Is BAP1 c.255+9del pathogenic?

BAP1 c.255+9del is classified Benign/Likely benign in BAP1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-12-16). Very rare (popmax 0.00348%, nfe); Associated with hereditary neoplastic syndrome.

What condition is associated with BAP1 c.255+9del?

BAP1 c.255+9del is associated with hereditary neoplastic syndrome, BAP1-related tumor predisposition syndrome (ClinVar).

How common is BAP1 c.255+9del in the general population?

BAP1 c.255+9del is very rare (popmax 0.00348%, nfe) (gnomAD).

BAP1 c.255+9del

rs769974242 · VCV490851

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00348%, nfe)

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +9	near-intronic (+9 nt from the splice site)
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.18	GERP -1.9, phastCons 0.015
Non-coding constraint	Z 1.97	1 kb window · o/e 0.86 · regional · uncalibrated
Overall
CADD	12.27	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00348% European (non-Finnish) · 41/1,178,162 alleles

Filtering AF 0.00259% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00233%

Overall 0.00255% 41/1,609,820 alleles · very rare exomes 40/1,457,804 · genomes 1/152,016 · joint denominator

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: BAP1
Coding: c.255+9del
MANE Select: NM_004656
dbSNP: rs769974242
Type: Deletion
Location: chr3:52408465 (GRCh38)
Gene constraint: LOEUF 0.324 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 63.87 · 4 PDB

Full BAP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: BAP1-related tumor predisposition syndrome

Similar variants

BAP1 c.123-10_129del Likely pathogenic ★★ same condition
BAP1 c.1729+1del Pathogenic ★★ same condition
BAP1 c.1984-3_1999del Likely pathogenic ★★ same condition
BAP1 c.659+1del Likely pathogenic ★★ same condition
BAP1 p.Ala138fs Pathogenic ★★ same condition
BAP1 p.Arg207fs Pathogenic ★★ same condition
BAP1 p.Arg518fs Pathogenic ★★ same condition
BAP1 p.Asn363fs 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-255-plus-9del (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown