SpliceAI

PARTIAL

## Connections

variant-classification splicing deep-learning

What It Does

Predicts splice site creation/disruption from DNA sequence
Four scores per variant: acceptor gain, acceptor loss, donor gain, donor loss
Score 0-1: >0.5 likely affects splicing, >0.8 high confidence
Distance to nearest affected splice site
Works for any variant type (SNV, indel) within 10kb of splice sites

How to Use

### Web Lookup

1. Go to https://spliceailookup.broadinstitute.org/

2. Enter variant: chr15-43600551-A-C (GRCh38)

3. View delta scores for each splice effect

### Python Package


        pip install spliceai


        from spliceai import predict
        # Requires reference genome FASTA
        # predict(variant, reference_fasta, annotation)

### Pre-computed Scores


        # Download pre-computed (SNVs only)
        # Available from Illumina: https://basespace.illumina.com/s/otSPW8hnhaZR
        tabix spliceai_scores.raw.snv.hg38.vcf.gz chr15:43600551-43600551

### Via VEP Plugin


        vep --input_file variants.vcf --plugin SpliceAI,snv=spliceai_scores.raw.snv.hg38.vcf.gz

Verified Status

PARTIAL — pip install works (v1.3.1) but runtime fails due to deprecated pkg_resources. API (spliceailookup-api.broadinstitute.org) TIMES OUT. Web lookup at spliceailookup.broadinstitute.org works for manual queries only. Pre-computed scores available via Illumina BaseSpace. For E1659A: must use web interface manually (API times out). As a missense in exon 29, major splice effects unlikely. AlphaGenome SPLICE output showed no significant splice junction changes at this position (all quantile scores ~0.99 for nearby genes, not STRC itself).

STRC Research Usage

Not yet used for E1659A
Critical for: evaluating any intronic STRC variants, assessing cryptic splice sites

STRC Research Usage

Not yet used for E1659A
Critical for: evaluating any intronic STRC variants, assessing cryptic splice sites