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BRCA1
Final classification
Uncertain Significance
BRCA1 c.5509T>G · p.Trp1837Gly
BRCA1

The BRCA1 c.5509T>G (p.Trp1837Gly; W1837G) variant has been reported in ClinVar with an expert-panel Pathogenic classification by the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel, and OncoKB classifies the variant as Likely Oncogenic with likely loss-of-function biological effect.

Gene
BRCA1
Transcript
NM_007294.4
HGVS · transcript:coding
NM_007294.4:c.5509T>G
Consequence
N/A
GRCh38
chr17:43045761 A>C
GRCh37
chr17:41197778 A>C
Basis Official ENIGMA BRCA1/BRCA2 v1.2 Table 3 final-classification framework was used. Applied pathogenic evidence comprises PP4_Moderate plus PM2_Supporting, PP3_Supporting, and PP5_Supporting; no benign criteria are applied. This combination does not meet ENIGMA Table 3 thresholds for Pathogenic or Likely Pathogenic, and no benign classification threshold is met.
Official ENIGMA BRCA1/BRCA2 v1.2 Table 3 final-classification framework was used. Applied pathogenic evidence comprises PP4_Moderate plus PM2_Supporting, PP3_Supporting, and PP5_Supporting; no benign criteria are applied. This combination does not meet ENIGMA Table 3 thresholds for Pathogenic or Likely Pathogenic, and no benign classification threshold is met.
Classification rationale
PM2PP3PP4PP5 Uncertain Significance
BRCA1 c.5509T>G

The BRCA1 c.5509T>G (p.Trp1837Gly; W1837G) variant has been reported in ClinVar with an expert-panel Pathogenic classification by the ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel, and OncoKB classifies the variant as Likely Oncogenic with likely loss-of-function biological effect.1 This variant is absent from gnomAD v2.1 and gnomAD v4.1, giving an observed population frequency of 0 in the available population datasets and supporting PM2_Supporting under the ENIGMA framework.2 ENIGMA curated functional data for c.5509T>G are discordant across calibrated studies, so neither PS3 nor BS3 is met for this variant.3 The variant lies in the BRCA1 BRCT repeats and has an ENIGMA supplementary BayesDel no-AF score of approximately 0.533, above the PP3 threshold of ≥0.28, while SpliceAI predicts no significant splice impact with a max delta score of 0.00.4 The BRCA1 clinical-history likelihood-ratio table reports c.5509T>G in 2 probands with LR 8.0617, exceeding the PP4_Moderate threshold of LR ≥4.3 and falling below the PP4_Strong threshold of LR ≥18.7.5

PM2 + PP3 + PP4 + PP5 Uncertain Significance
3 vcep_specifications_table9_v1_2_2024_11_18vcep_supplementarytables_v1_2_2024_11_18
4 vcep_appendices_v1_2_2024_11_18vcep_supplementarytables_v1_2_2024_11_18spliceai ↗cspec ↗
5 vcep_pmid_31853058_brca1_clinical_history_lrPMID:31853058 ↗cspec ↗
Gene diagram · NM_007294.4 · variants mapped to exon structure
BRCA1 NM_007294.4
Fetching transcript structure from UCSC…
Applied criteria · 4 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
      Absent from gnomAD v4.1.
      v2.1
      Absent from gnomAD v2.1.
      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.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Likely pathogenic (2 clinical laboratories) and as Pathogenic (2 clinical laboratories) and as Uncertain significance (1 clinical laboratory) and as Likely Pathogenic (1 clinical laboratory) and as Pathogenic by ClinGen ENIGMA BRCA1 and BRCA2 Variant Curation Expert Panel, ClinGen (expert panel).
      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 classifies this variant as Likely Oncogenic; biological effect: Likely Loss-of-function.
      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.
      Literature · how each cited paper was used
      1papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why.
      PMID PMID:31853058
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PP4 supports · met
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots