Filtering

VarLens provides a layered filtering system — from one-click presets to a structured query language — so you can narrow down variants at whatever level of detail you need.

Quick Filters (Toolbar)

The toolbar above the variant table provides instant-access filters:

Control	What it does
Search bar	Free-text search (gene, position, HGVS) or DSL expressions
Case / All	Scope annotation filters to current case or all cases
Star / Comment	Show only starred or commented variants
ACMG chips	Filter by classification (P, LP, VUS, LB, B)
Tags	Filter by assigned tags

The result count chip shows how many variants pass your filters (e.g., 12 / 245). It pulses briefly when the count changes.

Active Filter Bar

When filters are active, a bar appears below the toolbar showing each filter as a removable chip:

• Click the × on any chip to remove that filter
• Click Clear all to reset everything

Filter Drawer

Click Filters or press Ctrl+Shift+F to open the drawer. Filters are grouped into sections:

Variant Properties

• Search — Full-text search across all text fields
• Gene — Autocomplete by gene symbol
• Impact — Toggle HIGH / MODERATE / LOW impact chips
• Consequence — Grouped multi-select (Truncating, Missense, Splice, etc.)
• ClinVar — Grouped multi-select (Pathogenic, VUS, Benign, etc.)

Population & Scores

• Frequency — gnomAD allele frequency threshold (presets: ≤ 1%, ≤ 0.1%, ≤ 0.01%) with custom input
• CADD — Minimum CADD Phred score (presets: ≥ 10, ≥ 15, ≥ 20, ≥ 25) with custom input

Numeric filters are NULL-inclusive by default: variants without annotation data (e.g., novel variants with no gnomAD entry) pass through frequency and CADD filters.

Annotations

• Tags — Filter by assigned tags
• Star / Comment — Toggle starred or commented variants
• ACMG — Filter by ACMG classification

Collapsed Previews

When a filter panel is collapsed, its current value appears on the right (e.g., "≤ 1.00%" next to Frequency). This lets you see all active filters at a glance.

Per-Column Filters

Each column header has a filter icon. Click it to open a type-aware filter popup:

Numeric Columns (CADD, gnomAD AF, Quality)

• Choose an operator (<, >, <=, >=, =, !=)
• Enter a value or click a preset
• Toggle "Include missing values" for NULL-inclusive behavior
• The data range in the current case is shown at the bottom

Categorical Columns (Consequence, ClinVar, Function)

• Search within available values
• Check/uncheck individual values (with counts)
• Use "Select All" / "Clear" for bulk operations

Text Columns (Gene, Transcript, cDNA)

• Choose a match mode: Contains, Equals, Starts with, Ends with
• Type a search term — matching values are previewed

DSL Search Bar

For power users, the search bar supports a structured filter language:

Syntax

column:operator:value

Examples:

Expression	Meaning
gnomad_af:<:0.01	AF less than 1%
cadd:>=:20	CADD at least 20
gene:=:BRCA1	Exact gene match
consequence:~:missense	Consequence contains "missense"

Operators

Operator	Name	Column types
=	Equals	All
!=	Not equals	All
< > <= >=	Comparisons	Numeric
~	Contains	Text, Categorical

Combining Filters

Use AND or OR between expressions:

gnomad_af:<:0.01 AND cadd:>=:20

Use parentheses to group OR conditions:

(gene:=:BRCA1 OR gene:=:TP53) AND gnomad_af:<:0.01

WARNING

Mixing AND and OR without parentheses is not allowed — VarLens will ask you to add parentheses to clarify your intent.

Autocomplete

The search bar offers context-aware suggestions as you type:

1. Column names — type a few letters to see matching columns
2. Operators — after column:, valid operators for that column type appear
3. Values — after column:op:, common values are suggested (e.g., AF thresholds)
4. Combinators — after a complete expression, AND / OR are suggested

Preset References

Type @ followed by a preset name to apply a saved preset directly from the search bar:

@rare-pathogenic

Plain Text Search

If your input doesn't contain colons, it works as a regular full-text search:

• BRCA1 — search by gene symbol
• BRCA1 AND pathogenic — boolean operators
• c.5123C>T — HGVS cDNA notation
• p.Ala1708Glu — HGVS protein notation

Empty State

When filters produce no matching variants, VarLens shows a clear message with a button to reset all filters:

See Also

• Filter Presets — save and reuse filter combinations
• Keyboard Shortcuts — filter-related shortcuts