0%
complete
Final classification
VUS
BP1
BRCA1
c.2501G>A
p.Gly834Glu
missense · exon 10

BRCA1 encodes a large nuclear protein that helps maintain genomic stability by coordinating the repair of DNA double-strand breaks through homologous recombination, and it also regulates transcription and the cell cycle. It acts as a tumor suppressor, working with proteins such as RAD51, BRCA2, BARD1, and PALB2 to preserve genome integrity. Inherited alterations in BRCA1 cause hereditary breast and ovarian cancer syndrome, with elevated risks of breast, ovarian, prostate, and pancreatic cancers, and biallelic loss underlies a rare form of Fanconi anemia. Because BRCA1-driven tumors rely on impaired DNA repair, they are treatable with PARP inhibitors.

This variant

BRCA1 encodes a tumor suppressor whose loss-of-function germline alterations drive hereditary breast and ovarian cancer syndrome through impaired DNA double-strand-break repair, and this exon 11 missense substitution p.Gly834Glu falls outside the protein's clinically important functional domains.

Transcript
NM_007294.4
HGVS · transcript:coding
NM_007294.4:c.2501G>A
GRCh38
chr17:43093030 C>T
GRCh37
chr17:41245047 C>T
VUS: BP1 (strong) is the only met ENIGMA criterion, and a single benign-strong code satisfies no benign or likely-benign combination.
Classification rationale
BP1 VUS
BRCA1 c.2501G>A missense · exon 10

BP1 strong (met): p.Gly834Glu is a missense outside all clinically important BRCA1 domains (RING 2-101, coiled-coil 1391-1424, BRCT 1650-1857) with SpliceAI max delta 0.001, indicating no predicted splice impact.

BP1 VUS
Gene diagram · NM_007294.4 · variants mapped to exon structure
BRCA1 NM_007294.4
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 15 assessed
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
Applied · 1
Strength Supporting Moderate Strong Very strong
BP1 strong Benign
Met (BP1_Strong): p.Gly834Glu is a missense outside all clinically important domains (RING 2-101, coiled-coil 1391-1424, BRCT 1650-1857) with SpliceAI max delta 0.001 <= 0.1.
ENIGMA v1.2 specification Table 1 (BP1_Strong row): 'Apply BP1_Strong for silent substitution, missense or in-frame insertion, deletion or delins variants outside a (potentially) clinically important functional domain AND no splicing predicted (SpliceAI <=0.1). Missense prediction not applicable.' See Figure 1A; Appendix J.Domain check: specification Table 1 footnote ** defines the BRCA1 (potentially) clinically important functional domains as RING aa 2-101; coiled-coil aa 1391-1424; BRCT repeats aa 1650-1857. Residue 834 is not contained in any of these intervals.SpliceAI lookup for NM_007294.4:c.2501G>A: max delta score 0.001 (DS_AG 0.0, DS_AL 0.0, DS_DG 0.001, DS_DL 0.001), i.e., <=0.1 no-splicing-predicted threshold.
Assessed · not applied · 5 not met · 10 not assessed
Pathogenic
PS1 Not met: no pathogenic or likely pathogenic p.Gly834Glu exists in ClinVar (5 VUS, 1 likely benign, 1 benign), and only c.2501G>A can produce this amino acid change.
PS3 PS3 not assessed: ENIGMA Table 9/ST4 hold no calibrated functional assay entry for c.2501G>A (0/4,730 and 0/4,304 rows), and no published assay exists.
PS4 Not met: ENIGMA PS4 requires case-control p ≤ 0.05 and OR ≥ 4 (lower CI excluding 2.0); only a single VUS case observation (PMID:26306726) exists, with no OR or p-value.
PM2 Not assessed: ENIGMA PM2 (supporting) requires absence from gnomAD v2.1/v3.1 non-cancer controls, yet gnomAD data is unavailable and one submitter reports rs757383244 present at an unstated frequency.
PM3 Not met: ENIGMA v1.2 applies PM3 only to Fanconi-anemia phenotypes with co-occurrent same-gene variants; c.2501G>A has no second BRCA1 variant or phase data.
PP1 Not assessed: no pedigree or co-segregation LR for c.2501G>A; ENIGMA PP1 requires a quantitative segregation LR of at least 2.08:1 for supporting strength.
PP3 Not met: SpliceAI max delta 0.001 is far below the >=0.2 PP3 splice-impact threshold, and the BayesDel protein path does not apply to this out-of-domain missense.
PP4 Not assessed: ENIGMA PP4 needs a combined clinical likelihood ratio ≥ 2.08, but c.2501G>A has no variant-level LR (absent from the Li 2020 BRCA1 clinical-history LR table).
Benign
BA1 Not assessed: ENIGMA BA1 requires a gnomAD v2.1/v3.1 non-founder FAF above 0.1% (0.001), and no gnomAD allele-frequency value is available for this variant to test the threshold.
BS1 Not assessed: ENIGMA BS1 needs gnomAD v2.1/v3.1 non-founder FAF above 0.002% (supporting) or 0.01% (strong), but no gnomAD frequency value is available for this variant.
BS2 Not assessed: ENIGMA BS2 requires point-scored observations of biallelic (homozygous/in-trans) carriers without Fanconi anemia; no such observation exists for c.2501G>A.
BS3 BS3 not assessed: no well-established functional study shows a benign effect for c.2501G>A; ENIGMA Table 9 and ST4 contain zero entries.
BS4 Not assessed: no non-segregation data or co-segregation LR for c.2501G>A; ENIGMA BS4 requires a segregation LR of at most 0.48:1 for supporting strength.
BP4 Not met: ENIGMA BP4 (BayesDel <=0.15 AND SpliceAI <=0.1) applies only to missense inside clinically important domains; Gly834 lies outside RING, coiled-coil and BRCT.
BP5 Not assessed: ENIGMA BP5 needs a combined clinical likelihood ratio ≤ 0.48, but c.2501G>A has no variant-level LR (absent from the Li 2020 BRCA1 clinical-history LR table).
N/A · 12 PVS1 · PS2 · PM1 · PM4 · PM5 · PM6 · PP2 · PP5 · BP2 · BP3 · BP6 · BP7
Research & evidence
Population frequency
v4.1
This variant is absent from gnomAD v4.1.
v2.1
This variant is absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant has been reported in ClinVar as Uncertain significance (5 clinical laboratories) and as Benign (1 clinical laboratory). (ClinVarID = 462587)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. BRCA1, a tumor suppressor involved in the DNA damage response, is mutated in various cancer types.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV114744917, n = 1 times).
Hotspots
This variant does not lie in a statistically significant hotspot.
Literature · how each cited paper was used
1papers cited
Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 7 further PMIDs triaged but not cited — see Sources & references.
Rule & framework references · cited for criterion definitions, not variant evidence
31911673 ↗ Systematic misclassification of missense variants in BRCA1 and BRCA2 "coldspots".
Sources & reference links
9Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 7 PMIDs not cited in assessment
23918944 ↗ Tamoxifen and risk of contralateral breast cancer for BRCA1 and BRCA2 mutation carriers. CLINVAR
25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR
26306726 ↗ Clinical impact on ovarian cancer patients of massive parallel sequencing for BRCA mutation detection: the experience at Gemelli hospital and a literature review. CLINVAR
32438681 ↗ Spectrum of Germline BRCA1 and BRCA2 Variants Identified in 2351 Ovarian and Breast Cancer Patients Referring to a Reference Cancer Hospital of Rome. CLINVAR
25085752 ↗ Development and validation of a new algorithm for the reclassification of genetic variants identified in the BRCA1 and BRCA2 genes. CLINVAR
25394175 ↗ A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment. CLINVAR
26324357 ↗ American Society of Clinical Oncology Policy Statement Update: Genetic and Genomic Testing for Cancer Susceptibility. CLINVAR