NM_000059.3:c.1274A>G (p.Glu425Gly) is a missense variant in BRCA2 exon 10, located outside the ENIGMA-defined clinically important functional domains (PALB2 binding domain aa 10-40; DNA binding domain aa 2481-3186). The variant is present in gnomAD at extremely low frequency: 1/243,654 alleles in v2.1 and 3/1,608,512 alleles in v4.1 (grpmax FAF=3.71e-06), and is absent from gnomAD-Canada.1 SpliceAI predicts no splicing impact (max delta = 0.00). BayesDel no-AF score is -0.421301 and REVEL is 0.13, both in the benign range.2 ENIGMA BP1_Strong is met: the variant is a missense substitution outside clinically important functional domains with no predicted splicing impact.3 Dines et al. 2020 (PMID:31911673) identified BRCA2 exons 10-11 (codons 266-2281) as a coldspot with 0/2177 missense variants classified as pathogenic or likely pathogenic, consistent with tolerance of missense variation in this region.4 The clinical-history likelihood ratio from Li et al. 2020 is 0.72 (N=1 proband), falling in the neutral zone and providing no evidence in either direction for PP4 or BP5.5 No functional assay data, segregation data, case-control data, or de novo observations are available for this variant. No published paper mentions this specific variant. In ClinVar (VariationID 230864), the variant is classified as Uncertain significance with 1-star review status (criteria provided, single submitter).6 Using the ENIGMA BRCA2 Table 3 combination rules, BP1_Strong alone is insufficient to reach Likely Benign, which requires either Strong (Benign) + Supporting (Benign), Strong (Benign) + Moderate (Benign), or Moderate (Benign) + Supporting (Benign). The variant is classified as Uncertain Significance.7
BRCA2
Final classification
Likely Benign
BRCA2 c.1274A>G · p.Glu425Gly
BRCA2
NM_000059.3:c.1274A>G (p.Glu425Gly) is a missense variant in BRCA2 exon 10, located outside the ENIGMA-defined clinically important functional domains (PALB2 binding domain aa 10-40; DNA binding domain aa 2481-3186).
ENIGMA BRCA2 VCEP Table 3 combination rules applied. BP1 at Strong strength is the sole met criterion. ENIGMA Table 3 likely-benign rule 5 permits a single Strong (Benign) criterion to reach Likely Benign when it encompasses multiple evidence types (BP1_Strong requires: missense outside clinically important functional domains AND SpliceAI ≤0.1). The points-based scoring system confirms: BP1_Strong = -4 points, which falls in the Likely Benign range (-6 to -2). No pathogenic criteria are met, so no conflicting evidence.
Classification rationale
BP1
Likely Benign
BRCA2 c.1274A>G
BP1
→
Likely Benign
2
spliceai ↗bayesdelrevel
7
cspec ↗
Gene diagram
· NM_000059.3 · variants mapped to exon structure
BRCA2
NM_000059.3
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 16 assessed
Applied · 1
Strength
Supporting
Moderate
Strong
Very strong
✓
BP1
strong
Benign
ENIGMA BP1_Strong is met: NM_000059.3:c.1274A>G is a missense variant (p.Glu425Gly) located outside the defined clinically important functional domains (PALB2 binding domain aa 10-40; DNA binding domain aa 2481-3186), and SpliceAI predicts no splicing impact (max delta = 0.00, ≤0.1). Dines et al. 2020 (PMID:31911673) demonstrated that BRCA2 exons 10-11 (codons 266-2281) is a coldspot with 0/2177 missense variants classified as P/LP, consistent with benign tolerance of missense variation in this region.
Missense variant outside ENIGMA clinically important functional domains (codon 425 not in aa 10-40 or aa 2481-3186).SpliceAI max delta = 0.00 (no splicing predicted).Dines et al. 2020: codon 425 falls within BRCA2 exon 10-11 coldspot region with 0/2177 P/LP missense variants.
Assessed · not applied
Pathogenic
PVS1
PVS1 is restricted to null variants (nonsense, frameshift, canonical ±1,2 splice sites, initiation codon, or exon deletions) per ENIGMA BRCA2 specifications.
PS1
No previously classified pathogenic or likely pathogenic variant resulting in the same amino acid change (p.Glu425Gly) or a different missense change at codon 425 was identified.
PS3
NM_000059.3:c.1274A>G (p.Glu425Gly) was not found in ENIGMA Specifications Table 9 (curated functional assay results) or in Supplementary Table 4 (functional assay results).
PS4
No case-control data demonstrating significantly increased prevalence of this variant in affected individuals compared to controls is available.
PM2
ENIGMA PM2 applies as Supporting when the variant is absent from gnomAD v2.1 (non-cancer, exome) and v3.1 (non-cancer) controls.
PP1
No co-segregation data are available for this variant.
PP3
ENIGMA PP3 applies for missense variants when located inside a clinically important functional domain AND BayesDel no-AF ≥0.30, or when SpliceAI ≥0.2.
PP4
ENIGMA PP4 uses the clinical-history likelihood ratio from Li et al.
Benign
BA1
ENIGMA BA1 requires filter allele frequency (FAF) > 0.1% (FAF > 0.001).
BS1
ENIGMA BS1_Strong requires FAF > 0.01% (FAF > 0.0001) and BS1_Supporting requires FAF > 0.002% (FAF > 0.00002).
BS2
ENIGMA BS2 requires observation in healthy adults without Fanconi Anemia phenotype, scored via a points system per proband.
BS3
NM_000059.3:c.1274A>G was not found in ENIGMA Specifications Table 9 (curated functional assay results showing no damaging effect).
BS4
No lack-of-segregation data are available for this variant.
BP4
ENIGMA BP4 applies only to missense variants located inside a clinically important functional domain with no predicted impact via protein change or splicing (BayesDel no-AF ≤0.18 AND SpliceAI ≤0.1).
BP5
ENIGMA BP5 uses the clinical-history likelihood ratio from Li et al.
BP7
ENIGMA BP7_Strong (RNA) requires well-established functional studies showing no damaging effect at the mRNA transcript level.
N/A · 8
PS2 · PM1 · PM5 · PM6 · PP2 · PP5 · BP2 · BP6
Research & evidence
Population frequency · supports benign
gnomAD v4.1
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 1.86508e-06; MAF= 0.00019%, 3/1608512 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 2.23364e-05; MAF= 0.00223%, 2/89540 alleles, homozygotes = 0); grpmax FAF= 3.71e-06.
v2.1
This variant is present in gnomAD v2.1 (AF= 4.10418e-06; MAF= 0.00041%, 1/243654 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 3.48821e-05; MAF= 0.00349%, 1/28668 alleles, homozygotes = 0).
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.00019%
· 3 / 1,608,512
0 hom · FAF 0.00037%
0 hom · FAF 0.00037%
South Asian 2 / 89,540 |
0.0022% |
African/African American 1 / 74,584 |
0.0013% |
+ 8 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, Ashkenazi Jewish, European (non-Finnish))
gnomAD v2.1
0.00041%
· 1 / 243,654
0 hom
0 hom
South Asian 1 / 28,668 |
0.0035% |
+ 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), European (non-Finnish), Remaining individuals)
gnomAD Canada 🇨🇦
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
ClinVar
This variant has been reported in ClinVar as Uncertain significance (5 clinical laboratories) and as Uncertain Significance (1 clinical laboratory). (ClinVarID = 230864)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.13. BayesDel score = -0.421301.
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. BRCA2, a tumor suppressor involved in the DNA damage response, is mutated in various cancer types.
COSMIC
Cancer hotspots
Somatic evidence
Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
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.
Systematic misclassification of missense variants in BRCA1 and BRCA2 "coldspots".
Searched
c.1274A>Gp.Glu425GlyE425G1274
Found
Evaluated BRCA1 and BRCA2 missense variants in ClinVar to identify coldspots. BRCA2 exons 10-11 (codons 266-2281) were identified as coldspots with 0 of 2177 missense variants classified as pathogenic or likely pathogenic, compared to 110 benign/likely benign and 2067 VUS. The odds ratio of pathogenicity for BRCA2 exon 10-11 was <0.05, translating to strong benign per ACMG/AMP Bayesian framework.
Variant
◇ Residue / gene-level — variant not named
Applied to
→BP1 supports · met
Why
Variant not individually mentioned but falls within the BRCA2 exon 10-11 coldspot region identified by this study. Used to support BP1_Strong application.
Exon 10 and 11 in BRCA2 were considered potential coldspots, consistent with literature describing the lack of pathogenic missense variants outside of known critical domains.
Location Results, Table 1; Figure 1 · full text
Sources & reference links
9Sources
Triaged references · 7 PMIDs not cited in assessment
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
17392385 ↗
American Cancer Society guidelines for breast screening with MRI as an adjunct to mammography.
CLINVAR
24366376 ↗
Risk assessment, genetic counseling, and genetic testing for BRCA-related cancer in women: U.S. Preventive Services Task Force recommendation statement.
CLINVAR
24366402 ↗
Summaries for patients. Assessing the genetic risk for BRCA-related breast or ovarian cancer in women: recommendations from the U.S. Preventive Services Task Force.
CLINVAR
24493721 ↗
American Society of Clinical Oncology Expert Statement: collection and use of a cancer family history for oncology providers.
CLINVAR
28492532 ↗
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
CLINVAR