Is BRCA1 p.Leu1780= (c.5340G>A) pathogenic?

BRCA1 p.Leu1780= (c.5340G>A) is classified Likely benign in BRCA1 (ClinVar, Expert panel, 2 submitters; last evaluated 2017-06-29). Very rare (popmax 0.00133%, afr); Associated with breast-ovarian cancer, familial, susceptibility to, 1.

How common is BRCA1 p.Leu1780= (c.5340G>A) in the general population?

BRCA1 p.Leu1780= (c.5340G>A) is very rare (popmax 0.00133%, afr) (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.

BRCA1 p.Leu1780=

Q: What condition is associated with BRCA1 p.Leu1780= (c.5340G>A)?

BRCA1 p.Leu1780= (c.5340G>A) is associated with breast-ovarian cancer, familial, susceptibility to, 1, hereditary neoplastic syndrome (ClinVar).

c.5340G>A · rs766700840 · VCV427323

Likely benign Expert panel

Classification

Likely benign

ClinVar

Review

Expert panel ★★★☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00133%, afr)

Conditions

breast-ovarian cancer, familial, susceptibility to, 1

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 -0.56	GERP -1.6, phastCons 0.028
Overall
CADD	3.22	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00133% African / African-American · 1/74,924 alleles

Overall 0.000124% 2/1,613,934 alleles · very rare

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.00156%	64,038
African / African-Americangrpmax	0.00133%	74,924

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: BRCA1
Protein: p.Leu1780=
Coding: c.5340G>A
MANE Select: NM_007294
dbSNP: rs766700840
Type: single nucleotide variant
Location: chr17:43049187 (GRCh38)
Gene constraint: LOEUF 0.885 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 41.99 · 33 PDB
Residue 1780: a UniProt-annotated variant site (in fancs); the brct 2 domain; a UniProt-annotated variant site (in bc, brovca1 and oc; uncertain significance); an α-helix

Full BRCA1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

breast-ovarian cancer, familial, susceptibility to, 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: hereditary neoplastic syndrome

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

Inheritance: Autosomal dominant
Onset: Adult, Elderly

Similar variants

BRCA1 p.Leu1780Arg Likely pathogenic ★★★ same residue
BRCA1 p.Leu1780Pro Pathogenic/Likely pathogenic ★★ same residue
BRCA1 p.Leu1780fs Pathogenic ★★★ same residue
BRCA1 p.Leu1780Gln Likely pathogenic ★ same residue
BRCA1 p.Leu1780Val Uncertain significance ★ ⚠ same residue
BRCA1 c.134+3A>T Likely pathogenic ★★★ same condition
BRCA1 c.135-1G>T Pathogenic ★★★ same condition
BRCA1 c.212+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/brca1-p-leu1780 (accessed [today's date]).

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