Is BAP1 c.1116+10del pathogenic?

BAP1 c.1116+10del is classified Likely benign in BAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-11-12). Absent from gnomAD; Associated with hereditary neoplastic syndrome.

What condition is associated with BAP1 c.1116+10del?

BAP1 c.1116+10del is associated with hereditary neoplastic syndrome (ClinVar).

How common is BAP1 c.1116+10del in the general population?

BAP1 c.1116+10del is absent from gnomAD (gnomAD).

BAP1 c.1116+10del

rs1705105432 · VCV922623

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 +10	near-intronic (+10 nt from the splice site)
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.14	GERP -1.4

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: BAP1
Coding: c.1116+10del
MANE Select: NM_007212 · reported on NM_004656
dbSNP: rs1705105432
Type: Deletion
Location: chr3:52405100 (GRCh38)
Structure: AlphaFold pLDDT 78.27 · 28 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

Similar variants

BAP1 c.123-10_129del Likely pathogenic ★★ same condition
BAP1 c.1729+1del 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
BAP1 p.Asp400_Tyr401insTer 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-1116-plus-10del (accessed [today's date]).

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