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BARD1
Final classification
VUS
BARD1 c.928T>G · p.Ser310Ala
BARD1

This variant is a missense substitution in BARD1 (NM_000465.4:c.928T>G, p.Ser310Ala) located in exon 4. BARD1 is a tumor suppressor gene involved in the DNA damage response, with germline loss-of-function variants associated with hereditary breast and ovarian cancer susceptibility.

Gene
BARD1
Transcript
NM_000465.4
HGVS · transcript:coding
NM_000465.4:c.928T>G
Consequence
N/A
GRCh38
chr2:214780946 A>C
GRCh37
chr2:215645670 A>C
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting, BP4 supporting; combination = 1 supporting + 1 supporting benign, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting, BP4 supporting; combination = 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP4 VUS
BARD1 c.928T>G

This variant is a missense substitution in BARD1 (NM_000465.4:c.928T>G, p.Ser310Ala) located in exon 4. BARD1 is a tumor suppressor gene involved in the DNA damage response, with germline loss-of-function variants associated with hereditary breast and ovarian cancer susceptibility.1 This variant is absent from gnomAD v2.1 and is present at an extremely low frequency in gnomAD v4.1 (AF = 6.20e-6; 10/1,613,658 alleles, all in the European non-Finnish subpopulation; 0 homozygotes). This extremely low population frequency meets PM2 at supporting strength (well below the 0.1% threshold).2 Multiple lines of computational evidence predict a benign effect. REVEL score is 0.086 (strongly benign-leaning). BayesDel score is -0.575 (benign-leaning). SpliceAI max delta score is 0.02, predicting no splicing impact. Multiple independent clinical laboratories concurred that in silico tools predict a benign effect, with Labcorp noting five of five tools predicted no impact. This meets BP4 at supporting strength.3 No variant-specific functional studies, case-control data, segregation data, or de novo reports were identified. The variant has been reported in ClinVar predominantly as a Variant of Uncertain Significance (5 clinical laboratories) with one Likely benign classification (Ambry Genetics). No expert panel review has been performed.4 Applying generic ACMG/AMP 2015 combination rules (PMIDs:25741868): PM2 (supporting) + BP4 (supporting) results in a final classification of Variant of Uncertain Significance, as the evidence supporting pathogenicity and benign impact are insufficient to reach a more definitive classification.5

PM2 + BP4 VUS
Gene diagram · NM_000465.4 · variants mapped to exon structure
BARD1 NM_000465.4
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 20 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
This variant is absent from gnomAD v2.1 (exome) and has an extremely low allele frequency in gnomAD v4.1 (AF = 6.20e-6, 10/1,613,658 alleles, 0 homozygotes; grpmax FAF = 4.29e-06). The observed frequency of 0.00062% is well below the 0.1% threshold for PM2 in non-VCEP contexts. Absent from all subpopulations except European (non-Finnish) where it is present at 8.48e-6. Not available in gnomAD-Canada.
Absent from gnomAD v2.1 (exome). Present in gnomAD v4.1 at AF = 6.20e-06 (10/1613658 alleles
BP4 supporting Benign
Multiple lines of computational evidence predict no impact on the gene product. REVEL score is 0.086 (strongly benign-leaning). BayesDel score is -0.575 (benign-leaning). SpliceAI max delta score is 0.02 (no predicted splicing impact). Multiple independent ClinVar submitters (GeneDx, Labcorp/Women's Health and Genetics) concurred that in silico analysis predicts a benign effect, with Labcorp noting 'five of five in-silico tools predict a benign effect of the variant on protein function.'
REVEL 0.086 (strongly benign-leaning). BayesDel -0.575 (benign-leaning). SpliceAI max delta 0.02 (no splicing impact). Five of five in silico tools predict benign per Labcorp ClinVar submission.
Assessed · not applied
Pathogenic
PS1 No data available on whether the same amino acid change (p.Ser310Ala) has been previously reported as pathogenic.
PS2 No de novo data available for this variant.
PS3 No variant-specific functional studies have been reported for NM_000465.4:c.928T>G.
PS4 No variant-specific case-control or prevalence data available.
PM1 This variant does not lie in a statistically significant mutational hotspot in BARD1.
PM6 No de novo data available.
PP1 No segregation data available for this variant in affected families.
PP2 PP2 applies to genes where missense variants are a common mechanism of disease with a low rate of benign missense variation.
PP3 Multiple in silico tools predict a benign effect for this variant.
PP4 No specific patient phenotype information available for this variant.
PP5 This variant is classified as Uncertain Significance by 5 clinical laboratories in ClinVar and as Likely benign by 1 laboratory (Ambry Genetics).
Benign
BA1 The allele frequency in gnomAD v4.1 is 6.20e-6 (0.00062%), well below the 1% BA1 threshold.
BS1 The allele frequency in gnomAD v4.1 is 6.20e-6 (0.00062%), well below the 0.3% BS1 threshold.
BS2 No data on observation of this variant in healthy adult individuals with full penetrance expected at an early age.
BS3 No functional studies demonstrating no deleterious effect have been reported for this variant.
BS4 No segregation data available to assess lack of cosegregation with disease.
BP1 BP1 applies when a missense variant occurs in a gene where only truncating variants cause disease.
BP2 No data on observation of this variant in trans with a known pathogenic variant in BARD1 or another gene for a fully penetrant dominant disorder.
BP5 No data on an alternative molecular basis for disease in a case with this variant.
BP6 No expert panel or reputable source has classified this variant as benign.
N/A · 6 PVS1 · PM3 · PM4 · PM5 · BP3 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 6.1971e-06; MAF= 0.00062%, 10/1613658 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.47551e-06; MAF= 0.00085%, 10/1179870 alleles, homozygotes = 0); grpmax FAF= 4.29e-06.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Not available in gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.00062% · 10 / 1,613,658
0 hom · FAF 0.00043%
European (non-Finnish)
10 / 1,179,870
0.00085%
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant has been reported in ClinVar as Uncertain significance (5 clinical laboratories) and as Likely benign (1 clinical laboratory). (ClinVarID = 279698)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02). REVEL score = 0.086. BayesDel score = -0.575285.
Functional / OncoKB screenshot
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 screenshot
COSMIC
Cancer hotspots screenshot
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.
Sources & reference links
8Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 8 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
20301425 ↗ BRCA1- and BRCA2-Associated Hereditary Breast and Ovarian Cancer. CLINVAR
24432435 ↗ PMID 24432435 CLINVAR
26389258 ↗ Cancer Genetics Risk Assessment and Counseling (PDQ®): Health Professional Versi CLINVAR
26976419 ↗ Frequency of Germline Mutations in 25 Cancer Susceptibility Genes in a Sequential Series of Patients With Breast Cancer. CLINVAR
31429903 ↗ Risk Assessment, Genetic Counseling, and Genetic Testing for BRCA-Related Cancer: US Preventive Services Task Force Recommendation Statement. CLINVAR
31479213 ↗ PMID 31479213 CLINVAR
33471991 ↗ Breast Cancer Risk Genes - Association Analysis in More than 113,000 Women. CLINVAR