Variant classification summary

NM_000059.4:c.425G>A

BRCA2 · NP_000050.3:p.(Ser142Asn) · NM_000059.4

GRCh37: chr13:32899321 G>A · GRCh38: chr13:32325184 G>A

Gene: BRCA2 Transcript: NM_000059.4

Final call

VUS

PP3 supporting BS1 supporting

Variant details

Gene

BRCA2

Transcript

NM_000059.4

Protein

NP_000050.3:p.(Ser142Asn)

gnomAD AF

2.8479148732354255e-05 (v4.1)

ClinVar

Uncertain significance

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_000059.4:c.425G>A (p.Ser142Asn) is a missense variant in BRCA2 exon 4, located outside the established clinically important functional domains (PALB2-binding domain aa 10-40; DNA-binding domain aa 2481-3186).

2

This variant is absent from gnomAD v2.1 but present in gnomAD v4.1 in 44 of 1,544,990 alleles (AF=0.00285%), including 1 homozygote, with a grpmax filter allele frequency of 0.024% (0.00024125). The highest subpopulation frequency is in the South Asian population (30/89,438 alleles, AF=0.034%).

3

SpliceAI predicts a splicing alteration with a maximum delta score of 0.91, exceeding the ENIGMA PP3 threshold of ≥0.2 for missense variants, supporting a potential splice effect (PP3_Supporting). However, the specific SpliceAI sub-scores (donor gain/loss, acceptor gain/loss) are not available, and no RNA splicing assay has been performed to confirm this prediction.

4

The population frequency evidence meets ENIGMA BS1 at Supporting strength: the grpmax FAF of 0.00024125 exceeds the 0.01% threshold, and the observation of a homozygous individual in gnomAD v4.1 argues against high-penetrance pathogenicity. The variant is absent from gnomAD v2.1 per the ENIGMA-specified dataset, but the larger v4.1 release confirms population presence.

5

Multifactorial likelihood analysis from Parsons et al. 2019 (PMID:31131967) yields a combined LR of 1.383 (neutral), with segregation LR=1.554 and pathology LR=0.89. Neither PP1 (co-segregation) nor BS4 (lack of segregation) thresholds are met. The clinical-history LR from Li et al. 2020 (PMID:31853058) is 1.027 (1 proband, neutral zone); PP4 and BP5 are not met.

6

The variant is not listed in ENIGMA Table 9 for calibrated functional assay results (PS3/BS3 not assessed). No variant-specific functional evidence was identified in the literature or in OncoKB.

7

In ClinVar, this variant is classified as Uncertain Significance by 4 clinical laboratories, as Likely Pathogenic by 3, and as Pathogenic by 2 (ClinVar Variation ID: 197099), with review status of criteria provided, single submitter and no expert panel classification.

8

Under the ENIGMA BRCA1/2 v1.2.0 combining rules (Table 3): PP3_Supporting (1 pathogenic supporting) and BS1_Supporting (1 benign supporting) are the only met criteria. Neither Likely Pathogenic nor Likely Benign thresholds are reached. The variant is classified as a Variant of Uncertain Significance (VUS).

Final determination: ENIGMA Table 3 conflicting-evidence point system: when both pathogenic and benign criteria are met, points are summed (Supporting: +1 pathogenic / -1 benign). PP3_Supporting (+1) + BS1_Supporting (-1) = 0, which falls in the VUS range (-1 to 5).

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 not applicable: this is a missense substitution (p.Ser142Asn), not a null variant (nonsense, frameshift, or canonical ±1,2 splice site). ENIGMA PVS1 rules apply only to null variants and variants with demonstrated RNA-level splicing impact.	vcep_specifications_v1_2_2024_11_18
PS1	Not assessed	No previously classified pathogenic variant with the same amino acid change (Ser142Asn) was identified. No comparator variant at this residue with a definitive pathogenic classification is available in the VCEP materials or ClinVar.
PS2	N/A	PS2 is designated Not Applicable under the ENIGMA BRCA1/2 specification v1.2.0.	cspec
PS3	Not assessed	The variant is not listed in ENIGMA Specifications Table 9 (curated functional assay results). No calibrated functional assay data from well-established in vitro or in vivo studies measuring protein function were identified. The OncoKB entry notes gene-level curated context but no variant-specific functional evidence.	vcep_specifications_table9_v1_2_2024_11_18 oncokb
PS4	Not assessed	No case-control study with an odds ratio meeting ENIGMA criteria (OR ≥4, lower CI excluding 2.0, p ≤0.05) was identified for this variant. The variant has been observed in gnomAD with 44 alleles and in clinical testing cohorts, but no formal case-control comparison is available.	gnomad_v4 vcep_humu_40_1557_s001
PS5	Not assessed	No alternative missense variant at the same amino acid residue (Ser142) with a definitive pathogenic classification was identified in VCEP materials or ClinVar. No ENIGMA-specific PS5 rule exists; assessed under generic ACMG/AMP framework. Insufficient evidence to apply PS5.
PM1	N/A	PM1 is designated Not Applicable under the ENIGMA BRCA1/2 specification v1.2.0.	cspec
PM2	Not met	The variant is absent from gnomAD v2.1 (exome), but is present in gnomAD v4.1 with 44 alleles (AF=2.85e-05), including 1 homozygote, and a grpmax FAF of 0.00024125. The presence in the larger v4.1 dataset (1,544,990 alleles) indicates the variant is not truly absent from outbred population controls. ENIGMA PM2 (Supporting) requires absence from both gnomAD v2.1 and v3.1; the v4.1 data supersedes and shows presence. PM2 is therefore not met.	gnomad_v2 gnomad_v4
PM5	N/A	Under ENIGMA v1.2, PM5 is repurposed exclusively for PTC (protein termination codon) variants in exons where a different proven pathogenic PTC variant has been observed (PM5_PTC). This is a missense variant and does not qualify for ENIGMA PM5_PTC adjudication.	vcep_specifications_table4_v1_2_2024_11_18 cspec
PM6	N/A	PM6 is designated Not Applicable under the ENIGMA BRCA1/2 specification v1.2.0.	cspec
PP1	Not met	The co-segregation likelihood ratio from the Parsons et al. 2019 (PMID:31131967) multifactorial analysis is 1.5539, which falls below the ENIGMA PP1 Supporting threshold of LR ≥2.08. This does not provide sufficient evidence for co-segregation with disease.	vcep_humu_40_1557_s001 PMID:31131967
PP2	N/A	PP2 is designated Not Applicable under the ENIGMA BRCA1/2 specification v1.2.0.	cspec
PP3	Met	SpliceAI predicts a splicing impact with a maximum delta score of 0.91, which exceeds the ENIGMA PP3 threshold of ≥0.2 for missense variants irrespective of location in clinically important functional domains. Per ENIGMA Figure 1A, PP3 Supporting is applied for missense variants with predicted splicing alteration (SpliceAI ≥0.2). The variant is annotated as missense_variant/splice_region_variant. The amino acid substitution (p.Ser142Asn) is located outside the BRCA2 clinically important functional domains (PALB2-binding aa 10-40; DNA-binding aa 2481-3186), so protein-level prediction (BayesDel no-AF = -0.314, REVEL = 0.153) is not used for PP3; the splicing prediction alone supports PP3.	spliceai cspec
PP4	Not met	The clinical-history likelihood ratio from Li et al. 2020 (PMID:31853058) is 1.027 (1 proband), which falls in the ENIGMA neutral zone (>0.48 and <2.08). The combined multifactorial LR from Parsons et al. 2019 is 1.383, also neutral. Neither meets the PP4 Supporting threshold of LR ≥2.08. PP4 is not met.	vcep_pmid_31853058_brca2_clinical_history_lr PMID:31853058 vcep_humu_40_1557_s001 PMID:31131967
PP5	N/A	PP5 is designated Not Applicable under the ENIGMA BRCA1/2 specification v1.2.0.	cspec
BA1	Not met	The gnomAD v4.1 grpmax filter allele frequency (FAF) is 0.00024125 (0.024%), which is below the ENIGMA BA1 threshold of >0.1% (FAF >0.001). BA1 Stand-Alone is not met.	gnomad_v4
BS1	Met	The gnomAD v4.1 grpmax filter allele frequency (FAF) is 0.00024125 (0.024%), which exceeds the ENIGMA BS1 Strong threshold of FAF >0.01% (FAF >0.0001). However, the ENIGMA v1.2 rule specifies gnomAD v2.1 and v3.1; the variant is absent from gnomAD v2.1 and confirmed present only in the newer v4.1 release. Given this version discrepancy, BS1 is applied at Supporting strength rather than Strong. The variant is observed in 44 of 1,544,990 alleles (AF=0.00285%), including 1 homozygote, with highest frequency in the South Asian population (30/89,438 alleles, AF=0.034%). These observations support that the variant is unlikely to be a highly penetrant pathogenic allele.	gnomad_v2 gnomad_v4 cspec
BS2	Not assessed	BS2 requires proband-level assessment of Fanconi Anemia (FA) phenotype absence with a point-based system per ENIGMA Specifications Table 8. The gnomAD v4.1 observation of a homozygous individual suggests possible healthy adult carrier, but individual-level clinical data confirming the absence of FA features are not available. Insufficient data to apply BS2.	gnomad_v4 cspec
BS3	Not assessed	The variant is not listed in ENIGMA Specifications Table 9 (curated functional assay results for PS3/BS3). No well-established in vitro or in vivo functional studies demonstrating no damaging effect on protein function were identified. BS3 cannot be assessed without calibrated functional assay data.	vcep_specifications_table9_v1_2_2024_11_18
BS4	Not met	The segregation likelihood ratio from Parsons et al. 2019 is 1.5539, which is above the ENIGMA BS4 Supporting threshold of LR ≤0.48. This does not support lack of segregation with disease. BS4 is not met.	vcep_humu_40_1557_s001 PMID:31131967
BP1	Not met	BP1_Strong requires a missense variant outside clinically important functional domains AND no splicing predicted (SpliceAI ≤0.1). While this variant is located outside the BRCA2 functional domains (PALB2-binding aa 10-40; DNA-binding aa 2481-3186), SpliceAI predicts a splicing alteration with max delta score of 0.91, which exceeds the 0.1 threshold. BP1 is not met due to predicted splicing impact.	spliceai cspec
BP2	N/A	BP2 is designated Not Applicable under the ENIGMA BRCA1/2 specification v1.2.0.	cspec
BP4	Not met	ENIGMA BP4 for missense variants applies only when inside a clinically important functional domain with no predicted impact via protein change (BayesDel no-AF ≤0.18) AND no predicted splicing (SpliceAI ≤0.1). This variant is outside the functional domains, and SpliceAI predicts a splicing alteration (max delta=0.91), which exceeds the BP4 threshold of ≤0.1. BP4 is not met.	spliceai bayesdel cspec
BP5	Not met	The clinical-history likelihood ratio from Li et al. 2020 is 1.027 (1 proband), which is above the ENIGMA BP5 Supporting threshold of LR ≤0.48. The combined multifactorial LR from Parsons et al. 2019 is 1.383, also above the threshold. Neither supports benignity via clinical history. BP5 is not met.	vcep_pmid_31853058_brca2_clinical_history_lr PMID:31853058 vcep_humu_40_1557_s001 PMID:31131967
BP6	N/A	BP6 is designated Not Applicable under the ENIGMA BRCA1/2 specification v1.2.0.	cspec
BP7	N/A	ENIGMA BP7_Supporting applies only to silent or intronic variants meeting specific criteria. This is a missense variant. BP7_Strong (RNA) requires well-established mRNA assay evidence showing no damaging effect on splicing, which is not available for this variant. BP7 is not applicable.	cspec

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