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BRCA1
Final classification
VUS
BRCA1 c.4189A>G · p.Arg1397Gly
BRCA1

NM_007294.4:c.4189A>G (p.Arg1397Gly) is a rare missense variant in BRCA1 exon 12, located within the ENIGMA clinically important coiled-coil domain (aa 1391–1424).

Gene
BRCA1
Transcript
NM_007294.4
HGVS · transcript:coding
NM_007294.4:c.4189A>G
Consequence
N/A
GRCh38
chr17:43082572 T>C
GRCh37
chr17:41234589 T>C
Basis Only one pathogenic criterion (PM2_Supporting) is met. Under ENIGMA BRCA1/2 v1.2.0 Table 3 combination rules, a single Supporting-level criterion does not satisfy any Likely Pathogenic or Pathogenic combination threshold. No benign criteria are met. The evidence is insufficient to classify beyond Uncertain Significance.
Only one pathogenic criterion (PM2_Supporting) is met. Under ENIGMA BRCA1/2 v1.2.0 Table 3 combination rules, a single Supporting-level criterion does not satisfy any Likely Pathogenic or Pathogenic combination threshold. No benign criteria are met. The evidence is insufficient to classify beyond Uncertain Significance.
Classification rationale
PM2 VUS
BRCA1 c.4189A>G

NM_007294.4:c.4189A>G (p.Arg1397Gly) is a rare missense variant in BRCA1 exon 12, located within the ENIGMA clinically important coiled-coil domain (aa 1391–1424).1 The variant is absent from gnomAD v2.1 and observed at extremely low frequency in gnomAD v4.1 (2/1,614,142 alleles; grpmax FAF=2.8×10⁻⁷), meeting ENIGMA PM2_Supporting.2 In silico predictions are indeterminate: REVEL score is 0.594 (elevated), but the ENIGMA-specified BayesDel no-AF score of 0.153 falls between the BP4 threshold (≤0.15) and PP3 threshold (≥0.28), and SpliceAI predicts no splicing impact (max delta=0.04). Neither PP3 nor BP4 is met.3 No variant-specific functional data, clinical-history likelihood ratios, cosegregation analysis, or case-control data were identified in the ENIGMA VCEP materials or literature reviewed.4 With only PM2_Supporting met and no other applicable criteria, the evidence is insufficient to classify this variant beyond Uncertain Significance (VUS) under the ENIGMA BRCA1/2 v1.2.0 framework. The combination of a single supporting-level pathogenic criterion does not reach the Likely Pathogenic threshold.5

PM2 VUS
3 bayesdelrevelspliceai ↗cspec ↗
4 vcep_specifications_table9_v1_2_2024_11_18vcep_supplementarytables_v1_2_2024_11_18vcep_pmid_31853058_brca1_clinical_history_lr
Gene diagram · NM_007294.4 · variants mapped to exon structure
BRCA1 NM_007294.4
Fetching transcript structure from UCSC…
Applied criteria · 1 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= 1.23905e-06; MAF= 0.00012%, 2/1614142 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 1.69489e-06; MAF= 0.00017%, 2/1180020 alleles, homozygotes = 0); grpmax FAF= 2.8e-07.
      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
      0.00012% · 2 / 1,614,142
      0 hom · FAF 2.8e-05%
      European (non-Finnish)
      2 / 1,180,020
      0.00017%
      + 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 (2 clinical laboratories). (ClinVarID = 1508878)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.04). REVEL score = 0.594. BayesDel score = 0.15333.
      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. BRCA1, a tumor suppressor involved in the DNA damage response, is mutated in various cancer types.
      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 · 9 PMIDs not cited in assessment
      23918944 ↗ Tamoxifen and risk of contralateral breast cancer for BRCA1 and BRCA2 mutation carriers. CLINVAR
      12692171 ↗ American Society of Clinical Oncology policy statement update: genetic testing for cancer susceptibility. CLINVAR
      15604628 ↗ Genetic cancer risk assessment and counseling: recommendations of the national society of genetic counselors. CLINVAR
      17392385 ↗ American Cancer Society guidelines for breast screening with MRI as an adjunct to mammography. CLINVAR
      17508274 ↗ Risk assessment and genetic counseling for hereditary breast and ovarian cancer: recommendations of the National Society of Genetic Counselors. CLINVAR
      18163131 ↗ The emerging landscape of breast cancer susceptibility. CLINVAR
      19305347 ↗ ACOG Practice Bulletin No. 103: Hereditary breast and ovarian cancer syndrome. CLINVAR
      20065170 ↗ American Society of Clinical Oncology policy statement update: genetic and genomic testing for cancer susceptibility. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR