Inaccurate SpliceAI scores displayed

[slversch]

Describe the bug
Some SpliceAI scores are inaccurately displayed as 0.00 in Seqr.

Two examples:

Variant 1-6148879-C-T:
Seqr displayed SpliceAI score: 0.00
SpliceAI highest delta score: 0.59 (donor loss, position 1 bp)

Variant 11-9176771-C-T:
Seqr displayed SpliceAI score: 0.00
SpliceAI highest delta score: 0.15 (donor loss, position 1 bp)

In these examples, the highest delta score is not affected by changing the max distance from 50 bp to 1000 bp.

Scope of the bug
I noticed discrepancies in displayed SpliceAI scores in all families from the same project.

[bpblanken]

Hi @slversch,

We're aware of the discrepancies between the SpliceAI lookup tool and the scores displayed in seqr. The scores in seqr come from a precomputed batch with a fixed Gencode version and "MaxDistance" parameter that was delivered directly from Illumina, whereas the lookup tool is able to dynamically compute scores with variable parameters. The scores in seqr are, unfortunately, outdated and not as accurate as in the lookup tool. There's a tad more context on a gnomAD forum post.

We're currently evaluating a few paths forward to resolve these discrepancies, but an immediate fix is unfortunately not possible.

Thank you for the report!

[slversch]

Hi @bpblanken,

Thank you for the clear explanation! It's reassuring to know you're working on resolving this.