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c.862-11C>A

SpliceS3Likely benignCytoplasmic · predicted
Splice variant · splice site near at position 288 · N-terminal cytoplasmic (intrinsically disordered) · WFS1 (Wolframin)

S3 — Minimal predicted splicing impact (SpliceAI ΔS 0.01)

Interactive 3D Structure

Interactive structure
rotate · zoom · variant + 5 Å neighbors
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AlphaFold wild-type wolframin · the variant site near residue 288 (N-terminal cytoplasmic (intrinsically disordered)) is highlighted.

Variant Assessment

Variant type
Splice
Schema
S3
Minimal predicted splicing impact (SpliceAI ΔS 0.01)
Domain
N-terminal cytoplasmic (intrinsically disordered)
Status
—

Therapeutic Implication · S3

SpliceAI predicts little splicing disruption at this acceptor (3') site (max ΔS 0.01 < 0.2; acceptor-gain 0.00, acceptor-loss 0.01, donor-gain 0.00, donor-loss 0.00). The variant may be tolerated or act through a weak/again-tissue-specific mechanism; wet-lab RNA validation is the arbiter before any therapeutic call.

Clinical Evidence

ClinVar classificationLikely benign
Review statuscriteria provided, single submitter
Associated conditions—
Population frequency (gnomAD v4)Ultra-rare · AF 0.0029%
cDNA changec.862-11C>A
ClinVar variantNM_006005.3(WFS1):c.862-11C>A
ClinVar accessionVCV002417720
Last evaluated2023/12/11 00:00

Observed at very low frequency in gnomAD.

Therapeutic Strategy Handoff · prediction

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Full Variant Card

c.862-11C_A — WFS1 Molecular Atlas Card

Variant type: Splice site Boundary: acceptor (3' splice site) · intronic offset -11 Nearest protein position: ~288 (N-terminal cytoplasmic (intrinsically disordered))

Schema category: S3 — Minimal predicted splicing impact (SpliceAI ΔS 0.01)

SpliceAI predicts little splicing disruption at this acceptor (3') site (max ΔS 0.01 < 0.2; acceptor-gain 0.00, acceptor-loss 0.01, donor-gain 0.00, donor-loss 0.00). The variant may be tolerated or act through a weak/again-tissue-specific mechanism; wet-lab RNA validation is the arbiter before any therapeutic call.

Splice prediction

  • Affected site: acceptor (3' splice site), extended splice region
  • SpliceAI delta scores (GRCh38 chr4:6300646 C>A):
    • acceptor gain 0.00 · acceptor loss 0.01
    • donor gain 0.00 · donor loss 0.00
  • Predicted outcome: Minimal predicted splicing impact (SpliceAI ΔS 0.01)

Clinical evidence

  • Classification: Likely benign
  • Review status: criteria provided, single submitter
  • cDNA change: c.862-11C>A
  • ClinVar accession: VCV002417720
  • Last evaluated: 2023/12/11 00:00
  • Submissions: 1

Card generated by wolfram-atlas-batch (splice pipeline) on 2026-06-08T07:53:38.652735Z. Schema: reference/card_schema_extension.md (S1–S3). WFS1: UniProt O76024, AlphaFold v6.