Is BRCA2 p.Ser1971= (c.5913T>C) pathogenic?

BRCA2 p.Ser1971= (c.5913T>C) is classified Likely benign in BRCA2 (ClinVar, Expert panel, 2 submitters; last evaluated 2017-06-29). Very rare (popmax 6.2e-05%); Associated with breast-ovarian cancer, familial, susceptibility to, 2.

How common is BRCA2 p.Ser1971= (c.5913T>C) in the general population?

BRCA2 p.Ser1971= (c.5913T>C) is very rare (popmax 6.2e-05%) (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.Ser1971=

Q: What condition is associated with BRCA2 p.Ser1971= (c.5913T>C)?

BRCA2 p.Ser1971= (c.5913T>C) is associated with breast-ovarian cancer, familial, susceptibility to, 2, hereditary neoplastic syndrome (ClinVar).

c.5913T>C · rs751308094 · VCV232126

Likely benign Expert panel

Classification

Likely benign

ClinVar

Review

Expert panel ★★★☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 6.2e-05%)

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	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 4.1	GERP 1.1, phastCons 0.83
Overall
CADD	4.04	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 6.2e-05%

Overall 6.2e-05% 1/1,614,036 alleles · very rare exomes 1/1,461,712 · genomes 0/152,324 · joint denominator

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.Ser1971=
Coding: c.5913T>C
MANE Select: NM_000059
dbSNP: rs751308094
Type: single nucleotide variant
Location: chr13:32340268 (GRCh38)
Gene constraint: LOEUF 0.803 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Residue 1971: the 'interaction with rad51' 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 neoplastic syndrome

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

Inheritance: Autosomal dominant
Onset: Adult, Elderly

Similar variants

BRCA2 p.Ser1971Cys Conflicting classifications of pathogenicity ★ ⚠ same residue
BRCA2 p.Ser1971Phe Conflicting classifications of pathogenicity ★ ⚠ same residue
BRCA2 p.Ser1971Pro Conflicting classifications of pathogenicity ★ ⚠ same residue
BRCA2 p.Ser1971fs Pathogenic ★★★ same residue
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

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-ser1971 (accessed [today's date]).

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