diseases (the one shown in the Disease column). The Phenomatch score is calculated by Emedgene's proprietary algorithm and ranges from 0 to 1.
Prediction - summarized in silico pathogenicity prediction score. Tip: you can glance at the underlying scores in the pop-up tooltip. 🔻 Allows alphabetical sorting
Proband Quality - overall variant quality score in proband:
SNV/Indel - based on Base Quality, Depth, Mapping Quality, and Genotype Quality;
CNV - based on CNV Quality, Size, and Bin Count.
🔻 Allows alphabetical sorting
Proband Zygosity - variant zygosity in the proband. 🔻 Allows alphabetical sorting
Protein Change - protein change (transcript-specific).
Splice Prediction - summarized in silico splicing prediction score. Tip: you can glance at the underlying scores in the pop-up tooltip.
Tag - variant tag assigned by Emedgene or selected by a user.
Variant Details:
SNV/Indel: genomic coordinates, nucleotide change, and dbSNP identifier;
CNV: genomic coordinates and size.
🔻 Allows sorting by genomic start location
Variant Notes - indicates if the variant has Variant Interpretation notes.
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