Alphagenome Lookup

Variant Lookup

Predict splicing and expression effects using deep learning

Examples:

Analyses:

Expression Scores RNA Expression Tracks Splice Scores Splice Sites Splice Junctions

Tissues (optional): Leave empty for all tissues.

How it works

Enter a genomic variant in chr-position-ref-alt format (hg38). AlphaGenome predicts how single nucleotide changes affect gene expression and splicing across hundreds of human tissues and cell types.

What you get

Expression Scores — predicted log-fold-change in gene expression per tissue
RNA Tracks — REF vs ALT expression visualization
Splice Scores — changes in donor/acceptor site usage
Splice Sites & Junctions — detailed interpretation of splicing effects

Variant format

Use hg38 coordinates: chr-position-ref-alt. Supports all autosomes and sex chromosomes (chr1–chr22, chrX, chrY).

Gene Information

Gene: -

Expression Scores

- Expression Score

Samples: -

Range: -

Direction: -

Gene Name	Tissue	Output Type	Raw Score

Splicing Score Changes

Δ Type	Δ Score	Position	Severity

Clinical Significance

Finding	Value	Significance

Summary

In-Silico Mutagenesis

Scan a genomic region to find variants that affect expression or splicing

Mode:

Expression Splice

Region:

Gene Region Custom Coordinates

Gene:

Region:

Window:

Tissue (optional): Leave empty for all tissues average

How it works

Select a gene region or enter custom coordinates. AlphaGenome systematically tests every possible single nucleotide change across the region, revealing which positions are most sensitive to mutation — useful for identifying regulatory elements and potential therapeutic targets.

Region options

Promoter — TSS ±500bp, where transcription factor binding controls gene activation
5'UTR — first 200bp, affects mRNA stability and translation efficiency
3'UTR — last 500bp, miRNA binding sites that regulate mRNA degradation
Custom — any region up to 200bp

Output

SeqLogo — visual map of position-specific mutational sensitivity
Top variants — ranked lists of upregulating and downregulating mutations

SeqLogo

Top Variants

Top 10 Upregulating

Variant	Position	Ref	Alt	Score

Top 10 Downregulating

Variant	Position	Ref	Alt	Score