Starting
Initialising…
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BRCA1
Final classification
Pathogenic
BRCA1 c.2657_2676del · p.Ser886Ter
BRCA1

NM_007294.4:c.2657_2676del is a 20bp frameshift deletion in BRCA1 exon 10(11) that creates a premature termination codon at p.Ser886Ter. BRCA1 loss of function is an established mechanism for hereditary breast and ovarian cancer.

Gene
BRCA1
Transcript
NM_007294.4
HGVS · transcript:coding
NM_007294.4:c.2657_2676del
Consequence
N/A
GRCh38
chr17:43092854 TTAAGGACCCAGAGTGGGCAG>T
GRCh37
chr17:41244871 TTAAGGACCCAGAGTGGGCAG>T
Basis ENIGMA BRCA1 VCEP Specification v1.2.0 Table 3. No conflicting evidence: no benign criteria are met. Pathogenic criteria: PVS1 (Very Strong, 8 pts) + PM5 (Strong, 4 pts) + PM2 (Supporting, 1 pt). Table 3 pathogenic all_of rule satisfied: 1 Very Strong + >=1 Strong -> Pathogenic. ENIGMA point system confirms: 8+4+1 = 13, in Pathogenic range (>=10).
ENIGMA BRCA1 VCEP Specification v1.2.0 Table 3. No conflicting evidence: no benign criteria are met. Pathogenic criteria: PVS1 (Very Strong, 8 pts) + PM5 (Strong, 4 pts) + PM2 (Supporting, 1 pt). Table 3 pathogenic all_of rule satisfied: 1 Very Strong + >=1 Strong -> Pathogenic. ENIGMA point system confirms: 8+4+1 = 13, in Pathogenic range (>=10).
Classification rationale
PVS1PM2PM5 Pathogenic
BRCA1 c.2657_2676del

NM_007294.4:c.2657_2676del is a 20bp frameshift deletion in BRCA1 exon 10(11) that creates a premature termination codon at p.Ser886Ter. BRCA1 loss of function is an established mechanism for hereditary breast and ovarian cancer.1 Per ENIGMA BRCA1 VCEP Specifications Table 4, PTC variants in exon E10(11) are assigned PVS1 (Very Strong) as null variants in a gene where loss of function is a known disease mechanism, and PM5_Strong (PTC) because other proven pathogenic PTC variants have been reported in this exon.2 The variant is absent from gnomAD v2.1 and v4.1 population databases (allele count = 0), meeting PM2 at Supporting strength per ENIGMA population frequency rules.3 Applying the ENIGMA Table 3 point system: PVS1 Very Strong = 8 points, PM5 Strong = 4 points, PM2 Supporting = 1 point. Total = 13 points, which falls in the Pathogenic range (>=10).4

PVS1 + PM2 + PM5 Pathogenic
1 cspec ↗vcep_specifications_table4_v1_2_2024_11_18
2 vcep_specifications_table4_v1_2_2024_11_18
4 cspec ↗vcep_specifications_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
      This variant is absent from gnomAD-Canada.
      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 is absent from ClinVar.
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
      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
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 4 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