Is BRCA2 p.Asn679del (c.2033ATA[1]) pathogenic?

BRCA2 p.Asn679del (c.2033ATA[1]) is classified Uncertain significance in BRCA2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-02-19). Absent from gnomAD; Associated with hereditary neoplastic syndrome.

What condition is associated with BRCA2 p.Asn679del (c.2033ATA[1])?

BRCA2 p.Asn679del (c.2033ATA[1]) is associated with hereditary neoplastic syndrome, hereditary breast ovarian cancer syndrome (ClinVar).

How common is BRCA2 p.Asn679del (c.2033ATA[1]) in the general population?

BRCA2 p.Asn679del (c.2033ATA[1]) is absent from gnomAD (gnomAD).

BRCA2 p.Asn679del

c.2033ATA[1] · rs2548523020 · VCV2827570

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

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 -0.23	GERP -0.54

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.Asn679del
Coding: c.2033ATA[1]
MANE Select: NM_000059
dbSNP: rs2548523020
Type: Microsatellite
Location: chr13:32336386 (GRCh38)
Gene constraint: LOEUF 0.803 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Residue 679: the 'interaction with npm1' 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

Also linked: hereditary breast ovarian cancer syndrome

Similar variants

BRCA2 p.Asn679fs Pathogenic ★★★ same residue
BRCA2 p.Asn679Asp Conflicting classifications of pathogenicity ★ ⚠ same residue
BRCA2 p.Asn679His Conflicting classifications of pathogenicity ★ ⚠ same residue
BRCA2 p.Asn679Lys Conflicting classifications of pathogenicity ★ ⚠ same residue
BRCA2 p.Asn679Tyr Conflicting classifications of pathogenicity ★ ⚠ same residue
BRCA2 p.Ala1439fs Pathogenic ★★★ same condition
BRCA2 p.Ala1725Ter Pathogenic ★★★ same condition
BRCA2 p.Arg155_Asp156insTer 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-asn679del (accessed [today's date]).

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