Is BRCA2 p.Ser1676= (c.5028T>C) pathogenic?

BRCA2 p.Ser1676= (c.5028T>C) is classified Likely benign in BRCA2 (ClinVar, Expert panel, 11 submitters; last evaluated 2017-06-29). Very rare (popmax 0.00448%, eas); Associated with breast-ovarian cancer, familial, susceptibility to, 2.

What condition is associated with BRCA2 p.Ser1676= (c.5028T>C)?

BRCA2 p.Ser1676= (c.5028T>C) is associated with breast-ovarian cancer, familial, susceptibility to, 2, hereditary breast ovarian cancer syndrome, medulloblastoma (ClinVar).

How common is BRCA2 p.Ser1676= (c.5028T>C) in the general population?

BRCA2 p.Ser1676= (c.5028T>C) is very rare (popmax 0.00448%, eas) (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.Ser1676=

c.5028T>C · rs762458631 · VCV215608

Likely benign Expert panel

Classification

Likely benign

ClinVar

Review

Expert panel ★★★☆

ClinVar · 11 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00448%, eas)

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 -4.7, phastCons 0.012
Overall
CADD	0.34	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00448% East Asian · 2/44,692 alleles

Filtering AF 0.000742% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000278%

Overall 0.000188% 3/1,595,382 alleles · very rare exomes 2/1,443,188 · genomes 1/152,194 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00448%	22,346
European (non-Finnish)	8.53e-05%	1,172,305

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.Ser1676=
Coding: c.5028T>C
MANE Select: NM_000059
dbSNP: rs762458631
Type: single nucleotide variant
Location: chr13:32339383 (GRCh38)
Gene constraint: LOEUF 0.803 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Residue 1676: the 'interaction with rad51' region; the 'interaction with polh' region

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 breast ovarian cancer syndrome medulloblastoma prostate cancer Wilms tumor 1 Fanconi anemia complementation group D1 glioma susceptibility 3 pancreatic cancer, susceptibility to, 2 hereditary neoplastic syndrome hereditary breast carcinoma BRCA2-related cancer predisposition

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

Inheritance: Autosomal dominant
Onset: Adult, Elderly

Similar variants

BRCA2 p.Ser1676Thr Uncertain significance ★★ same residue
BRCA2 p.Ser1676Arg Conflicting classifications of pathogenicity ★ same residue
BRCA2 p.Ser1676Asn Conflicting classifications of pathogenicity ★ ⚠ same residue
BRCA2 p.Ser1676Gly Conflicting classifications of pathogenicity ★ ⚠ same residue
BRCA2 p.Ser1676Ile Conflicting classifications of pathogenicity ★ same residue
BRCA2 p.Ser1676del 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-ser1676 (accessed [today's date]).

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