Is BRCA2 c.6396dupA pathogenic?

BRCA2 c.6396dupA is classified Pathogenic in BRCA2 (ClinVar, Expert panel, 4 submitters; last evaluated 2016-10-18). Absent from gnomAD; Associated with breast-ovarian cancer, familial, susceptibility to, 2.

What condition is associated with BRCA2 c.6396dupA?

BRCA2 c.6396dupA is associated with breast-ovarian cancer, familial, susceptibility to, 2, hereditary breast ovarian cancer syndrome (ClinVar).

How common is BRCA2 c.6396dupA in the general population?

BRCA2 c.6396dupA is absent from gnomAD (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.6396dupA

rs886040654 · VCV266944

Pathogenic Expert panel

Classification

Pathogenic

ClinVar

Review

Expert panel ★★★☆

ClinVar · 4 submitters

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 · substitutions only
Constraint at this position
Conservation	phyloP 1.6	GERP -3.2, phastCons 0.034
Non-coding constraint	Z 0.53	1 kb window · o/e 0.96 · regional · uncalibrated

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: BRCA2
Coding: c.6396dupA
MANE Select: NM_000059
dbSNP: rs886040654
Type: Duplication
Location: chr13:32340750 (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 breast ovarian cancer syndrome

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

Inheritance: Autosomal dominant
Onset: Adult, Elderly

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BRCA2 c.7806-2_7806-1dup Pathogenic ★★★ same condition
BRCA2 n.6325_6326insT Pathogenic ★★★ same condition
BRCA2 n.7696_7697insT Pathogenic ★★★ same condition
BRCA2 p.Ala127fs Pathogenic ★★★ same condition
BRCA2 p.Ala2595fs 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-6396dupa (accessed [today's date]).

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