Is BRCA1 p.Arg979Ser (c.2935C>A) pathogenic?

BRCA1 p.Arg979Ser (c.2935C>A) is classified Conflicting classifications of pathogenicity in BRCA1 (ClinVar, Conflicting submitters, 7 submitters; last evaluated 2025-12-13). AlphaMissense: likely benign (0.1208); Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with BRCA1 p.Arg979Ser (c.2935C>A)?

BRCA1 p.Arg979Ser (c.2935C>A) is associated with hereditary neoplastic syndrome, hereditary breast ovarian cancer syndrome, breast-ovarian cancer, familial, susceptibility to, 1 (ClinVar).

How common is BRCA1 p.Arg979Ser (c.2935C>A) in the general population?

BRCA1 p.Arg979Ser (c.2935C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BRCA1 p.Arg979Ser (c.2935C>A)?

AlphaMissense predicts likely benign (score 0.1208) — an in-silico prediction, not a clinical call.

BRCA1 p.Arg979Ser

c.2935C>A · rs80356970 · VCV182078

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 7 submitters

AlphaMissense

likely benign

0.1208 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
AlphaMissense	0.1208	likely benign
REVEL	0.275	benign-leaning
SaProt	LLR -5.21	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.4	GERP -2.8, phastCons 0.16
Regional constraint	o/e 0.91	unconstrained · MANE · 78 kb · p 4.8e-05 · regional, not allelic
Overall
CADD	10.23	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: BRCA1
Protein: p.Arg979Ser
Coding: c.2935C>A
MANE Select: NM_007294
dbSNP: rs80356970
Type: single nucleotide variant
Location: chr17:43092596 (GRCh38)
Gene constraint: LOEUF 0.885 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 41.99 · 33 PDB
Residue 979: a UniProt-annotated variant site (in fancs)

Full BRCA1 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, 1

Similar variants

BRCA1 p.Arg979= Likely benign ★★ same residue
BRCA1 p.Arg979Cys Likely benign ★★ same residue
BRCA1 p.Arg979Gly Uncertain significance ★ ⚠ same residue
BRCA1 p.Arg979His Conflicting classifications of pathogenicity ★ ⚠ same residue
BRCA1 p.Arg979Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
BRCA1 p.Arg979fs Pathogenic ★ same residue
BRCA1 c.134+3A>T Likely pathogenic ★★★ same condition
BRCA1 c.135-1G>T 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-arg979ser (accessed [today's date]).

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