Variant search

The variant search box on top of the Filters/Presets panel allows you to quickly find specific variants within a case by applying customized filters.

How variant search works with filters and filter presets

Variant search uses AND logic with any active filters or filter presets.

This means that only variants matching all selected criteria—from both the search and the filters/presets—will be displayed.

Applying multiple filters

You can apply multiple filters in variant search box, one at a time, from the same or different categories.

Individual search queries are combined under either:

AND logic

A variant must meet all selected criteria to appear in the results. This narrows your search.

Example

Search query: Phenotype = Hyporeflexia AND Phenotype = Dilated cardiomyopathy AND Phenotype = Calf muscle pseudohypertrophy

Search result will include:

• Variants in gene(s) that are associated with all three specified phenotypes

OR logic

A variant will appear in the results if it meets any of the selected criteria. This broadens your search.

Example

Search query: Gene = BRCA1 OR Disease = Breast-ovarian cancer, familial, 2

Search result will include:

• Variants in the BRCA1 gene

• Variants in gene(s) associated with Breast-ovarian cancer, familial, 2

Variant search filter categories

Gene

Criterion	How to use	Query example	Output
Gene symbol	Search by a single gene name	"BRCA1"	Variants in the BRCA1 gene
Multiple gene symbols (batch)	Search multiple genes in one query	"BRCA1, BRCA2, UBE3A"	Variants in the BRCA1, BRCA2, UBE3A genes
Gene list	Search by a predefined gene list name	"Cardiomyopathy panel"	Variants in the genes included in the Cardiomyopathy panel gene list

Multiple gene search queries are joined (OR logic)

Combined gene search query: "FBN1" , "TGFBR1, TGFBR2, SMAD3, TGFB2, TGFB3" , "Ehlers-Danlos syndrome panel"

The query returns:

• Variants in the FBN1 gene

• Variants in the TGFBR1, TGFBR2, SMAD3, TGFB2, TGFB3 genes

• Variants in the Ehlers-Danlos syndrome gene list

Phenotype

Criterion	How to use	Query example	Output
Phenotype	Search by a phenotype name	"Mandibular prognathia"	Variants in genes where at least one associated disease includes Mandibular prognathia as one of it's phenotypes

Multiple phenotype search queries are intersected (AND logic)

Combined phenotype search query: "Brainstem dysplasia", "Generalized-onset seizure", "Clinodactyly"

The query will return:

• Variants in genes where at least one associated disease has an exact phenotype match with all three specified phenotypes: Brainstem dysplasia, Generalized-onset seizure, and Clinodactyly

Disease

Criterion	How to use	Query example	Output
Disease	Search by a disease name	"Kabuki syndrome 1"	Variants in genes where at least one associated disease has a name that exactly matches the query disease
Disease inheritance mode	Search by a disease inheritance mode	"Autosomal dominant"	Variants in genes where at least one associated disease has an inheritance mode that matches the query

Multiple disease search queries are joined (OR logic)

Combined disease search query: "Genitopatellar syndrome" , "Arthrogryposis, distal, type 3" , "Dysosteosclerosis"

The query returns:

• Variants in genes where at least one associated disease is Genitopatellar syndrome

• Variants in genes where at least one associated disease is Arthrogryposis, distal, type 3

• Variants in genes where at least one associated disease is Dysosteosclerosis

Due to a current limitation, the dropdown may display duplicate entries for the same disease. To ensure complete results, please select all matching entries, not just one.

Variant notation

Criterion	How to use	Query example	Output
Specific SNV/Indel	Search by exact variant notation	"chr1:27089776G>T"	Variant that exactly matches the specified genomic position, reference allele, and alternate allele
Specific MNV (39.0+)	Search by exact variant notation	"chr1:100AT>GC"	Variant that exactly matches the specified genomic position, reference allele, and alternate allele

Multiple variant notation queries are joined (OR logic)

Combined variant notation search query: "chr1:27089776G>T" , "chr1:100AT>GC"

The query returns:

• chr1:27089776G>T variant

• chr1:100AT>GC variant

Genomic position or range

Criterion	How to use	Query example	Output
Genomic position	Search by a single coordinate	"chr11:2686616"	SNVs/indels that match the specified genomic position CNVs whose starting position matches the specified genomic position
Genomic range	Search by a range of positions	"chr11:2686616-2886620"	SNVs/indels whose positions fall within the specified genomic range, including both start and end coordinates CNVs whose starting position falls within the specified genomic range, including both start and end coordinates

Multiple genomic position queries are joined (OR logic)

Combined genomic position search query: "chr1:27089776" , "chr11:2686616-2886620"

The query returns:

• SNVs/indels whose positions either match chr1:27089776 or fall within chr11:2686616-2886620, inclusive of both start and end coordinates

• CNVs whose starting position either match chr1:27089776 or fall within chr11:2686616-2886620, inclusive of both start and end coordinates

Use gene symbol searches when exploring CNVs; this can often give more reliable results than coordinate-based CNV queries.

Free text

Free text search is performed within variant characteristics using substring matching, meaning the query can match any part of a word. See the table below for example use cases.

Criterion	Use case	Query example	Output
Free text	Search by variant main effect full name	"Stop lost"	Variants where the main effect is "Stop lost"
Free text	Search by variant main effect partial name	"Stop"	Variants where the main effect is "Stop lost", "Stop gained", "Stop retained variant"
Free text	Search by partial gene symbol	"CYP"	Variants in genes whose symbols include "CYP" (cytochrome P450 genes)
Free text	Search by dbSNP ID	"rs2488992"	Variant with dbSNP ID "rs2488992"
Free text	Search by cytoband	"1p36.33"	Variants located within the 1p36.33 cytoband

Multiple free text search queries are intersected (AND logic)

Combined free text search query: "BRCA", "Frameshift"

The query will return:

• Variants in genes whose symbols include "BRCA" (ie, BRCA1, BRCA2) where the main effect is "Frameshift variant"