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Variant interpretation report

BRCA2 c.3995A>G, p.(His1332Arg)

NM_000059.4:c.3995A>G NP_000050.3:p.(His1332Arg) View identifiers
Classification
Uncertain significance

Variant description:

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.

In plain language

Gene-level background from the recorded interpretation.

About BRCA2

No gene-level summary was recorded for this case.

LYFE Sciences is an AI system, and it can make mistakes. Criteria may be applied incorrectly, sources may be misread, and a confident-looking classification can still be wrong. Double-check every criterion and its underlying evidence before relying on any call.
01The reasoning

How it was classified

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.

Recorded applied criteria

The applied criteria and their strengths are shown as assessed under the stated framework.

Pathogenic evidence criteria: 0 Benign evidence criteria: 1
Pathogenic criteria applied · 0

No pathogenic criterion marked as applied in the recorded assessment.

Benign criteria applied · 1
BP1Strong
BP1 · strong

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.

Recorded classification: Uncertain significance

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.

02The sources

Evidence at a glance

Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.

gnomAD v4.1
gnomAD v2.1
Population frequency
2 / 1,585,794 alleles

gnomAD v4.1: 2 / 1,585,794 alleles. Recorded AF 1.2612e-06. Recorded homozygote count 0.

gnomAD 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).

gnomAD-Canada

Not available in gnomAD-Canada v1.0.

SpliceAI score
0.000 maximum delta

Recorded SpliceAI maximum delta score: 0.000. Refer to the recorded PP3/BP4 rationale for interpretation.

No listed criterion applied SpliceAI ↗
ClinVar submissions
4 reported laboratory submissions

3 Uncertain significance · 1 Likely benign. ClinVar API review status: criteria provided, conflicting classifications.

Context only ClinVar ↗
Functional evidence
Statement recorded

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.

No listed criterion applied OncoKB ↗
COSMIC
Cancer Hotspots
Somatic evidence
No matching record reported

This variant has not previously been reported in somatic cancers (COSMIC).

Cancer Hotspots

This variant does not lie in a statistically significant hotspot.

For specialists

Technical detail

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.

Met Not met Not assessed Not applicable

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.

Met · 1

BP1 StrongThis 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. Details ▾Hide ▴
Evidence considered
  • Position 1332 is outside PALB2 binding domain (aa 10-40) and DNA binding domain (aa 2481-3186).
  • SpliceAI max delta = 0.00
  • no predicted splicing impact.
  • The BRC repeats region (aa 1008-2082) within exon 11 has been reported as a coldspot with 0 pathogenic missense variants in ClinVar (PMID:31911673).
Sources

Not met · 9 · evaluated, threshold not reached

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. Details ▾Hide ▴
Evidence considered
  • ClinVar contains no pathogenic missense variants at codon 1332 of BRCA2.
Sources
PS3 This variant is not listed in ENIGMA Table 9 of calibrated functional assay results. No variant-specific functional data identified in the literature or from OncoKB for NM_000059.4:c.3995A>G (p.His1332Arg). Details ▾Hide ▴
Evidence considered
  • ENIGMA Table 9 does not list any functional assay code for this variant.
  • OncoKB reports unknown oncogenic effect with no variant-specific functional evidence.
Still missing
  • No mammalian functional assay data available for this missense variant.
Sources
vcep_specifications_table9_v1_2_2024_11_18oncokb ↗
PM2 This variant is present in gnomAD population databases (v2.1: 1/228,162 alleles; v4.1: 2/1,585,794 alleles). ENIGMA PM2_Supporting requires absence from outbred population controls in both gnomAD v2.1 and v3.1 non-cancer subsets. Details ▾Hide ▴
Evidence considered
  • gnomAD v2.1: 1/228
  • 162 exome alleles (AF = 4.38e-6)
  • highest in NFE (1/106
  • 914).
  • gnomAD v4.1: 2/1
  • 585
  • 794 alleles (AF = 1.26e-6)
  • grpmax FAF = 2.8e-7.
Sources
PP3 Variant (p.His1332Arg) is outside the ENIGMA-defined clinically important functional domains (PALB2 binding aa 10-40; DNA binding aa 2481-3186). SpliceAI delta = 0.00 (<0.2 threshold). BayesDel no-AF score = -0.576 (<0.30 threshold). No computational evidence supports a deleterious effect per ENIGMA PP3 rules. Details ▾Hide ▴
Evidence considered
  • SpliceAI max delta = 0.00
  • no predicted splicing impact.
  • BayesDel no-AF score = -0.576
  • below PP3 threshold of ≥0.30.
  • REVEL score = 0.135
  • low
  • consistent with no predicted pathogenicity.
Sources
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). Details ▾Hide ▴
Evidence considered
  • gnomAD v2.1 exome AF = 4.38e-06 (0.00044%).
  • gnomAD v4.1 grpmax FAF = 2.8e-07 (0.000028%).
Sources
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). The variant's overall frequency (v2.1 AF = 0.00044%) also falls below the 0.002% threshold. Details ▾Hide ▴
Evidence considered
  • gnomAD v4.1 grpmax FAF = 2.8e-07 (< 0.00002 BS1_Supporting threshold).
  • gnomAD v2.1 overall AF = 0.00044% (< 0.002% BS1_Supporting threshold).
Sources
BS3 This variant is not listed in ENIGMA Table 9 of calibrated functional assay results. No well-established functional data indicate a benign effect for p.His1332Arg. Details ▾Hide ▴
Evidence considered
  • ENIGMA Table 9 does not list any BS3 code for this variant.
Sources
vcep_specifications_table9_v1_2_2024_11_18
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. This variant at position 1332 is outside both domains. Details ▾Hide ▴
Evidence considered
  • Position 1332 is outside ENIGMA-defined clinically important functional domains.
  • BayesDel no-AF = -0.576
  • SpliceAI = 0.00 — both consistent with no predicted impact but BP4 domain requirement is not met.
Sources
BP7 No mRNA transcript assay data available for this variant. ENIGMA BP7_Strong (RNA) requires well-established functional studies showing no damaging effect on splicing. BP7_Supporting is only applicable for silent or intronic variants; this is a missense substitution. Details ▾Hide ▴
Evidence considered
  • SpliceAI delta = 0.00 predicts no splicing impact but no confirmatory RNA assay data exist.
  • Variant is missense
  • not silent or intronic
  • BP7_Supporting rules do not apply.
Still missing
  • No mRNA transcript assay data available.
Sources

Not assessed · 6 · no assessment recorded

PS4 No case-control data available to evaluate prevalence of this variant in affected individuals versus controls. ENIGMA PS4 requires case-control study with p-value ≤0.05 and OR ≥4. Details ▾Hide ▴
Still missing
  • No case-control study data available for this variant.
PP1 No co-segregation data available for this variant. ENIGMA PP1 requires quantitative co-segregation analysis with LR ≥2.08:1. Details ▾Hide ▴
Still missing
  • No co-segregation analysis data available.
PP4 Variant not found in Li et al. 2020 (PMID:31853058) clinical-history likelihood ratio table for BRCA2. No multifactorial clinical data available to calculate PP4 likelihood ratio. Details ▾Hide ▴
Evidence considered
  • The BRCA2 clinical-history LR table (PMID_31853058_BRCA2_clinical_history_LR.xlsx) does not contain this variant.
Still missing
  • No multifactorial likelihood clinical data available.
Sources
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. Details ▾Hide ▴
Still missing
  • No individual proband-level data available for BS2 evaluation.
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. Details ▾Hide ▴
Still missing
  • No co-segregation analysis data available.
BP5 Variant not found in Li et al. 2020 (PMID:31853058) clinical-history likelihood ratio table for BRCA2. No multifactorial clinical data available to calculate BP5 likelihood ratio. Details ▾Hide ▴
Evidence considered
  • The BRCA2 clinical-history LR table does not contain this variant.
Still missing
  • No multifactorial likelihood clinical data available.
Sources
Not applicable · 10· recorded as not applicable Show reasons ▾Hide reasons ▴
PVS1 N/APVS1 is reserved for null variants (nonsense, frameshift, canonical splice sites, initiation codon, exon deletion) per ENIGMA BRCA2 v1.2; NM_000059.4:c.3995A>G is a missense substitution. Details ▾Hide ▴

No further detail was recorded.

PS2 VCEPDe novo occurrence is not calibrated for BRCA1/2-related cancers which occur relatively commonly per ENIGMA BRCA2 v1.2. Details ▾Hide ▴

No further detail was recorded.

PM1 VCEPPM1 is not independently applicable per ENIGMA BRCA2 v1.2; domain location is considered within the PP3/BP4 bioinformatic analysis framework. Details ▾Hide ▴
Evidence considered
  • ENIGMA v1.2 considers PM1 as a component of bioinformatic analysis (PP3/BP4).
Sources
PM5 N/APM5 is repurposed for PTC/truncating variant logic (PM5_PTC) per ENIGMA BRCA2 v1.2; not applicable for missense substitutions. No same-residue pathogenic missense comparators were identified. Details ▾Hide ▴

No further detail was recorded.

PM6 VCEPDe novo occurrence is not calibrated for BRCA1/2-related cancers which occur relatively commonly per ENIGMA BRCA2 v1.2. Details ▾Hide ▴

No further detail was recorded.

PP2 VCEPPP2 is not applicable per ENIGMA BRCA2 v1.2 due to high frequency of benign missense variants in BRCA2. Details ▾Hide ▴

No further detail was recorded.

PP5 VCEPPP5 is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee per ENIGMA BRCA2 v1.2. Details ▾Hide ▴

No further detail was recorded.

BP2 VCEPBP2 is applied only in the context of BS2 per ENIGMA BRCA2 v1.2. Details ▾Hide ▴

No further detail was recorded.

BP6 VCEPBP6 is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee per ENIGMA BRCA2 v1.2. Details ▾Hide ▴

No further detail was recorded.

PS5 N/APS5 is not defined in the ENIGMA BRCA1 and BRCA2 Expert Panel Specifications v1.2. Details ▾Hide ▴

No further detail was recorded.

Identifiers

Gene
BRCA2
Transcript
NM_000059.4
Coding (HGVS c.)
NM_000059.4:c.3995A>G
Protein (HGVS p.)
NP_000050.3:p.(His1332Arg)
GRCh38
chr13:32338350 A>G
GRCh37
chr13:32912487 A>G
ClinVar
91811

Gene diagram

Every interpreted variant in BRCA2, mapped onto the exon structure of NM_000059.4. Select a row to find it on the plot.

BRCA2NM_000059.4
Fetching transcript structure from UCSC…
gnomAD v4.1 2 / 1,585,794 alleles AF 1.26e-06 · 0 homozygotes · FAF 2.8e-07
gnomAD v2.1 1 / 228,162 alleles AF 4.38e-06 · 0 homozygotes
gnomAD-Canada v1.0 Allele count data not recorded

By genetic ancestry

gnomAD v4.1

AF 1.3e-06 · 2 / 1,585,794 alleles · 0 hom · FAF 2.8e-07
European (non-Finnish)2 / 1,168,842 1.7e-06
0 alternate alleles recorded in 9 other groups: Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American.

gnomAD v2.1

AF 4.4e-06 · 1 / 228,162 alleles · 0 hom
European (non-Finnish)1 / 106,914 9.4e-06
0 alternate alleles recorded in 7 other groups: African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian.

Statements

gnomAD 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.

gnomAD 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).

gnomAD-Canada

Not available in gnomAD-Canada v1.0.

SpliceAI and Pangolin

SpliceAI acceptor lossat +119 bp
0.000
SpliceAI acceptor gainat -72 bp
0.000
SpliceAI donor lossat -149 bp
0.000
SpliceAI donor gainat +206 bp
0.000
Pangolin splice lossmagnitude shown
-0.000
Pangolin splice gain
0.000

Other predictors

REVEL
0.135
BayesDel
-0.576

How the predictions were used

PP3 Variant (p.His1332Arg) is outside the ENIGMA-defined clinically important functional domains (PALB2 binding aa 10-40; DNA binding aa 2481-3186). SpliceAI delta = 0.00 (<0.2 threshold). BayesDel no-AF score = -0.576 (<0.30 threshold). No computational evidence supports a deleterious effect per ENIGMA PP3 rules. Details ▾Hide ▴
Evidence considered
  • SpliceAI max delta = 0.00
  • no predicted splicing impact.
  • BayesDel no-AF score = -0.576
  • below PP3 threshold of ≥0.30.
  • REVEL score = 0.135
  • low
  • consistent with no predicted pathogenicity.
Sources
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. This variant at position 1332 is outside both domains. Details ▾Hide ▴
Evidence considered
  • Position 1332 is outside ENIGMA-defined clinically important functional domains.
  • BayesDel no-AF = -0.576
  • SpliceAI = 0.00 — both consistent with no predicted impact but BP4 domain requirement is not met.
Sources
BP7 No mRNA transcript assay data available for this variant. ENIGMA BP7_Strong (RNA) requires well-established functional studies showing no damaging effect on splicing. BP7_Supporting is only applicable for silent or intronic variants; this is a missense substitution. Details ▾Hide ▴
Evidence considered
  • SpliceAI delta = 0.00 predicts no splicing impact but no confirmatory RNA assay data exist.
  • Variant is missense
  • not silent or intronic
  • BP7_Supporting rules do not apply.
Still missing
  • No mRNA transcript assay data available.
Sources

Statement

In silico

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.

Cited in the classification

  • Systematic misclassification of missense variants in BRCA1 and BRCA2 "coldspots".
    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.
    → BP1 Does not name this variant
    PMID 31911673 ↗
    Source detail
    BRCA2 Exon 10 and 11 266–2281 0 (0) 110 (5.1) 2067 (94.9) 2177 (100.0)

    Location Results section, Table 1

Other recorded publications

  • Tamoxifen and risk of contralateral breast cancer for BRCA1 and BRCA2 mutation carriers.
    Phillips et al. 2013 study of tamoxifen and contralateral breast cancer risk in BRCA1/2 mutation carriers. Reports aggregate outcomes for 1,583 BRCA1 and 881 BRCA2 carriers but does not discuss any specific variants.
    Does not name this variant
    PMID 23918944 ↗
  • 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.
    Richards et al. 2015 ACMG/AMP standards and guidelines for sequence variant interpretation. Provides the generic classification framework but does not discuss any specific variants.
    Does not name this variant
    PMID 25741868 ↗
  • American Cancer Society guidelines for breast screening with MRI as an adjunct to mammography.
    Saslow D et al. · 2007
    Saslow et al. 2007 American Cancer Society guidelines for breast MRI screening. Provides screening recommendations for women at elevated breast cancer risk but does not discuss any specific genetic variants.
    Does not name this variant
    PMID 17392385 ↗
  • BRCA1- and BRCA2-Associated Hereditary Breast and Ovarian Cancer.
    Adam MP et al. · 1993
    GeneReviews summary for BRCA1- and BRCA2-associated hereditary breast and ovarian cancer. Provides general clinical and genetic information about BRCA2 but does not discuss specific variants.
    Does not name this variant
    PMID 20301425 ↗
  • 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.
    USPSTF patient summary on genetic risk assessment for BRCA-related breast or ovarian cancer. General screening guidance; does not discuss specific variants.
    Does not name this variant
    PMID 24366402 ↗
  • Risk assessment and genetic counseling for hereditary breast and ovarian cancer syndromes-Practice resource of the National Society of Genetic Counselors.
    Berliner et al. 2021 NSGC practice resource for hereditary breast and ovarian cancer risk assessment and genetic counseling. Provides general guidance for HBOC but does not discuss any specific variants.
    Does not name this variant
    PMID 33410258 ↗

Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.

All source links

Statements for reports

The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.

gnomAD 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.

gnomAD 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).

gnomAD-Canada

Not available in gnomAD-Canada v1.0.

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

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.

Somatic

This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).

Cancer Hotspots

This variant does not lie in a statistically significant hotspot.