Variant table columns

The variant table displays all variants identified in your case, along with key annotations, quality metrics, pathogenicity data, and interpretation details. Each column provides specific information to help you review and prioritize variants effectively.

This guide explains the meaning of each column for proband analysis and trio analysis, with sorting features and scoring details.

1. Core variant information

Variant details	Displays genomic coordinates and basic variant identifiers. SNV/Indel: Genomic position, nucleotide change, and dbSNP ID CNV/SV: Genomic coordinates and variant size Allows sorting by genomic start location.
Gene	Gene identifier. SNV/Indel/single-gene CNV: An HGNC-approved gene symbol Multi-gene CNVs: A list of HGNC-approved gene symbols and the 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.
Variant type	Specifies whether the variant is SNV, Indel, CNV, SV, STR, or other. Allows alphabetical sorting.
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

2. Clinical and phenotypic data

Disease	Lists the count of disease associations, mode(s) of inheritance, and the name of one of the diseases. Tip: Hover over the line to see the full disease list in a pop-up window. Allows alphabetical sorting.
Tag	Variant tag assigned by Emedgene or by a user. Allows alphabetical sorting.
Known variants	Classification(s) of the variant in ClinVar and your curated variant database. Allows alphabetical sorting.
Variant notes	Indicates if Variant interpretation notes are available. Allows alphabetical sorting.

3. AI and Phenotype scoring

AI rank	Indicates potential causative variants: Most Likely Candidates and Candidates. Variants with identical scores share the same rank. Ranges from 1 to 220; lower numbers indicate higher rank. Case reanalysis causes Al ranks to be recalculated. Allows numerical sorting.
Phenomatch score	Proprietary phenotypic match score ranging from 0 to 1. Case reanalysis causes Phenomatch score to be recalculated. Allows numerical sorting.
PhenomeId score	Proprietary phenotypic match score outperforming previous Phenomatch 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 Phenomeld score to be recalculated. Allows numerical sorting.

4. Quality metrics

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.
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.
Alternate read	Number of alternate reads. Available only for SNVs. Allows numerical sorting.
Allele bias	Percentage of reads that include an alternate allele out of all reads. Available only for SNVs. Allows numerical sorting.
Bin count	Number of bins supporting CNV detection. Allows numerical sorting.

5. Population frequency data

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.
Emedgene DB frequency (%)	Variant frequency in the Emedgene internal control database. Allows numerical sorting.
Emedgene DB frequency (#)	Variant allele count in the Emedgene internal control database. Allows numerical sorting.
gnomAD All AF	Overall alternative allele frequency across gnomAD populations (also called Total AF in the Summary section). Allows numerical sorting.
gnomaAD allele count	Number of observed alternate alleles in gnomAD dataset. Allows numerical sorting.
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.
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.
Max AF (#)	The highest alternative allele count among all public population databases. Note: Not to be confused with Max AF in Summary section that only considers gnomAD statistics. Allows numerical sorting.
Historic AF (%)	Variant frequency in the organization’s Historic database, containing results of previously analyzed internal cases. SNV/Indel: Percentage of samples carrying the variant CNV/SV: Percentage of cases containing overlapping CNV/SV events, based on internal historic calls Allows numerical sorting.
Historic AF (#)	Variant allele count in the organization’s Historic database. SNV/Indel: Number of probands with the same variant. CNV/SV: Number of cases with overlapping CNV/SV regions. Allows numerical sorting.

6. Prediction and conservation metrics

Prediction	Summarized in silico pathogenicity prediction score. Tip: You can glance at the underlying scores in a pop-up tooltip. Allows alphabetical sorting.
Conservation	Summarized nucleotide conservation score. Tip: You can glance at the underlying scores in a pop-up tooltip. Allows alphabetical sorting.
Splice prediction	Summarized splicing impact prediction score. Tip: You can glance at the underlying scores in a pop-up tooltip. Allows alphabetical sorting.

7. Genetic notation and structural details

Coding change	HGVS-compliant coding sequence change notation. Allows alphabetical sorting.
Protein change	HGVS-compliant protein change notation. Allows alphabetical sorting.
Variant length	Variant size in kilobases (relevant for CNVs/SVs). Allows numerical sorting.
Cytoband	Chromosomal cytogenetic band where variant is located. Allows alphanumeric sorting.
ISCN	Cytogenetic description of a chromosomal abnormality, using the International System for Human Cytogenomic Nomenclature (ISCN). Allows alphanumeric sorting.

8. Classification fields

Pathogenicity	Pathogenicity classification assigned in the Evidence section. Allows alphabetical sorting.
Manual classification	Displays pathogenicity classifications previously assigned by members of the organization to the same variant in earlier cases. Badge color indicates pathogenicity class while badge number indicates count. Tip: hover over the badge to see pathogenicity. Allows alphabetical sorting.
Networks classification	Displays pathogenicity classifications assigned by partnering organizations. Badge color indicates pathogenicity class while badge number indicates count. Tip: hover over the badge to see pathogenicity. Allows alphabetical sorting.

9. Trio-specific columns

Proband zygosity	Variant zygosity status in the proband. Allows alphabetical sorting
Mother zygosity	Variant zygosity status in mother. Allows alphabetical sorting
Father zygosity	Variant zygosity status in father. Allows alphabetical 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
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.
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
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