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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 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      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