Is BRCA2 p.Arg2502= (c.7506C>A) pathogenic?

BRCA2 p.Arg2502= (c.7506C>A) is classified Likely benign in BRCA2 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-07-24). Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with BRCA2 p.Arg2502= (c.7506C>A)?

BRCA2 p.Arg2502= (c.7506C>A) is associated with hereditary neoplastic syndrome (ClinVar).

How common is BRCA2 p.Arg2502= (c.7506C>A) in the general population?

BRCA2 p.Arg2502= (c.7506C>A) is absent from gnomAD v4.1 (gnomAD).

BRCA2 p.Arg2502=

c.7506C>A · rs140693106 · VCV1759233

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 carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>T here scores Δ0.27 · evaluated, not missing
Constraint at this position
Conservation	phyloP -0.43	GERP -4.6
Overall
CADD	0.205	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.Arg2502=
Coding: c.7506C>A
MANE Select: NM_000059
dbSNP: rs140693106
Type: single nucleotide variant
Location: chr13:32356498 (GRCh38)
Gene constraint: LOEUF 0.803 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Residue 2502: a UniProt-annotated variant site (in bc; uncertain significance); a UniProt-annotated variant site (in); the 'interaction with fancd2' region; the 'interaction with sem1' region

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 p.Arg2502His Benign ★★★ same residue
BRCA2 p.Arg2502Cys Conflicting classifications of pathogenicity ★ same residue
BRCA2 p.Arg2502Leu Conflicting classifications of pathogenicity ★ same residue
BRCA2 p.Arg2502Pro Conflicting classifications of pathogenicity ★ same residue
BRCA2 p.Arg2502Ser Conflicting classifications of pathogenicity ★ same residue
BRCA2 p.Arg2502Gly Uncertain significance ★ same residue
BRCA2 c.316+1G>T Pathogenic ★★★ same condition
BRCA2 c.316+2T>C 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-arg2502 (accessed [today's date]).

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