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.

• Sorting: Allows sorting by genomic start location.

Gene

• HGNC-approved gene symbol(s) where the variant occurs.

  • Single-gene CNVs: One gene symbol.

  • Multi-gene CNVs: Multiple gene symbols (hover to see full list).

• Sorting: Alphabetical.

Variant Type

• Specifies whether the variant is SNV, Indel, CNV, SV, STR, or other.

• Sorting: Alphabetical.

2. Clinical and phenotypic data

Disease

• Displays the number of disease associations, disease name and inheritance modes derived from OMIM, CGD and ORPHANET. Shows complete list of disease names and inheritance on hovering.

• Sorting: Alphabetical.

Tag

• Indicates variant tags assigned by Emedgene or manually by users (e.g., "Candidate," "Reviewed").

• Sorting: Alphabetical.

Known Variants

• Shows existing classifications from ClinVar and your Curate database.

• Sorting: Alphabetical.

Variant Notes

• Indicates if Variant Interpretation notes are available.

• Sorting: Alphabetical.

3. AI and Phenotype scoring

AI Rank

• AI-based ranking of potential causative variants. Lower numbers indicate higher rank. Variants with identical scores share the same rank (1–220).

• Sorting: Numerical.

Note: AI ranks are recalculated upon case reanalysis.

Phenomatch Score

• Proprietary phenotype-matching score ranging from 0–1.

• Sorting: Numerical.

Phenomeld Score

• Enhanced phenotype-matching score (range 0–2).

  • 0 = No match

  • 0.15 = Moderate match

  • 0.7 = High match

• Sorting: Numerical.

Note: Recalculated during reanalysis.

4. Quality metrics

Proband Quality

• Overall variant quality for the proband.

  • SNV/Indel: Based on Base Quality, Depth, Mapping Quality, Genotype Quality.

  • CNV: Based on CNV Quality, Size, Bin Count.

• Sorting: Alphabetical.

Depth

• Sequencing depth of coverage.

  • SNV/Indel: Depth at variant position.

  • CNV: Depth across CNV region.

• Sorting: Numerical.

Alternate Read

• Number of reads supporting the alternate allele.

• Sorting: Numerical.

Allele Bias

• Percentage of alternate allele reads out of total reads (0–100). Available only for SNVs.

• Sorting: Numerical.

Bin Count

• Number of bins supporting CNV detection.

• Sorting: Numerical.

5. Population frequency data

Allele Freq

• Variant frequency category based on highest allele frequency across public databases.

  • Private: 0

  • Rare: <0.01

  • Low Frequency: 0.01–0.05

  • Polymorphism: >0.05

• Sorting: Alphabetical.

Emedgene DB Frequency (% / #)

• Frequency of variant in Emedgene's internal control database, shown as percentage and count.

• Sorting: Numerical.

gnomAD All AF (% / #)

• Overall alternative allele frequency across gnomAD populations.

• Sorting: Numerical.

gnomAD Hom / Hemi

• Number of gnomAD subjects who are homozygous or hemizygous for the variant.

• Sorting: Numerical.

gnomAD Allele Count

• Number of observed alternate alleles in gnomAD dataset.

• Sorting: Numerical.

Max AF (% / #)

• Maximum alternative allele frequency across public databases.

• Sorting: Numerical.

6. Prediction and conservation metrics

Prediction

• Summarized in silico pathogenicity prediction score. Hover to view detailed predictions (SIFT, REVEL, CADD, etc.).

• Sorting: Alphabetical.

Conservation

• Summarized nucleotide conservation score. Tooltip displays detailed scores.

• Sorting: Alphabetical.

Splice Prediction

• Summarized splicing impact prediction score (SpliceAI and others).

• Sorting: Alphabetical.

7. Genetic notation and structural details

Coding Change

• HGVS coding-level description of variant.

• Sorting: Alphabetical.

Protein Change

• HGVS protein-level description of variant.

• Sorting: Alphabetical.

Variant Length (kbp)

• Size of variant in kilobases (relevant for CNVs/SVs).

• Sorting: Numerical.

Cytoband

• Chromosomal cytogenetic band where variant is located.

• Sorting: Alphanumeric.

ISCN

• International System for Human Cytogenomic Nomenclature description of chromosomal abnormality.

• Sorting: Alphanumeric.

8. Classification fields

Pathogenicity

• Pathogenicity classification (Pathogenic, Likely Pathogenic, VUS, Likely Benign, Benign).

• Sorting: Alphabetical.

Manual Classification

• User-assigned pathogenicity from previous cases. Badge color indicates class; number indicates count. Hover for details.

• Sorting: Alphabetical.

Networks Classification

• Pathogenicities assigned by partner organizations. Same badge system as Manual Classification.

• Sorting: Alphabetical.

9. Trio-specific columns

Mother Zygosity / Father Zygosity

• Variant zygosity status in mother and father.

• Sorting: Alphabetical.

Mother Quality / Father Quality

• Overall variant quality for mother/father.

• Sorting: Alphabetical.

Mother Depth / Father Depth

• Sequencing depth for mother/father.

• Sorting: Numerical.