Starting
Initialising…
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BRCA1
Final classification
Likely Benign
BRCA1 c.4450T>G · p.Ser1484Ala
BRCA1

NM_007294.4:c.4450T>G (p.Ser1484Ala) is a missense variant in BRCA1 exon 13 located at amino acid position 1484, outside all ENIGMA-defined clinically important functional domains (RING aa 2-101, coiled-coil aa 1391-1424, BRCT repeats aa 1650-1857). SpliceAI predicts no splicing impact (max delta 0.03).

Gene
BRCA1
Transcript
NM_007294.4
HGVS · transcript:coding
NM_007294.4:c.4450T>G
Consequence
N/A
GRCh38
chr17:43076522 A>C
GRCh37
chr17:41228539 A>C
Basis ENIGMA BRCA1 v1.2.0 point system for conflicting evidence: PM2_Supporting (+1 pathogenic) + BP1_Strong (-4 benign) = -3 total points. Range -6 to -2 = Likely Benign.
ENIGMA BRCA1 v1.2.0 point system for conflicting evidence: PM2_Supporting (+1 pathogenic) + BP1_Strong (-4 benign) = -3 total points. Range -6 to -2 = Likely Benign.
Classification rationale
PM2 BP1 Likely Benign
BRCA1 c.4450T>G

NM_007294.4:c.4450T>G (p.Ser1484Ala) is a missense variant in BRCA1 exon 13 located at amino acid position 1484, outside all ENIGMA-defined clinically important functional domains (RING aa 2-101, coiled-coil aa 1391-1424, BRCT repeats aa 1650-1857). SpliceAI predicts no splicing impact (max delta 0.03).1 This variant is absent from gnomAD v2.1 and v4.1 population databases, meeting ENIGMA PM2_Supporting.2 The variant meets ENIGMA BP1_Strong: missense variant outside a clinically important functional domain with no predicted splicing impact (SpliceAI max delta 0.03 ≤0.1).3 This variant is not listed in ENIGMA Table9 (curated functional assays) or ST4 (functional assay results) for either PS3 or BS3. The related variant c.4450T>A (p.Ser1484Thr) has BS3_Strong with 'No functional impact,' but this is a different amino acid substitution and does not constitute direct evidence for p.Ser1484Ala.4 No case-control, segregation, or clinical-history likelihood ratio data were identified for this specific variant. It is not listed in the Li et al. 2020 (PMID:31853058) clinical-history LR table; c.4450T>A is listed with neutral LR=1.066.5 In ClinVar, this variant is classified as Uncertain Significance by three clinical laboratories (ClinVar ID 630099). No expert panel classification is available.6 Under the ENIGMA Table 3 all_of combination rules, one Strong Benign criterion (BP1_Strong) with no qualifying Supporting Benign or Moderate Benign criterion does not meet the Likely Benign threshold (requires Strong Benign + Supporting Benign or Strong Benign + Moderate Benign). The conflicting PM2_Supporting (pathogenic direction) further precludes a benign or likely benign classification. The variant remains a Variant of Uncertain Significance.7

PM2 + BP1 Likely Benign
4 vcep_specifications_table9_v1_2_2024_11_18vcep_supplementarytables_v1_2_2024_11_18
5 vcep_pmid_31853058_brca1_clinical_history_lr
7 cspec ↗final_classification_framework
Gene diagram · NM_007294.4 · variants mapped to exon structure
BRCA1 NM_007294.4
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 · supports benign
      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 has been reported in ClinVar as Uncertain significance (3 clinical laboratories). (ClinVarID = 630099)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.03). REVEL score = 0.15. BayesDel score = -0.314566.
      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
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      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
      25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. 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
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR