> 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+/filters_presets_panel/variant_search.md). # Variant search The variant search box at the top of the **Filtering panel** lets you quickly narrow the variant list by applying custom query terms. Variant search queries act as **refinement filters**: * In the **Filters tab**: Variant search conditions intersect (**AND logic**) with the active filters, returning only variants that satisfy both. * In the **Presets tab:** Variant search conditions intersect (**AND logic**) with each preset in the active preset group, returning only variants that satisfy both the preset logic and the search terms. The refinements are **temporary** and do not modify the saved logic of any preset. ## 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:** {% columns %} {% column width="50%" %} **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 {% endcolumn %} {% column width="50%" %} **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 {% endcolumn %} {% endcolumns %} ## 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

{% hint style="warning" %} 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.

{% endhint %} ### 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 (v100.39.0+)	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

{% hint style="info" %} Use gene symbol searches when exploring CNVs; this can often give more reliable results than coordinate-based CNV queries. {% endhint %} ### 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"

--- # 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: ``` GET https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/reviewing_a_case/analysis-tools-tab-beta-v100.39.0+/filters_presets_panel/variant_search.md?ask= ``` The question should be specific, self-contained, and written in natural language. 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.