Is BRCA2 c.6937+978A>T pathogenic?

BRCA2 c.6937+978A>T is classified Benign in BRCA2 (ClinVar, Expert panel, 1 submitter; last evaluated 2015-01-12). Low-frequency (popmax 4.64%, eas); Associated with breast-ovarian cancer, familial, susceptibility to, 2.

What condition is associated with BRCA2 c.6937+978A>T?

BRCA2 c.6937+978A>T is associated with breast-ovarian cancer, familial, susceptibility to, 2 (ClinVar).

How common is BRCA2 c.6937+978A>T in the general population?

BRCA2 c.6937+978A>T is low-frequency (popmax 4.64%, 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 c.6937+978A>T

rs11571676 · VCV209709

Benign Expert panel

Classification

Benign

ClinVar

Review

Expert panel ★★★☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

low-frequency (popmax 4.64%, eas)

Conditions

breast-ovarian cancer, familial, susceptibility to, 2

Computational evidence

Protein change
Missense predictors do not apply to this variant type.
Splicing
Splice region	donor +978	deep intronic (+978 nt into the intron)
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Non-coding constraint	Z 1.88	1 kb window · o/e 0.86 · regional · uncalibrated
Overall
CADD	8.393	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 4.64% East Asian · 241/5,192 alleles

Filtering AF 4.16% ClinGen BA1/BS1 input FAF95, joint · FAF99 3.97%

Overall 0.653% 993/152,138 alleles · low-frequency

Ancestry group	Frequency	1 in
East Asiangrpmax	4.64%	22
Admixed American	3.95%	25
Remaining individualsnot grpmax-eligible	0.9%	111
Finnishnot grpmax-eligible	0.349%	287
South Asian	0.29%	345
African / African-American	0.0987%	1,014
European (non-Finnish)	0.0545%	1,835

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
Coding: c.6937+978A>T
MANE Select: NM_000059
dbSNP: rs11571676
Type: single nucleotide variant
Location: chr13:32345631 (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

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

Inheritance: Autosomal dominant
Onset: Adult, Elderly

Similar variants

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
BRCA2 c.475+1G>A Pathogenic ★★★ same condition
BRCA2 c.475+1G>T Pathogenic ★★★ same condition
BRCA2 c.476-2A>G Pathogenic ★★★ same condition
BRCA2 c.517-2A>G 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-c-6937-plus-978a-t (accessed [today's date]).

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