Variant classification summary

NM_000059.4:c.3995A>G

BRCA2 · NP_000050.3:p.(His1332Arg) · NM_000059.4

GRCh37: chr13:32912487 A>G · GRCh38: chr13:32338350 A>G

Gene: BRCA2 Transcript: NM_000059.4

Final call

VUS

BP1 Strong (Benign)

Variant details

Gene

BRCA2

Transcript

NM_000059.4

Protein

NP_000050.3:p.(His1332Arg)

gnomAD AF

1.2611978605039494e-06 (v4.1)

ClinVar

Uncertain significance

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

1

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.

2

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.

3

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.

4

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.

5

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.

Final determination: BP1_Strong alone (single evidence type) does not satisfy any ENIGMA Table 3 Likely Benign combination rule because the Strong (Benign)-only rule requires multiple evidence types; no pathogenic criteria are met; default classification is VUS.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	PVS1 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.
PS1	Not met	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.	clinvar
PS2	N/A	De novo occurrence is not calibrated for BRCA1/2-related cancers which occur relatively commonly per ENIGMA BRCA2 v1.2.
PS3	Not met	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).	vcep_specifications_table9_v1_2_2024_11_18 oncokb
PS4	Not assessed	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.
PS5	N/A	PS5 is not defined in the ENIGMA BRCA1 and BRCA2 Expert Panel Specifications v1.2.
PM1	N/A	PM1 is not independently applicable per ENIGMA BRCA2 v1.2; domain location is considered within the PP3/BP4 bioinformatic analysis framework.	cspec
PM2	Not met	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.	gnomad_v2 gnomad_v4
PM5	N/A	PM5 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.
PM6	N/A	De novo occurrence is not calibrated for BRCA1/2-related cancers which occur relatively commonly per ENIGMA BRCA2 v1.2.
PP1	Not assessed	No co-segregation data available for this variant. ENIGMA PP1 requires quantitative co-segregation analysis with LR ≥2.08:1.
PP2	N/A	PP2 is not applicable per ENIGMA BRCA2 v1.2 due to high frequency of benign missense variants in BRCA2.
PP3	Not met	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.	spliceai bayesdel revel cspec
PP4	Not assessed	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.	PMID:31853058
PP5	N/A	PP5 is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee per ENIGMA BRCA2 v1.2.
BA1	Not met	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).	gnomad_v2 gnomad_v4
BS1	Not met	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.	gnomad_v2 gnomad_v4
BS2	Not assessed	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	Not met	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.	vcep_specifications_table9_v1_2_2024_11_18
BS4	Not assessed	No co-segregation data available to evaluate lack of segregation per ENIGMA BS4, which requires quantitative co-segregation analysis with LR ≤0.48:1.
BP1	Met	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.	spliceai cspec
BP2	N/A	BP2 is applied only in the context of BS2 per ENIGMA BRCA2 v1.2.
BP4	Not met	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.	cspec bayesdel spliceai
BP5	Not assessed	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.	PMID:31853058
BP6	N/A	BP6 is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee per ENIGMA BRCA2 v1.2.
BP7	Not met	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.	spliceai

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