BAP1 c.1729+3G>A
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
2
hereditary neoplastic syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +3 | donor splice region (+3, within the first 6 intronic nt) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.37 | GERP -2.9, phastCons 0.84 |
| Non-coding constraint | Z 4.03 | 1 kb window · o/e 0.76 · regional · uncalibrated |
| Overall | ||
| CADD | 16.24 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- BAP1
- Coding
- c.1729+3G>A
- MANE Select
- NM_004656
- dbSNP
- rs2153226566
- Type
- single nucleotide variant
- Location
- chr3:52403413 (GRCh38)
- Gene constraint
- LOEUF 0.324 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.87 · 4 PDB
Similar variants
- BAP1 c.1117-1G>A Likely pathogenic ★★ same condition
- BAP1 c.122+1G>A Pathogenic ★★ same condition
- BAP1 c.122+1G>T Pathogenic/Likely pathogenic ★★ same condition
- BAP1 c.122+5G>A Pathogenic/Likely pathogenic ★★ same condition
- BAP1 c.122+5G>C Likely pathogenic ★★ same condition
- BAP1 c.1251-1G>A Likely pathogenic ★★ same condition
- BAP1 c.1251-1G>C Likely pathogenic ★★ same condition
- BAP1 c.1251-2A>G Likely pathogenic ★★ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/bap1-c-1729-plus-3g-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown