SpliceAI Lookup

Enter a variant below to see its SpliceAI scores. This can be any SNV or simple InDel within an exon or intron defined by GENCODE v38.

more details...

Examples (on hg38):
chr8-140300616-T-G
chr8 140300616 T G
NM_000552.4(VWF):c.3797C>A (p.Pro1266Gln)

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 exapmle

Genome version:

hg19

hg38

Score type:

masked

raw

Max distance:

Use Illumina's pre-computed scores:

yes

What's New

To post issues or feature requests related to this web interface, please use SpliceAI-lookup/issues. For questions about SpliceAI itself or the SpliceAI pre-computed scores, see SpliceAI/issues.

Feb 5, 2023
- show Pangolin scores in addition to SpliceAI scores.
- update to Gencode v42 (was previously on v38)

June 2, 2021
- show RefSeq ids for the subset of Ensembl ENST ids (~30%) that have one or more matching RefSeq NM ids according to Ensembl. See issue #8 for details.
- update to Gencode v38 (was previously on v37)

April 11, 2021
- show gray background for non-coding transcripts
- switch to showing all non-coding transcripts. (Previously, transcripts with Gencode biotypes like lncRNA, processed_pseudogene, processed_transcript, retained_intron, and nonsense_mediated_decay were filtered out if they overlapped protein_coding transcripts). See issue #6 for details.
- update to Gencode v37 (was previously on v36)

Related web tools:
liftover - simple hg19 <=> hg38 conversion for variants, positions, intervals
CMA search - search OMIM by genomic region, gene name, phenotype, etc.