NM_000059.4:c.3995A>G (p.His1332Arg) is a missense substitution located outside the ENIGMA-defined clinically important functional domains of BRCA2 (PALB2 binding aa 10-40; DNA binding aa 2481-3186) with no predicted splicing impact (SpliceAI delta = 0.00), satisfying BP1_Strong.1 This variant is present at extremely low frequency in gnomAD (v2.1: 1/228,162 alleles; v4.1: 2/1,585,794 alleles), not meeting BA1 or BS1 population frequency criteria for benign classification.2 No variant-specific functional data, case-control studies, co-segregation analysis, or clinical-history likelihood ratio data are available for this variant. It is not listed in ENIGMA Table 9 (PS3/BS3) or in the Li et al. 2020 clinical-history LR table.3 The variant is reported in ClinVar as Uncertain significance by 3 clinical laboratories and Likely benign by 1 laboratory (ClinVar ID: 91811), with review status 'criteria provided, single submitter.' No expert panel classification is available.4 With BP1_Strong as the only met criterion (-4 points in the ENIGMA point system, falling in the -1 to +5 VUS range), the overall classification is Variant of Uncertain Significance per ENIGMA BRCA2 v1.2.5
BRCA2
Final classification
VUS
BRCA2 c.3995A>G · p.His1332Arg
BRCA2
NM_000059.4:c.3995A>G (p.His1332Arg) is a missense substitution located outside the ENIGMA-defined clinically important functional domains of BRCA2 (PALB2 binding aa 10-40; DNA binding aa 2481-3186) with no predicted splicing impact (SpliceAI delta = 0.00), satisfying BP1_Strong.
ENIGMA BRCA2 v1.2 Table 3 combination rules applied. BP1 is met at Strong (Benign) strength as the only adjudicated criterion. Under Table 3, a single Strong (Benign) criterion requires multiple evidence types to reach Likely Benign (requires_multiple_evidence_types: true). BP1 represents a single evidence type (bioinformatic coldspot domain analysis + SpliceAI). No Likely Benign combination rule is satisfied. No pathogenic criteria are met. The result falls to VUS by default per ENIGMA v1.2.
Classification rationale
BP1
VUS
BRCA2 c.3995A>G
BP1
→
VUS
3
vcep_specifications_table9_v1_2_2024_11_18PMID:31853058 ↗
5
cspec ↗
Gene diagram
· NM_000059.4 · variants mapped to exon structure
BRCA2
NM_000059.4
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 15 assessed
Applied · 1
Strength
Supporting
Moderate
Strong
Very strong
✓
BP1
strong
Benign
This missense variant (p.His1332Arg) is located outside ENIGMA-defined clinically important functional domains (PALB2 binding aa 10-40; DNA binding aa 2481-3186). SpliceAI delta = 0.00 (≤0.1), confirming no predicted splicing impact. BP1_Strong applies per ENIGMA BRCA2 v1.2 Specifications Figure 1A.
Position 1332 is outside PALB2 binding domain (aa 10-40) and DNA binding domain (aa 2481-3186).SpliceAI max delta = 0.00no predicted splicing impact.
Assessed · not applied
Pathogenic
PS1
No previously classified pathogenic or likely pathogenic missense variant has been identified at the same amino acid residue (His1332) to satisfy PS1 per ENIGMA BRCA2 v1.2.
PS3
This variant is not listed in ENIGMA Table 9 of calibrated functional assay results.
PS4
No case-control data available to evaluate prevalence of this variant in affected individuals versus controls.
PM2
This variant is present in gnomAD population databases (v2.1: 1/228,162 alleles; v4.1: 2/1,585,794 alleles).
PP1
No co-segregation data available for this variant.
PP3
Variant (p.His1332Arg) is outside the ENIGMA-defined clinically important functional domains (PALB2 binding aa 10-40; DNA binding aa 2481-3186).
PP4
Variant not found in Li et al.
Benign
BA1
gnomAD filter allele frequency (v4.1 grpmax FAF = 2.8e-07; v2.1 overall AF = 4.38e-06) is well below the ENIGMA BA1 threshold of FAF > 0.1% (0.001).
BS1
gnomAD filter allele frequency (v4.1 grpmax FAF = 2.8e-07) is below the ENIGMA BS1_Supporting threshold of FAF > 0.002% (0.00002).
BS2
No individual-level clinical observations are available to evaluate the ENIGMA BS2 point system, which requires scoring probands for absence of Fanconi anemia phenotype.
BS3
This variant is not listed in ENIGMA Table 9 of calibrated functional assay results.
BS4
No co-segregation data available to evaluate lack of segregation per ENIGMA BS4, which requires quantitative co-segregation analysis with LR ≤0.48:1.
BP4
ENIGMA BP4_Supporting for missense variants requires location inside a clinically important functional domain (PALB2 binding aa 10-40 or DNA binding aa 2481-3186) with BayesDel no-AF ≤0.18 and SpliceAI ≤0.1.
BP5
Variant not found in Li et al.
BP7
No mRNA transcript assay data available for this variant.
N/A · 9
PVS1 · PS2 · PM1 · PM5 · PM6 · PP2 · PP5 · BP2 · BP6
Research & evidence
Population frequency
gnomAD v4.1
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 1.2612e-06; MAF= 0.00013%, 2/1585794 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 1.7111e-06; MAF= 0.00017%, 2/1168842 alleles, homozygotes = 0); grpmax FAF= 2.8e-07.
v2.1
This variant is present in gnomAD v2.1 (AF= 4.38285e-06; MAF= 0.00044%, 1/228162 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 9.35331e-06; MAF= 0.00094%, 1/106914 alleles, homozygotes = 0).
🇨🇦 CA
Not available in gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.00013%
· 2 / 1,585,794
0 hom · FAF 2.8e-05%
0 hom · FAF 2.8e-05%
European (non-Finnish) 2 / 1,168,842 |
0.00017% |
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
gnomAD v2.1
0.00044%
· 1 / 228,162
0 hom
0 hom
European (non-Finnish) 1 / 106,914 |
0.00094% |
+ 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian)
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 (3 clinical laboratories) and as Likely benign (1 clinical laboratory). (ClinVarID = 91811)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.135. BayesDel score = -0.576408.
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. 6 further PMIDs triaged but not cited — see Sources & References.
Systematic misclassification of missense variants in BRCA1 and BRCA2 "coldspots".
Searched
c.3995A>Gp.His1332ArgH1332R13323995
Found
Dines et al. 2020 analysis of missense variant classification in BRCA1/2 coldspots. Reports that BRCA2 exon 10 and 11 (aa 266-2281) and the BRC repeats region (aa 1008-2082) harbor 0 pathogenic missense variants out of 2,177 and 1,200 variants respectively, supporting coldspot designation for the region containing p.His1332Arg.
Variant
◇ Residue / gene-level — variant not named
Applied to
→BP1 supports · met
Why
Variant not individually identified, but regional coldspot data from this paper supports BP1_Strong application.
BRCA2 Exon 10 and 11 266–2281 0 (0) 110 (5.1) 2067 (94.9) 2177 (100.0)
Location Results section, Table 1 · full text
Sources & reference links
9Sources
Triaged references · 6 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
17392385 ↗
American Cancer Society guidelines for breast screening with MRI as an adjunct to mammography.
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
33410258 ↗
Risk assessment and genetic counseling for hereditary breast and ovarian cancer syndromes-Practice resource of the National Society of Genetic Counselors.
CLINVAR