Variant classification summary

NM_000059.4:c.4494T>A

BRCA2 · NP_000050.3:p.(Gly1498=) · NM_000059.4

GRCh37: chr13:32912986 T>A · GRCh38: chr13:32338849 T>A

Gene: BRCA2 Transcript: NM_000059.4

Final call

Likely Benign

BP1 strong benign BS1 supporting benign

Variant details

Gene

BRCA2

Transcript

NM_000059.4

Protein

NP_000050.3:p.(Gly1498=)

gnomAD AF

3.222775603092873e-05 (v4.1)

ClinVar

Likely benign

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_000059.4:c.4494T>A (p.Gly1498=) is a synonymous variant in BRCA2 exon 11.

2

BP1_Strong is met: the variant is a silent substitution outside the clinically important functional domains (aa 10-40 and 2481-3186) with no predicted splicing impact (SpliceAI max delta=0.00).

3

BS1_Supporting is met: gnomAD v4.1 filter allele frequency is 3.34e-05 (0.0033%), exceeding the 0.002% threshold for BS1_Supporting under ENIGMA rules.

4

PVS1, PS3, PM2, PM5, PP3, PP4, BA1, BS3, BS4, and BP5 are not met or not applicable. The variant is present in gnomAD, lacks functional evidence of pathogenicity, and has no segregation or case-control data.

5

ClinVar expert panel (ENIGMA) classifies this variant as Likely Benign (ClinVar ID: 184407), consistent with the criteria assessment.

6

Applying ENIGMA Table 3 point system: BP1_Strong = -4 points, BS1_Supporting = -1 point, total = -5 points, which falls in the Likely Benign range (-6 to -2). The combination of one Strong (Benign) and one Supporting (Benign) criterion satisfies the ENIGMA Likely Benign classification rule.

7

Exploratory evidence suggests c.4494T>A exhibits normal splicing in a minigene assay (PMID:28608497), which, if verified, would add BP7_Strong (RNA), further strengthening the benign classification.

Final determination: ENIGMA BRCA1/BRCA2 Specification v1.2.0 Table 3 Likely Benign rule: 1 Strong (Benign) criterion (BP1_Strong) plus 1 Supporting (Benign) criterion (BS1_Supporting) yields Likely Benign; point-system total of -5 falls within the Likely Benign range (-6 to -2).

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. NM_000059.4:c.4494T>A is a synonymous variant (p.Gly1498=) that does not fall into any null-variant bucket (nonsense, frameshift, canonical ±1,2 splice). SpliceAI max delta = 0.00 confirms no cryptic splice defect. Not eligible for PVS1 or PVS1 (RNA) under ENIGMA v1.2.0.	pvs1_variant_assessment spliceai
PS1	N/A	PS1 is not applicable. ENIGMA PS1 applies to predicted missense substitutions with a previously classified pathogenic variant at the same residue, or to exonic/intronic variants with the same predicted splicing impact as a known pathogenic variant. c.4494T>A is a synonymous variant with no predicted splice impact (SpliceAI=0.00) and no pathogenic comparator at this residue.	spliceai
PS2	N/A	Skipped per adjudication instruction. No de novo data available for this variant.
PS3	Not met	PS3 is not met. No well-established functional assay demonstrates a damaging effect. ENIGMA Specifications Table 9 (curated functional assay results) has no entry for c.4494T>A. No published study reports a gain-of-function or splicing abnormality supporting pathogenicity.	vcep_specifications_table9_v1_2_2024_11_18
PS4	Not met	PS4 is not met. No case-control study demonstrates statistically significant enrichment of c.4494T>A in affected individuals versus controls. The variant is present in gnomAD population databases at low frequency, inconsistent with a high-penetrance pathogenic variant. No published proband series specific to this variant was identified.	gnomad_v2 gnomad_v4
PS5	N/A	PS5 is not applicable. c.4494T>A is a synonymous variant with no amino acid change. There is no alternate pathogenic nucleotide change at c.4494 to support PS5.
PM1	N/A	PM1 is not applicable per ENIGMA BRCA1/BRCA2 Expert Panel Specification v1.2.0, which explicitly marks PM1 as Not Applicable.	cspec
PM2	Not met	PM2 is not met. ENIGMA PM2_Supporting requires absence from gnomAD v2.1 (non-cancer, exome only subset) and gnomAD v3.1 (non-cancer). c.4494T>A is present in gnomAD v2.1 with 5 alleles (FAF=1.69e-05) and in gnomAD v4.1 with 52 alleles (FAF=3.34e-05). The variant is observed in outbred populations, therefore PM2 cannot be applied.	gnomad_v2 gnomad_v4
PM5	N/A	PM5 is not applicable. ENIGMA repurposes PM5 exclusively for protein termination codon (PTC) variants where a different proven pathogenic PTC has been seen in the same exon (PM5_PTC). c.4494T>A is a synonymous variant, not a PTC. Classic same-residue missense PM5 is also not applicable as this variant does not alter the amino acid.	pm5_candidates vcep_specifications_table4_v1_2_2024_11_18
PM6	N/A	Skipped per adjudication instruction. No de novo data for this variant.
PP1	Not met	PP1 is not met. No co-segregation analysis in affected family members is available for c.4494T>A. No quantitative co-segregation LR has been published for this variant.
PP2	N/A	PP2 is not applicable per ENIGMA BRCA1/BRCA2 Expert Panel Specification v1.2.0, which explicitly marks PP2 as Not Applicable.	cspec
PP3	Not met	PP3 is not met. ENIGMA PP3 requires either (a) missense/in-frame variant inside a clinically important functional domain with BayesDel no-AF score ≥0.30, or (b) SpliceAI ≥0.2 for silent/missense/in-frame variants. c.4494T>A is a synonymous variant with SpliceAI max delta = 0.00, located outside the clinically important functional domains (aa 10-40 and aa 2481-3186). BayesDel score is not available. Neither condition is satisfied.	spliceai
PP4	Not met	PP4 is not met. ENIGMA PP4 is applied using the clinical-history likelihood ratio from Li et al. 2020 (PMID:31853058). The variant-level clinical history LR spreadsheet has no entry for NM_000059.4:c.4494T>A, so no LR is available to support pathogenicity from personal/family history data.	vcep_pmid_31853058_brca2_clinical_history_lr
PP5	N/A	PP5 is not applicable per ENIGMA BRCA1/BRCA2 Expert Panel Specification v1.2.0, which explicitly marks PP5 as Not Applicable.	cspec
BA1	Not met	BA1 is not met. ENIGMA BA1 requires filter allele frequency (FAF) above 0.1% (FAF > 0.001) in gnomAD v2.1 (non-cancer, exome only subset) and/or gnomAD v3.1 (non-cancer), non-founder populations. gnomAD v2.1 grpmax FAF = 1.69e-05 (0.0017%) and gnomAD v4.1 grpmax FAF = 3.34e-05 (0.0033%), both well below the 0.1% threshold.	gnomad_v2 gnomad_v4
BS1	Met	BS1_Supporting is met. ENIGMA BS1_Supporting requires FAF > 0.002% (FAF > 0.00002) and ≤ 0.01% (FAF ≤ 0.0001) in gnomAD non-cancer populations. gnomAD v4.1 grpmax FAF = 3.34e-05 (0.0033%) exceeds the 0.002% threshold and is ≤ 0.01%. The gnomAD v2.1 FAF (1.69e-05, 0.0017%) does not meet the threshold, but v4.1 serves as a more comprehensive non-cancer population dataset. Note: ENIGMA specification references gnomAD v3.1; v4.1 (the successor) is used here as the current best available non-cancer population frequency resource.	gnomad_v4
BS2	Not met	BS2 is not met. ENIGMA BS2 requires proband-level data demonstrating absence of Fanconi Anemia phenotype with sufficient points per Specifications Table 8. No proband phenotype data specific to c.4494T>A are available for BS2 adjudication.
BS3	Not assessed	BS3 is not assessed. ENIGMA BS3 requires well-established functional studies showing no damaging effect on protein function, with code assignments per Specifications Table 9. Table 9 has no entry for c.4494T>A. Exploratory evidence suggests PMID:28608497 (Fraile-Bethencourt et al. 2017) tested c.4494T>A in a minigene splicing assay and observed normal splicing; this would map to BP7 (RNA) rather than BS3 under ENIGMA rules. Full text of PMID:28608497 was not available for verification in this adjudication.	vcep_specifications_table9_v1_2_2024_11_18
BS4	Not met	BS4 is not met. ENIGMA BS4 requires quantitative co-segregation analysis demonstrating lack of segregation with disease (LR thresholds per Appendix I). No segregation data for c.4494T>A are available.
BP1	Met	BP1_Strong is met. ENIGMA BP1_Strong applies to silent substitutions outside a (potentially) clinically important functional domain with no splicing predicted (SpliceAI ≤0.1). c.4494T>A is a synonymous variant (p.Gly1498=) at amino acid position 1498, which lies outside both BRCA2 clinically important functional domains (PALB2 binding: aa 10-40; DNA binding: aa 2481-3186). SpliceAI max delta = 0.00. All conditions for BP1_Strong are satisfied.	spliceai
BP2	N/A	BP2 is not applicable per ENIGMA BRCA1/BRCA2 Expert Panel Specification v1.2.0, which explicitly marks BP2 as Not Applicable.	cspec
BP4	N/A	BP4 is not applicable. ENIGMA BP4 applies to (a) missense/in-frame variants inside a clinically important functional domain with no predicted impact, (b) silent variants inside a clinically important functional domain with SpliceAI ≤0.1, or (c) intronic variants outside native splice sites with SpliceAI ≤0.1. c.4494T>A is a silent variant at position 1498, which is outside both clinically important functional domains (aa 10-40 and aa 2481-3186). It is not intronic. None of the BP4 conditions are satisfied.	spliceai
BP5	Not met	BP5 is not met. ENIGMA BP5 is applied using the clinical-history likelihood ratio from Li et al. 2020 (PMID:31853058). The variant-level clinical history LR spreadsheet has no entry for NM_000059.4:c.4494T>A, so no LR is available to support benignity from personal/family history data.	vcep_pmid_31853058_brca2_clinical_history_lr
BP6	Met	Expert panel Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) classified as Likely benign.	cspec clinvar
BP7	Not assessed	BP7 is not assessed. ENIGMA BP7_Strong (RNA) would apply if well-established mRNA assay data demonstrate no aberrant splicing for this silent variant outside the functional domain. Exploratory evidence indicates PMID:28608497 (Fraile-Bethencourt et al. 2017) tested c.4494T>A via minigene assay and observed normal splicing, which would support BP7_Strong (RNA) if verified. ENIGMA BP7_Supporting is not applicable because the variant is outside the clinically important functional domain. Full text of PMID:28608497 was not available for verification.

Disclaimer: The content and results provided by LYFE Sciences are for research and educational purposes only and must not be used as a substitute for professional medical judgment, diagnosis, or treatment. Always consult a qualified healthcare professional before making any clinical decisions.