Variant table columns

Name	Function
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.
AI Rank	Indicates potential causative variants: Most Likely Candidates and Candidates. Lower numbers represent a higher rank. Variants with the same score calculated by AI Shortlist share the same rank. Ranges from 1 to 220. Case reanalysis causes AI ranks to be recalculated. 🔻 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 a pop-up tooltip.
Depth	Variant depth in proband. SNV/Indel - sequencing depth of coverage at the variant position; CNV - depth of coverage across the CNV region. 🔻 Allows numerical sorting.
Disease	The number of disease associations and corresponding mode(s) of inheritance derived from OMIM and CGD, and the name of one of the diseases are listed. Tip: hover over the partially displayed disease name to see the full name in the pop-up window.
Emedgene DB Frequency	Variant frequency in the internal control database.
Father Depth	Variant depth in father. 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 classification(s) of the variant in ClinVar and your 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	Variant depth in mother. 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	Proprietary phenotypic match score. Ranges from 0 to 1. Case reanalysis causes Phenomatch score to be recalculated.
Phenomeld Score	Proprietary phenotypic match score outperforming previous models. Ranges from 0 to 2. A score of 0 means no match, a score above 0.15 suggests a moderate match, and scores above 0.7 indicate a high phenotypic match. Case reanalysis causes Phenomatch score to be recalculated.
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.
Variant Type	Variant type.
Cytoband	Cytoband. 🔻 Allows alphanumeric sorting.
Bin count	Bin count. 🔻 Allows numeric sorting.
ISCN	Cytogenetic description of a chromosomal abnormality, using the International System for Human Cytogenomic Nomenclature (ISCN). 🔻 Allows alphanumeric sorting.