Is BRCA2 p.Ser3041= (c.9123A>T) pathogenic?

BRCA2 p.Ser3041= (c.9123A>T) is classified Likely benign in BRCA2 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-10-08). Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with BRCA2 p.Ser3041= (c.9123A>T)?

BRCA2 p.Ser3041= (c.9123A>T) is associated with hereditary neoplastic syndrome (ClinVar).

How common is BRCA2 p.Ser3041= (c.9123A>T) in the general population?

BRCA2 p.Ser3041= (c.9123A>T) is absent from gnomAD v4.1 (gnomAD).

BRCA2 p.Ser3041=

c.9123A>T · rs2137624515 · VCV1765887

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.41	acceptor gain · deltas
Pangolin	Δ0.33	gain · loss 0.12 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 0.084	GERP -4.6, phastCons 0.23
Overall
CADD	15.02	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: BRCA2
Protein: p.Ser3041=
Coding: c.9123A>T
MANE Select: NM_000059
dbSNP: rs2137624515
Type: single nucleotide variant
Location: chr13:32380012 (GRCh38)
Gene constraint: LOEUF 0.803 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)

Full BRCA2 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

BRCA2 c.316+1G>T Pathogenic ★★★ same condition
BRCA2 c.316+2T>C Pathogenic ★★★ same condition
BRCA2 c.316+5G>A Pathogenic ★★★ same condition
BRCA2 c.316+5G>C Pathogenic ★★★ same condition
BRCA2 c.475+1G>A Pathogenic ★★★ same condition
BRCA2 c.475+1G>T Pathogenic ★★★ same condition
BRCA2 c.476-2A>G Pathogenic ★★★ same condition
BRCA2 c.517-2A>G 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/brca2-p-ser3041 (accessed [today's date]).

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