Is BRCA2 p.Leu613= (c.1839A>G) pathogenic?

BRCA2 p.Leu613= (c.1839A>G) is classified Likely benign in BRCA2 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-01-19). Very rare (popmax 0.00112%, sas); Associated with hereditary neoplastic syndrome.

What condition is associated with BRCA2 p.Leu613= (c.1839A>G)?

BRCA2 p.Leu613= (c.1839A>G) is associated with hereditary neoplastic syndrome, hereditary breast ovarian cancer syndrome, breast-ovarian cancer, familial, susceptibility to, 2 (ClinVar).

How common is BRCA2 p.Leu613= (c.1839A>G) in the general population?

BRCA2 p.Leu613= (c.1839A>G) is very rare (popmax 0.00112%, sas) (gnomAD).

BRCA2 p.Leu613=

c.1839A>G · rs1057520988 · VCV381242

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00112%, sas)

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 · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.058	GERP -4.2
Overall
CADD	0.739	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00112% South Asian · 1/89,456 alleles

Overall 0.000124% 2/1,608,538 alleles · very rare exomes 2/1,456,190 · genomes 0/152,348 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00112%	89,456
European (non-Finnish)	8.48e-05%	1,178,724

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.Leu613=
Coding: c.1839A>G
MANE Select: NM_000059
dbSNP: rs1057520988
Type: single nucleotide variant
Location: chr13:32333317 (GRCh38)
Gene constraint: LOEUF 0.803 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Residue 613: a UniProt-annotated variant site (in bc; uncertain significance)

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 breast-ovarian cancer, familial, susceptibility to, 2

Similar variants

BRCA2 p.Leu613Arg Conflicting classifications of pathogenicity ★ ⚠ same residue
BRCA2 p.Leu613Gln Uncertain significance ★ ⚠ same residue
BRCA2 p.Leu613Val Conflicting classifications of pathogenicity ★ ⚠ 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
BRCA2 c.475+1G>A 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-leu613 (accessed [today's date]).

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