> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/variant_table/variant_table_columns.md). # 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 Supports 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. Supports alphabetical sorting.
Variant type	Specifies whether the variant is SNV, Indel, CNV, SV, STR, or other. Supports 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. Supports 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. Supports alphabetical sorting.
Tag	Variant tag assigned by Emedgene or by a user. Supports alphabetical sorting.
Known variants	Classification(s) of the variant in ClinVar and your curated variant database. Supports alphabetical sorting.
Variant notes	Indicates if Variant interpretation notes are available. Supports 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 AI ranks to be recalculated. Supports numerical sorting.
Phenomatch score	Proprietary phenotypic match score ranging from 0 to 1. Case reanalysis causes Phenomatch scores to be recalculated. Supports numerical sorting.
Phenomeld score	Proprietary phenotypic match score that outperforms 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 strong phenotypic match. Case reanalysis causes Phenomeld scores to be recalculated. Supports numerical sorting.
Weighted Phenomeld	Phenomeld score recalculated after adjusting phenotype weights in Phenomatch filters Advanced mode (v100.40.0+). When phenotype weights are modified or new phenotypes are added, Weighted Phenomeld replaces the Phenomeld score column. 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 strong phenotypic match. Sorting is not supported.

### 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 Supports 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 Supports numerical sorting.
Alternate read	Number of alternate reads. Available only for SNVs. Supports numerical sorting.
Allele bias	Percentage of reads that include an alternate allele out of all reads. Available only for SNVs. Supports numerical sorting.
Bin count	Number of bins supporting CNV detection. Supports 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 Supports alphabetical sorting.
Emedgene DB frequency (%)	Variant frequency in the Emedgene internal control database. Supports numerical sorting.
Emedgene DB frequency (#)	Variant allele count in the Emedgene internal control database. Supports numerical sorting.
gnomAD All AF	Overall alternative allele frequency across gnomAD populations (also called Total AF in the Summary section). Supports numerical sorting.
gnomAD allele count	Number of observed alternate alleles in gnomAD dataset. Supports 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. Supports 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. Supports numerical sorting.
[Organization DB] AF (%)	Variant frequency in a specific historic or noise organization database. SNV/Indel: Percentage of database samples carrying the variant CNV/SV: Percentage of database samples containing overlapping CNV/SV events Supports numerical sorting.
[Organization DB] AF (#)	Variant allele count in a specific historic or noise organization database. SNV/Indel: Number of database samples carrying the variant CNV/SV: Number of database samples containing overlapping CNV/SV events Supports 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. Supports alphabetical sorting.
Conservation	Summarized nucleotide conservation score. Tip: You can glance at the underlying scores in a pop-up tooltip. Supports alphabetical sorting.
Splice prediction	Summarized splicing impact prediction score. Tip: You can glance at the underlying scores in a pop-up tooltip. Supports alphabetical sorting.

Prediction

Summarized in silico pathogenicity prediction score.

Tip: You can glance at the underlying scores in a pop-up tooltip.

Supports alphabetical sorting.

Conservation

Summarized nucleotide conservation score.

Tip: You can glance at the underlying scores in a pop-up tooltip.

Supports alphabetical sorting.

Splice prediction

Summarized splicing impact prediction score.

Tip: You can glance at the underlying scores in a pop-up tooltip.

Supports alphabetical sorting.

### 7. Genetic notation and structural details


Coding change	HGVS-compliant coding sequence change notation. Supports alphabetical sorting.
Protein change	HGVS-compliant protein change notation. Supports alphabetical sorting.
Variant length	Variant size in kilobases (relevant for CNVs/SVs). Supports numerical sorting.
Cytoband	Chromosomal cytogenetic band where variant is located. Supports alphanumeric sorting.
ISCN	Cytogenetic description of a chromosomal abnormality, using the International System for Human Cytogenomic Nomenclature (ISCN). Supports alphanumeric sorting.
Phasing	Variant phasing information: Phase block identifier Phased genotype (when available) that indicates which haplotype within the block the variant is on: `A`, `B`, `AB` Supports alphanumeric sorting. Available on v100.40.0+ for cases run on TruPath Genome data and analysed with DRAGEN 4.5+.

### 8. Classification fields


Pathogenicity	Pathogenicity classification assigned in the Evidence section. Supports 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. Supports 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. Supports alphabetical sorting.

Pathogenicity

Pathogenicity classification assigned in the Evidence section.

Supports 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.

Supports 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.

Supports alphabetical sorting.

### 9. Trio-specific columns


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

[^1]: HUGO Gene Nomenclature Committee [^2]: Human Genome Variation Society [^3]: Genotype `1|0` [^4]: Genotype `0|1` [^5]: Genotype `1|1` --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter: ``` GET https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/variant_table/variant_table_columns.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.