Is BRCA2 p.Phe2795Val (c.8383T>G) pathogenic?

BRCA2 p.Phe2795Val (c.8383T>G) is classified Likely benign in BRCA2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-08). AlphaMissense: likely benign (0.1511); Very rare (popmax 6.2e-05%); Associated with hereditary neoplastic syndrome.

What condition is associated with BRCA2 p.Phe2795Val (c.8383T>G)?

BRCA2 p.Phe2795Val (c.8383T>G) is associated with hereditary neoplastic syndrome (ClinVar).

How common is BRCA2 p.Phe2795Val (c.8383T>G) in the general population?

BRCA2 p.Phe2795Val (c.8383T>G) is very rare (popmax 6.2e-05%) (gnomAD).

What do computational predictors say about BRCA2 p.Phe2795Val (c.8383T>G)?

AlphaMissense predicts likely benign (score 0.1511) — an in-silico prediction, not a clinical call.

BRCA2 p.Phe2795Val

c.8383T>G · rs761952204 · VCV1763171

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1511 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 6.2e-05%)

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
AlphaMissense	0.1511	likely benign
REVEL	0.499	indeterminate
SaProt	—	not scored · why
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 2.4	GERP 2, phastCons 1
Regional constraint	o/e 0.87	unconstrained · MANE · 35 kb · p 0.00024 · regional, not allelic
Overall
CADD	20.7	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL is an independent agreement signal.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 6.2e-05%

Overall 6.2e-05% 1/1,614,082 alleles · very rare exomes 1/1,461,718 · genomes 0/152,364 · 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.Phe2795Val
Coding: c.8383T>G
MANE Select: NM_000059
dbSNP: rs761952204
Type: single nucleotide variant
Location: chr13:32370453 (GRCh38)
Gene constraint: LOEUF 0.803 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Residue 2795: the 'interaction with sem1' region

Full BRCA2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BRCA2 p.Phe2795= Likely benign ★★ same residue
BRCA2 p.Phe2795Cys Conflicting classifications of pathogenicity ★ same residue
BRCA2 p.Phe2795_Arg2799delinsTer Pathogenic ★★★ same residue
BRCA2 p.Phe2795Ile Likely benign ★ 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-phe2795val (accessed [today's date]).

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