Is BRCA2 p.Cys3069= (c.9207T>C) pathogenic?

BRCA2 p.Cys3069= (c.9207T>C) is classified Likely benign in BRCA2 (ClinVar, Expert panel, 2 submitters; last evaluated 2017-06-29). Absent from gnomAD v4.1; Associated with breast-ovarian cancer, familial, susceptibility to, 2.

How common is BRCA2 p.Cys3069= (c.9207T>C) in the general population?

BRCA2 p.Cys3069= (c.9207T>C) is absent from gnomAD v4.1 (gnomAD).

How is Hereditary breast and/or ovarian cancer syndrome inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

BRCA2 p.Cys3069=

Q: What condition is associated with BRCA2 p.Cys3069= (c.9207T>C)?

BRCA2 p.Cys3069= (c.9207T>C) is associated with breast-ovarian cancer, familial, susceptibility to, 2, hereditary neoplastic syndrome (ClinVar).

c.9207T>C · rs80359183 · VCV232494

Likely benign Expert panel

Classification

Likely benign

ClinVar

Review

Expert panel ★★★☆

ClinVar · 2 submitters

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

breast-ovarian cancer, familial, susceptibility to, 2

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.9	GERP -0.016, phastCons 1
Overall
CADD	6.421	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.Cys3069=
Coding: c.9207T>C
MANE Select: NM_000059
dbSNP: rs80359183
Type: single nucleotide variant
Location: chr13:32380096 (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

breast-ovarian cancer, familial, susceptibility to, 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: hereditary neoplastic syndrome

For Hereditary breast and/or ovarian cancer syndrome (Orphanet):

Inheritance: Autosomal dominant
Onset: Adult, Elderly

Similar variants

BRCA2 p.Cys3069Ter Pathogenic ★★★ same residue
BRCA2 p.Cys3069Arg Conflicting classifications of pathogenicity ★ ⚠ same residue
BRCA2 p.Cys3069Gly Conflicting classifications of pathogenicity ★ same residue
BRCA2 p.Cys3069Phe Conflicting classifications of pathogenicity ★ same residue
BRCA2 p.Cys3069Tyr Conflicting classifications of pathogenicity ★ same residue
BRCA2 p.Cys3069fs Pathogenic ★ 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-cys3069 (accessed [today's date]).

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