SpliceAI Lookup

Enter a variant below to see its SpliceAI and Pangolin scores

[more details]

Examples (on hg38):
chr8-140300616-T-G
chr8 140300616 T G
NM_001089.3(ABCA3):c.875A>T (p.Glu292Val)	[show more examples]
8:140300616 T>G	'chr' prefix is optional
1:930130:C:G	position with overlapping genes
1-1042601-A-AGAGAG	insertion of GAGAG
1-1042466-GGGC-G	deletion of GGC
NM_000249.4(MLH1):c.116G>A	another HGVS example

Genome version:

hg19

hg38

Max distance:

masked scores

REF & ALT score columns

SpliceAI-lookup/issues: issues or feature requests for this website

Related web tools:
liftover: for variants/positions/intervals (hg19 <=> hg38 <=> T2T)
CMA search: search OMIM by interval, gene or phenotype
TGG Viewer: igv.js-based web viewer for public reference tracks and, optionally, private data in Google Storage buckets

November 30, 2023
- changed default search settings to "not masked" due to confusion and issues with how masked scores are computed.
- when looking at hg19 variants, the visualization checkboxes now make it clear which IGV.js tracks are or aren't available on hg19.

[show older updates]

Visualizations:
SpliceAI & Pangolin results	GTEx RNA: average per sample	GTEx RNA: all splice junctions	SpliceAI: all precomputed scores	Reference
variant track SpliceAI REF & ALT scores SpliceAI Δ scores Pangolin Δ scores	blood fibroblasts muscle LCLs brain cortex	blood fibroblasts muscle LCLs brain cortex	gain ≥ 0.5 loss ≥ 0.5 gain ≥ 0.2 loss ≥ 0.2	100-mer mappability segmental duplications