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BRCA1
Final classification
Pathogenic
BRCA1 c.2182A>T · p.Arg728Ter
BRCA1

NM_007294.4:c.2182A>T (p.Arg728Ter) is a nonsense variant in BRCA1 exon 10 (legacy exon 11), predicted to undergo nonsense-mediated decay (>1900 nt upstream of the terminal exon junction).

Gene
BRCA1
Transcript
NM_007294.4
HGVS · transcript:coding
NM_007294.4:c.2182A>T
Consequence
N/A
GRCh38
chr17:43093349 T>A
GRCh37
chr17:41245366 T>A
Basis ENIGMA BRCA1/2 VCEP point system (Table 3): PVS1 Very Strong (8 points) + PM5 Strong (4 points) + PM2 Supporting (1 point) = 13 points, exceeding the Pathogenic threshold (≥10). Also satisfies the categorical rule: 1 Very Strong (PVS1) + ≥1 Strong (PM5) → Pathogenic.
ENIGMA BRCA1/2 VCEP point system (Table 3): PVS1 Very Strong (8 points) + PM5 Strong (4 points) + PM2 Supporting (1 point) = 13 points, exceeding the Pathogenic threshold (≥10). Also satisfies the categorical rule: 1 Very Strong (PVS1) + ≥1 Strong (PM5) → Pathogenic.
Classification rationale
PVS1PM2PM5 Pathogenic
BRCA1 c.2182A>T

NM_007294.4:c.2182A>T (p.Arg728Ter) is a nonsense variant in BRCA1 exon 10 (legacy exon 11), predicted to undergo nonsense-mediated decay (>1900 nt upstream of the terminal exon junction).1 Per ENIGMA Specification Table 4, BRCA1 exon 10 PTC variants are assigned PVS1 (Very Strong) weight. Loss of function is an established disease mechanism for BRCA1.2 ENIGMA Specification Table 4 assigns PM5_Strong (PTC) for nonsense variants in BRCA1 exon 10, where multiple proven pathogenic PTC variants have been observed. This is supported by ≥4 evidence points across functional assay, case-control, personal/family history, and CIMBA data (Supplementary Table 1).3 The variant is absent from gnomAD v2.1 (non-cancer, exome only), gnomAD v4.1 (non-cancer), and gnomAD-Canada v1.0, meeting ENIGMA PM2_Supporting.4 ENIGMA point-based combining rules (Table 3): PVS1 Very Strong (8 points) + PM5 Strong (4 points) + PM2 Supporting (1 point) = 13 points, meeting the Pathogenic threshold (≥10 points).5

PVS1 + PM2 + PM5 Pathogenic
1 cspec ↗vcep_specifications_table4_v1_2_2024_11_18
2 cspec ↗vcep_specifications_table4_v1_2_2024_11_18
3 cspec ↗vcep_specifications_table4_v1_2_2024_11_18vcep_supplementarytables_v1_2_2024_11_18
Gene diagram · NM_007294.4 · variants mapped to exon structure
BRCA1 NM_007294.4
Fetching transcript structure from UCSC…
Applied criteria · 3 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 · supports pathogenic
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      Absent from gnomAD v4.1.
      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
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      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 Pathogenic (2 clinical laboratories). (ClinVarID = 2811747)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). BayesDel score = 0.179714.
      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 · 9 PMIDs not cited in assessment
      11358863 ↗ Tumorigenesis in mice carrying a truncating Brca1 mutation. ONCOKB
      12483515 ↗ The cancer connection: BRCA1 and BRCA2 tumor suppression in mice and humans. ONCOKB
      12947386 ↗ Roles of BRCA1 and BRCA2 in homologous recombination, DNA replication fidelity and the cellular response to ionizing radiation. ONCOKB
      20608970 ↗ BRCA1 16 years later: risk-associated BRCA1 mutations and their functional implications. ONCOKB
      20104584 ↗ Characterization of BRCA1 and BRCA2 deleterious mutations and variants of unknown clinical significance in unilateral and bilateral breast cancer: the WECARE study. CLINVAR
      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
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR