About BRCA2
No gene-level summary was recorded for this case.
No variant summary was recorded for this case.
Five-step scale from benign to pathogenic. This variant is uncertain. Select a step to read what it means.
Uncertain.The recorded classification is uncertain significance.
Gene-level background from the recorded interpretation.
Words with a dotted underline have a short definition. Hover or tap them.No gene-level summary was recorded for this case.
The recorded framework is ClinGen BRCA2 VCEP v1.2. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.
The applied criteria and their strengths are shown as assessed under the stated framework.
No pathogenic criterion marked as applied in the recorded assessment.
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.
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.
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1: 2 / 1,585,794 alleles. Recorded AF 1.2612e-06. Recorded homozygote count 0.
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).
Not available in gnomAD-Canada v1.0.
Recorded SpliceAI maximum delta score: 0.000. Refer to the recorded PP3/BP4 rationale for interpretation.
3 Uncertain significance · 1 Likely benign. ClinVar API review status: criteria provided, conflicting classifications.
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.
This variant has not previously been reported in somatic cancers (COSMIC).
This variant does not lie in a statistically significant hotspot.
ACMG/AMP criteria under ClinGen BRCA2 VCEP v1.2, with the data and sources behind each one.
26 criteria with recorded statuses: 1 met · 9 not met · 6 not assessed · 10 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
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.
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.
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.
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.
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.
No criteria match.
No further detail was recorded.
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Every interpreted variant in BRCA2, mapped onto the exon structure of NM_000059.4. Select a row to find it on the plot.
| Protein | Location | Classification | Link |
|---|
| European (non-Finnish)2 / 1,168,842 | 1.7e-06 |
| European (non-Finnish)1 / 106,914 | 9.4e-06 |
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.
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).
Not available in gnomAD-Canada v1.0.
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.135. BayesDel score = -0.576408.
7 paper records listed. 1 cited in the classification. None of the listed paper records explicitly indicates that the variant is named.
BRCA2 Exon 10 and 11 266–2281 0 (0) 110 (5.1) 2067 (94.9) 2177 (100.0)
Location Results section, Table 1
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
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.
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).
Not available in gnomAD-Canada v1.0.
This variant has been reported in ClinVar as Uncertain significance (3 clinical laboratories) and as Likely benign (1 clinical laboratory). (ClinVarID = 91811)
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.135. BayesDel score = -0.576408.
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.
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
This variant does not lie in a statistically significant hotspot.