Classification rationale

PM2 BP1BP4 Likely Benign

BARD1 c.1325C>T

NM_000465.4:c.1325C>T (p.Pro442Leu) is a missense variant in BARD1 present at extremely low frequency in population databases (gnomAD v2.1 AF=0.00119%; v4.1 AF=0.00236%), meeting PM2 at supporting level.¹ Multiple in silico tools consistently predict a benign effect: REVEL score 0.208, BayesDel score -0.244, and SpliceAI max delta 0.07, meeting BP4 at supporting level.² BARD1 is a tumor suppressor gene where primarily loss-of-function variants cause disease; this missense variant meets BP1 at supporting level.³ No functional studies, case-control data, de novo observations, co-segregation data, or pathogenic same-residue comparators exist for this variant. ClinVar classifies it as a Variant of Uncertain Significance (9 clinical laboratories).⁴ Two supporting benign criteria (BP1 and BP4) are met with no moderate or strong criteria on either side. Per generic ACMG/AMP 2015 combination rules, two supporting benign criteria warrant a classification of Likely Benign.⁵

PM2 + BP1 + BP4 → Likely Benign

1 gnomad_v2 ↗gnomad_v4 ↗gnomad_canada ↗

2 revelbayesdelspliceai ↗

3 pvs1_gene_context

4 clinvar ↗pm5_candidates

5 generic_acmg_combination_rules

Gene diagram · NM_000465.4 · variants mapped to exon structure

BARD1 NM_000465.4

Fetching transcript structure from UCSC…

Applied criteria · 3 applied · 19 assessed

Applied · 3

Strength Supporting Moderate Strong Very strong

✓

PM2 supporting Pathogenic

This variant is present at extremely low frequency in population databases. gnomAD v2.1: 3/251,198 alleles (AF=0.00119%); gnomAD v4.1: 38/1,612,910 alleles (AF=0.00236%); absent from gnomAD-Canada. All allele frequencies are well below the 0.1% PM2 threshold. No homozygotes observed.

gnomAD v2.1 AF=0.00119% (3/251198 alleles0 homozygotes)

gnomad_v2 ↗gnomad_v4 ↗gnomad_canada ↗

✓

BP1 supporting Benign

BARD1 is a tumor suppressor gene where primarily loss-of-function (truncating, nonsense, splice-disrupting) variants are known to cause disease. NM_000465.4:c.1325C>T is a missense variant (p.Pro442Leu), and missense variants are not the established disease mechanism for BARD1.

BARD1 germline LoF mechanism is supported by disease literature (PVS1 gene context). Missense variants are not the primary pathogenic mechanism.

✓

BP4 supporting Benign

Multiple lines of computational evidence support a benign effect: REVEL score 0.208 (well below the pathogenic threshold of ~0.5), BayesDel score -0.243647 (negative/benign), and SpliceAI max delta score 0.07 (no predicted splice impact). These independent in silico tools consistently suggest this missense change is tolerated.

REVEL=0.208 (benign)BayesDel=-0.244 (benign)SpliceAI max delta=0.07 (no splice impact). ClinVar submitter Ambry Genetics notes the alteration is predicted to be tolerated by in silico analysis.

spliceai ↗

Assessed · not applied

Pathogenic

PS1 No known pathogenic variant at amino acid position 442 (Pro442) with a different substitution has been identified in ClinVar or the reviewed literature.

PS2 No de novo data are available for this variant.

PS3 No functional studies have directly tested BARD1 Pro442Leu or a systematically characterized range that includes position 442.

PS4 No case-control studies or sufficient enrichment data in affected individuals are available for this variant.

PM1 The variant (p.Pro442Leu) does not lie in a statistically significant mutational hotspot as assessed by cancerhotspots.org.

PM6 No de novo observation has been reported for this variant.

PP1 No co-segregation data are available for this variant.

PP2 BARD1 is a tumor suppressor gene where loss-of-function (truncating, nonsense, splice) variants are the established disease mechanism.

PP3 Multiple in silico tools predict a benign effect for this variant: REVEL score 0.208 (well below the pathogenic threshold of ~0.5), BayesDel score -0.243647 (negative, benign), and SpliceAI max delta 0.07 (no predicted splice impact).

PP4 No patient phenotype or specific clinical data are available for the individuals carrying this variant.

PP5 This variant is classified as Uncertain Significance (VUS) in ClinVar by 9 clinical laboratories, not Pathogenic or Likely Pathogenic.

Benign

BA1 The allele frequency of this variant in gnomAD v2.1 (0.00119%) and v4.1 (0.00236%) is well below the 1% BA1 threshold.

BS1 The allele frequency of this variant (gnomAD v2.1: 0.00119%, v4.1: 0.00236%) is below the 0.3% BS1 threshold.

BS2 No evidence is available that this variant has been observed in healthy adults with full penetrance expected at an early age.

BS3 No functional studies demonstrating a neutral or benign effect exist for this variant.

BS4 No co-segregation data demonstrating lack of segregation with disease are available.

BP2 No evidence that this variant has been observed in trans with a known pathogenic variant in BARD1.

BP5 No observation of this variant in a case with an alternate molecular basis for disease has been reported.

BP6 ClinVar classifies this variant as Uncertain Significance, not Benign or Likely Benign.

N/A · 6 PVS1 · PM3 · PM4 · PM5 · BP3 · BP7

Research & evidence

Population frequency · supports benign

gnomAD v4.1

gnomAD v2.1

v4.1

This variant is present in gnomAD v4.1 (AF= 2.35599e-05; MAF= 0.00236%, 38/1612910 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 3.20195e-05; MAF= 0.00320%, 2/62462 alleles, homozygotes = 0); grpmax FAF= 2.155e-05.

v2.1

This variant is present in gnomAD v2.1 (AF= 1.19428e-05; MAF= 0.00119%, 3/251198 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 2.64117e-05; MAF= 0.00264%, 3/113586 alleles, homozygotes = 0); grpmax FAF= 7.02e-06.

🇨🇦 CA

Absent from gnomAD-Canada v1.0.

Allele frequency by ancestry

three datasets · side by side

gnomAD v4.1

0.0024% · 38 / 1,612,910
0 hom · FAF 0.0022%

Remaining individuals 2 / 62,462	0.0032%
European (non-Finnish) 35 / 1,178,998	0.003%
African/African American 1 / 74,996	0.0013%

+ 7 not observed (Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish)

gnomAD v2.1

0.0012% · 3 / 251,198
0 hom · FAF 0.0007%

European (non-Finnish)

3 / 113,586

0.0026%

+ 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian)

gnomAD Canada 🇨🇦

Absent · 0 / ?
0 hom

Not observed in any ancestry group.

gnomAD v4 ↗ gnomAD v2 ↗ gnomAD 🇨🇦 ↗

ClinVar

This variant has been reported in ClinVar as Uncertain significance (9 clinical laboratories). (ClinVarID = 182045)

ClinVar ↗

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.07). REVEL score = 0.208. BayesDel score = -0.243647.

SpliceAI ↗

Functional Unknown Oncogenic Effect

OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. BARD1, a tumor suppressor involved in the DNA damage response, is altered by mutation in breast and ovarian cancers.

OncoKB ↗

COSMIC

Cancer hotspots

Somatic evidence Not in COSMIC / hotspots

COSMIC

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

Hotspots

This variant does not lie in a statistically significant hotspot.

COSMIC ↗ Hotspots ↗

Sources & reference links

8Sources

ClinVar

gnomAD v2.1

gnomAD v4.1

gnomAD-Canada

SpliceAI

OncoKB

COSMIC

Cancer hotspots

Triaged references · 6 PMIDs not cited in assessment

25741868 ↗ 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. CLINVAR

34242744 ↗ Customizing local and systemic therapies for women with early breast cancer: the St. Gallen International Consensus Guidelines for treatment of early breast cancer 2021. CLINVAR

24366402 ↗ 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. CLINVAR

26389258 ↗ Cancer Genetics Risk Assessment and Counseling (PDQ®): Health Professional Version. CLINVAR

31479213 ↗ PMID 31479213 CLINVAR

35802134 ↗ ACMG SF v3.1 list for reporting of secondary findings in clinical exome and genome sequencing: A policy statement of the American College of Medical Genetics and Genomics (ACMG). CLINVAR