Is BRCA2 p.Arg2502Cys (c.7504C>T) pathogenic?

BRCA2 p.Arg2502Cys (c.7504C>T) is classified Conflicting classifications of pathogenicity in BRCA2 (ClinVar, Conflicting submitters, 27 submitters; last evaluated 2026-02-04). AlphaMissense: likely benign (0.0861); Rare (popmax 0.296%, afr); Associated with hereditary neoplastic syndrome.

What condition is associated with BRCA2 p.Arg2502Cys (c.7504C>T)?

BRCA2 p.Arg2502Cys (c.7504C>T) is associated with hereditary neoplastic syndrome, hereditary breast ovarian cancer syndrome, breast-ovarian cancer, familial, susceptibility to, 2 (ClinVar).

How common is BRCA2 p.Arg2502Cys (c.7504C>T) in the general population?

BRCA2 p.Arg2502Cys (c.7504C>T) is rare (popmax 0.296%, afr) (gnomAD).

What do computational predictors say about BRCA2 p.Arg2502Cys (c.7504C>T)?

AlphaMissense predicts likely benign (score 0.0861) — an in-silico prediction, not a clinical call.

BRCA2 p.Arg2502Cys

c.7504C>T · rs55716624 · VCV41563

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 27 submitters

AlphaMissense

likely benign

0.0861 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.296%, afr)

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
AlphaMissense	0.0861	likely benign
REVEL	0.519	indeterminate
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>G here scores Δ0.20 · evaluated, not missing
Constraint at this position
Conservation	phyloP 0.2	GERP 0.54
Regional constraint	o/e 1.03	unconstrained · MANE · 47 kb · p 0.059 · regional, not allelic
Overall
CADD	8.722	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.296% African / African-American · 222/75,038 alleles

Filtering AF 0.264% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.252%

Overall 0.0173% 280/1,614,150 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.296%	338
Remaining individualsnot grpmax-eligible	0.0224%	4,465
Admixed American	0.01%	10,005
South Asian	0.00439%	22,773
Finnishnot grpmax-eligible	0.00312%	32,012
European (non-Finnish)	0.00271%	36,875

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: BRCA2
Protein: p.Arg2502Cys
Coding: c.7504C>T
MANE Select: NM_000059
dbSNP: rs55716624
Type: single nucleotide variant
Location: chr13:32356496 (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

Also linked: hereditary breast ovarian cancer syndrome breast-ovarian cancer, familial, susceptibility to, 2

Similar variants

BRCA2 p.Arg2502His Benign ★★★ 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.Arg2502= Likely benign ★ same residue
BRCA2 p.Arg2502fs Pathogenic ★★★ same residue
BRCA2 p.Arg2502Gly Uncertain significance ★ same residue
BRCA2 c.316+1G>T 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-arg2502cys (accessed [today's date]).

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