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BARD1
Final classification
VUS
BARD1 c.1217G>A · p.Arg406Gln
BARD1

NM_000465.4:c.1217G>A (p.Arg406Gln) is a missense variant in BARD1 exon 4.

Gene
BARD1
Transcript
NM_000465.4
HGVS · transcript:coding
NM_000465.4:c.1217G>A
Consequence
N/A
GRCh38
chr2:214780657 C>T
GRCh37
chr2:215645381 C>T
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.1217G>A

NM_000465.4:c.1217G>A (p.Arg406Gln) is a missense variant in BARD1 exon 4. This variant is present at very low frequency in population databases: gnomAD v2.1 allele frequency 0.006% (17/282,356 alleles, 0 homozygotes) and gnomAD v4.1 allele frequency 0.002% (39/1,613,954 alleles, 1 homozygote), meeting PM2 (supporting).1 Multiple lines of computational evidence predict a benign effect: REVEL score 0.117, BayesDel score -0.406678, and SpliceAI max delta 0.05, meeting BP4 (supporting).2 Functional studies show conflicting results: p.R406Q is fully functional in homology-directed repair (149% of wild-type activity; PMID:26350354) but shows partially impaired apoptosis in patient-derived lymphoblastoid cells (TUNEL and Annexin V assays; PMID:31371347). Neither PS3 nor BS3 is met due to inconsistent evidence across assay types.3 This variant has been reported in two unrelated patients with early-onset colorectal cancer (ages 24 and 37; PMID:31371347), but colorectal cancer is not the classic BARD1-associated phenotype (hereditary breast and ovarian cancer).4 In ClinVar (Variation ID 127713), this variant is classified as Uncertain Significance by 8 clinical laboratories and Likely Benign by 1 laboratory, with no expert panel review available.5 No de novo, segregation, or case-control data are available. No pathogenic missense variant at the same residue has been identified (PM5 not met).

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= 2.41643e-05; MAF= 0.00242%, 39/1613954 alleles, homozygotes = 1) and has highest observed frequency in the South Asian population (AF= 0.000263499; MAF= 0.02635%, 24/91082 alleles, homozygotes = 0); grpmax FAF= 0.00018075.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 6.02077e-05; MAF= 0.00602%, 17/282356 alleles, homozygotes = 0) and has highest observed frequency in the East Asian population (AF= 0.000451128; MAF= 0.04511%, 9/19950 alleles, homozygotes = 0); grpmax FAF= 0.00021575.
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.0024% · 39 / 1,613,954
      1 hom · FAF 0.018%
      South Asian
      24 / 91,082
      0.026%
      East Asian
      7 / 44,890
      0.016%
      Remaining individuals
      4 / 62,478
      0.0064%
      1 hom
      African/African American
      1 / 74,918
      0.0013%
      European (non-Finnish)
      3 / 1,179,980
      0.00025%
      + 5 not observed (Admixed American, European (Finnish), Amish, Middle Eastern, Ashkenazi Jewish)
      gnomAD v2.1
      0.006% · 17 / 282,356
      0 hom · FAF 0.022%
      East Asian
      9 / 19,950
      0.045%
      South Asian
      8 / 30,606
      0.026%
      + 6 not observed (African/African American, Admixed American, Ashkenazi Jewish, European (Finnish), European (non-Finnish), Remaining individuals)
      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 (8 clinical laboratories) and as Likely benign (1 clinical laboratory). (ClinVarID = 127713)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.05). REVEL score = 0.117. BayesDel score = -0.406678.
      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 previously been reported in somatic cancers (COSMIC; COSV53611525, n = 2 times).
      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
      23012255 ↗ ESMO Consensus Guidelines for management of patients with colon and rectal cancer. a personalized approach to clinical decision making. CLINVAR
      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
      26350354 ↗ Functional Analysis of BARD1 Missense Variants in Homology-Directed Repair of DNA Double Strand Breaks. CLINVAR
      31371347 ↗ Functional analysis of clinical BARD1 germline variants. CLINVAR
      25006736 ↗ Multitarget stool DNA testing for colorectal-cancer screening. CLINVAR
      25373533 ↗ Updated guidelines for biomarker testing in colorectal carcinoma: a national consensus of the Spanish Society of Pathology and the Spanish Society of Medical Oncology. CLINVAR
      25394175 ↗ A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment. CLINVAR
      19042984 ↗ National Academy of Clinical Biochemistry laboratory medicine practice guidelines for use of tumor markers in testicular, prostate, colorectal, breast, and ovarian cancers. CLINVAR