Small variants (SNVs & indels)

Small variants are single-nucleotide variants (SNVs) and short insertions or deletions (indels). In long-read WGS they are called per-sample, joint-called across a family where applicable, and phased so that you can see which variants sit on the same chromosome copy.

The candidate table

Each row is one variant. You can search, sort, filter, and customize the columns in the table using the Columns dropdown.

The default columns in the candidate table include:

Column	Description
User Classification	The classification manually assigned to the variant by a reviewer (e.g., Pathogenic, Likely Pathogenic, VUS, Benign).
Automated Classification	The automated classification generated by the system's pipeline rules or algorithms.
Chrom	The chromosome where the variant is located.
Pos	The genomic coordinate (position) of the variant.
REF	The reference allele at the variant position.
ALT	The alternative allele observed.
Gene Symbol	The standard HGNC gene symbol of the affected gene.
Max AF	The maximum allele frequency observed for the variant across any sub-populations in reference datasets.
1000G AF	The allele frequency of the variant in the 1000 Genomes Project cohort.
gnomAD Exome AF	The allele frequency of the variant in the gnomAD exomes database.
gnomAD Genome AF	The allele frequency of the variant in the gnomAD genomes database.
Biotype	The biological classification of the transcript (e.g., protein_coding, lncRNA).
Consequence	The predicted functional effect of the variant on the transcript (e.g., missense_variant, frameshift_variant).
Impact	The predicted severity impact of the variant's consequence (e.g., HIGH, MODERATE, LOW, MODIFIER).
Phenotype Association	Known clinical phenotypes, traits, or diseases associated with the gene.
Variant Class	The structural classification of the variant (e.g., SNV, Insertion, Deletion).
Exomiser Rank	The gene ranking generated by Exomiser based on phenotype relevance and variant pathogenicity.
Exomiser Inheritance	The predicted mode of inheritance for the disease matching the phenotypes.
Exomiser Variant Score	The score computed by Exomiser assessing the potential pathogenicity of the variant.
Exomiser Functional Class	The functional consequence class predicted by Exomiser.
Exomiser ACMG Classification	The pathogenicity classification assigned by Exomiser following ACMG guidelines.
Exomiser ACMG Disease	The specific disease associated with the gene that matches the patient's phenotypes according to Exomiser.
Genotype	The zygosity and phase of the variant in the sample.

Filters

The filter drawer offers:

• User Classification: Pathogenic, Likely Pathogenic, VUS, Likely Benign, Benign.

• Gene: filter by gene symbol.

• Chromosome: chr1 to chr22, chrX, chrY.

• Position: a genomic-coordinate range.

How to review

1. Sort or filter the table to bring the most relevant candidates to the top, typically rare, predicted-damaging variants in phenotype-relevant genes.

2. Select a variant to open its detail view, where you can inspect the supporting reads and annotations.

3. Record a decision (e.g. include, exclude, follow up) so it carries into the report.

Phasing matters for recessive conditions. When two heterozygous variants fall in the same gene, phasing tells you whether they are on the same copy (likely benign together) or on opposite copies (a potential compound heterozygote). See the phasing background on the Paralogs page.