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BRCA1
Final classification
VUS
BRCA1 c.5432A>G · p.Gln1811Arg
BRCA1

PS3_Strong is met: three independent calibrated functional studies (Findlay 2018, Petitalot 2019, Fernandes 2019) demonstrate that p.Gln1811Arg exhibits protein function comparable to pathogenic control variants (ENIGMA Table 9; functional impact complete, IARC class 5).

Gene
BRCA1
Transcript
NM_007294.3
HGVS · transcript:coding
NM_007294.3:c.5432A>G
Consequence
N/A
GRCh38
chr17:43047678 T>C
GRCh37
chr17:41199695 T>C
Basis ENIGMA BRCA1 Table 3 combining rules applied: one Strong criterion (PS3) plus one Supporting criterion (PM2) does not satisfy any Likely Pathogenic combination (requires 2 Strong, or 1 Strong + 2 Supporting, or 1 Strong + 1-2 Moderate). No benign criteria are met. Under the ENIGMA point-based scoring system, PS3_Strong (4 pts) + PM2_Supporting (1 pt) = 5 pts, which falls within the Uncertain Significance range (-1 to 5). The variant is classified as a Variant of Uncertain Significance (VUS).
ENIGMA BRCA1 Table 3 combining rules applied: one Strong criterion (PS3) plus one Supporting criterion (PM2) does not satisfy any Likely Pathogenic combination (requires 2 Strong, or 1 Strong + 2 Supporting, or 1 Strong + 1-2 Moderate). No benign criteria are met. Under the ENIGMA point-based scoring system, PS3_Strong (4 pts) + PM2_Supporting (1 pt) = 5 pts, which falls within the Uncertain Significance range (-1 to 5). The variant is classified as a Variant of Uncertain Significance (VUS).
Classification rationale
PS3PM2 VUS
BRCA1 c.5432A>G

PS3_Strong is met: three independent calibrated functional studies (Findlay 2018, Petitalot 2019, Fernandes 2019) demonstrate that p.Gln1811Arg exhibits protein function comparable to pathogenic control variants (ENIGMA Table 9; functional impact complete, IARC class 5).1 PM2_Supporting is met: the variant is absent from gnomAD v2.1 (non-cancer exomes) and observed at extremely low frequency in gnomAD v4.1 (1/1,614,234 alleles; AF=6.19×10⁻⁷).2 PP3 and BP4 are not met: BayesDel no-AF score of 0.192 falls in the intermediate range between the BP4 threshold (≤0.15) and the PP3 threshold (≥0.28) for variants inside the BRCT clinically important domain.3 PP4 and BP5 are not met: the clinical-history likelihood ratio (LR=0.993 from Li et al. 2020, N=3 probands) falls within the neutral zone, neither supporting pathogenicity nor benignity.4 PVS1, PM5, and BP1 are not applicable: PVS1 is restricted to null variants; PM5_PTC is N/A for exon E21(22) per ENIGMA Table 4; BP1 requires location outside a clinically important functional domain (Gln1811 is within the BRCT domain).5 Under ENIGMA Table 3 combining rules, the evidence profile of one Strong criterion (PS3) plus one Supporting criterion (PM2) is insufficient to classify as Likely Pathogenic (requires ≥2 Strong, or 1 Strong + ≥2 Supporting, or 1 Strong + 1–2 Moderate). The variant is classified as a Variant of Uncertain Significance (VUS).6

PS3 + PM2 VUS
1 vcep_specifications_table9_v1_2_2024_11_18
3 bayesdelcspec ↗
4 vcep_pmid_31853058_brca1_clinical_history_lrPMID:31853058 ↗
5 cspec ↗vcep_specifications_table4_v1_2_2024_11_18
Gene diagram · NM_007294.3 · variants mapped to exon structure
BRCA1 NM_007294.3
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= 6.19489e-07; MAF= 0.00006%, 1/1614234 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.47426e-07; MAF= 0.00008%, 1/1180044 alleles, homozygotes = 0).
      v2.1
      Absent from gnomAD v2.1.
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      6.2e-05% · 1 / 1,614,234
      0 hom
      European (non-Finnish)
      1 / 1,180,044
      8.5e-05%
      + 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 Likely pathogenic (6 clinical laboratories) and as Uncertain significance (2 clinical laboratories) and as Likely Pathogenic (1 clinical laboratory) and as pathogenic (1 clinical laboratory). (ClinVarID = 55578)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.709. BayesDel score = 0.192033.
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.
      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
      9Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 7 PMIDs not cited in assessment
      15172985 ↗ Structure-based assessment of missense mutations in human BRCA1: implications for breast and ovarian cancer predisposition. ONCOKB
      20516115 ↗ Comprehensive analysis of missense variations in the BRCT domain of BRCA1 by structural and functional assays. ONCOKB
      10946236 ↗ The BRCA1 C-terminal domain: structure and function. CLINVAR
      12496477 ↗ Mutations in the BRCT domain confer temperature sensitivity to BRCA1 in transcription activation. CLINVAR
      14534301 ↗ Detection of protein folding defects caused by BRCA1-BRCT truncation and missense mutations. CLINVAR
      15235020 ↗ Analysis of missense variation in human BRCA1 in the context of interspecific sequence variation. CLINVAR
      37733863 ↗ Accurate proteome-wide missense variant effect prediction with AlphaMissense. CLINVAR