Is BRCA2 p.Pro3054Val (c.9160_9161delinsGT) pathogenic?

BRCA2 p.Pro3054Val (c.91609161delinsGT) is classified Uncertain significance in BRCA2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-03-03). No gnomAD frequency available for this variant; Associated with hereditary neoplastic syndrome.

What condition is associated with BRCA2 p.Pro3054Val (c.9160_9161delinsGT)?

BRCA2 p.Pro3054Val (c.9160_9161delinsGT) is associated with hereditary neoplastic syndrome (ClinVar).

How common is BRCA2 p.Pro3054Val (c.9160_9161delinsGT) in the general population?

BRCA2 p.Pro3054Val (c.9160_9161delinsGT) is no gnomAD frequency available for this variant (gnomAD).

BRCA2 p.Pro3054Val

c.9160_9161delinsGT · rs2548556099 · VCV1766012

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

hereditary neoplastic syndrome

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 0.57	GERP -0.99, phastCons 0.036
Regional constraint	o/e 0.87	unconstrained · MANE · 35 kb · p 0.00024 · regional, not allelic

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
Protein: p.Pro3054Val
Coding: c.9160_9161delinsGT
MANE Select: NM_000059
dbSNP: rs2548556099
Type: Indel
Location: chr13:32380049 (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

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

Similar variants

BRCA2 p.Pro3054Ala Uncertain significance ★★ same residue
BRCA2 p.Pro3054Arg Uncertain significance ★ same residue
BRCA2 p.Pro3054His Conflicting classifications of pathogenicity ★ same residue
BRCA2 p.Pro3054Leu Conflicting classifications of pathogenicity ★ same residue
BRCA2 p.Pro3054Ser Conflicting classifications of pathogenicity ★ same residue
BRCA2 p.Pro3054= Likely benign ★ same residue
BRCA2 c.1587delinsCA Pathogenic ★★★ same condition
BRCA2 c.8954-1_8955delinsAA 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-pro3054val (accessed [today's date]).

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