Starting
Initialising…
0%
BRCA1
Final classification
Likely Benign
BRCA1 c.4720G>T · p.Asp1574Tyr
BRCA1

NM_007294.4:c.4720G>T (p.Asp1574Tyr) is a missense variant in BRCA1 exon 15, located outside all three clinically important functional domains (RING aa 2-101, coiled-coil aa 1391-1424, BRCT aa 1650-1857). It is absent from gnomAD v2.1 and v4.1 population databases.

Gene
BRCA1
Transcript
NM_007294.4
HGVS · transcript:coding
NM_007294.4:c.4720G>T
Consequence
N/A
GRCh38
chr17:43071194 C>A
GRCh37
chr17:41223211 C>A
Basis ENIGMA BRCA1/2 v1.2.0 Table 3 point system for conflicting evidence: PM2_Supporting (+1) + BP1_Strong (-4) = -3 total points. Score of -3 falls in the Likely Benign range (-6 to -2). The variant has only one met criterion on each side (1 supporting pathogenic, 1 strong benign), triggering the ENIGMA conflicting-evidence point-based resolution rather than a simple all_of table match.
ENIGMA BRCA1/2 v1.2.0 Table 3 point system for conflicting evidence: PM2_Supporting (+1) + BP1_Strong (-4) = -3 total points. Score of -3 falls in the Likely Benign range (-6 to -2). The variant has only one met criterion on each side (1 supporting pathogenic, 1 strong benign), triggering the ENIGMA conflicting-evidence point-based resolution rather than a simple all_of table match.
Classification rationale
PM2 BP1 Likely Benign
BRCA1 c.4720G>T

NM_007294.4:c.4720G>T (p.Asp1574Tyr) is a missense variant in BRCA1 exon 15, located outside all three clinically important functional domains (RING aa 2-101, coiled-coil aa 1391-1424, BRCT aa 1650-1857). It is absent from gnomAD v2.1 and v4.1 population databases.1 The variant meets PM2_Supporting: absent from gnomAD controls in outbred populations, per ENIGMA specifications.2 The variant meets BP1_Strong: missense substitution outside clinically important functional domains with no predicted splicing impact (SpliceAI max delta 0.02). Per ENIGMA Figure 1A, missense variants outside domains with SpliceAI ≤0.1 receive BP1_Strong.3 PVS1, PS1, PM5, and several other criteria are not applicable as this is a missense variant without a same-residue pathogenic comparator and without null-variant features.4 PS3 could not be assessed through the ENIGMA framework as the variant is not listed in Table 9 (calibrated functional assays). External functional evidence (Carvalho 2007 PMID:17308087, Starita 2018 PMID:29892012) suggests a damaging effect in yeast transcription and multiplex HDR assays, but these have not been calibrated through ENIGMA standards. Human review is recommended. PP4 and BP5 could not be assessed: the variant is absent from the Li et al. 2020 (PMID:31853058) BRCA1 clinical-history likelihood-ratio table.5 PS4, PP1, BS2, BS4, and BP7 have no supporting evidence available for this variant. BS3 is not met as functional evidence points toward damaging effect rather than benign.6

PM2 + BP1 Likely Benign
4 pvs1_variant_assessmentpm5_candidatescspec ↗
5 vcep_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 · 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
      Population frequency
      Absent from gnomAD v4.1.
      Absent from gnomAD v2.1.
      This variant is absent from gnomAD-Canada.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Uncertain significance (1 clinical laboratory). (ClinVarID = 936973)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02). REVEL score = 0.604. BayesDel score = 0.108762.
      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.
      Literature · 21 PMIDs triaged · 8 high-priority
      21papers screened
      Papers triaged by theme: functional/splicing/segregation/case_observation. high_priority_papers include abstract snippets. Use these to support PS3/BS3/PS4/PP1/PP3/PP5.
      23918944 ↗ splicing rna
      Tamoxifen and risk of contralateral breast cancer for BRCA1 and BRCA2 mutation carriers.
      To determine whether adjuvant tamoxifen treatment for breast cancer (BC) is associated with reduced contralateral breast cancer (CBC) risk for BRCA1 and/or BRCA2 mutation carriers. Analysis of pooled observational cohort data, self-reported at enrollment and at follow-up from the International BRCA1, and BRCA2 Carrier Cohort Study, Kathleen Cuningham Foundation Consortium for Research into Familia
      BP7PP3PP5PS4PVS1
      12692171 ↗ case observation
      American Society of Clinical Oncology policy statement update: genetic testing for cancer susceptibility.
      As the leading organization representing cancer specialists involved in patient care and clinical research, the American Society of Clinical Oncology (ASCO) reaffirms its commitment to integrating cancer risk assessment and management, including molecular analysis of cancer predisposition genes, into the practice of oncology and preventive medicine. The primary goal of this effort is to foster exp
      PP5PS4
      15604628 ↗ case observation
      Genetic cancer risk assessment and counseling: recommendations of the national society of genetic counselors.
      These cancer genetic counseling recommendations describe the medical, psychosocial, and ethical ramifications of identifying at-risk individuals through cancer risk assessment with or without genetic testing. They were developed by members of the Practice Issues Subcommittee of the National Society of Genetic Counselors Cancer Genetic Counseling Special Interest Group. The information contained in
      PP5PS4
      17392385 ↗ case observation
      American Cancer Society guidelines for breast screening with MRI as an adjunct to mammography.
      New evidence on breast Magnetic Resonance Imaging (MRI) screening has become available since the American Cancer Society (ACS) last issued guidelines for the early detection of breast cancer in 2003. A guideline panel has reviewed this evidence and developed new recommendations for women at different defined levels of risk. Screening MRI is recommended for women with an approximately 20-25% or gre
      PP5PS4
      17508274 ↗ case observation
      Risk assessment and genetic counseling for hereditary breast and ovarian cancer: recommendations of the National Society of Genetic Counselors.
      These cancer genetic counseling recommendations describe the medical, psychosocial and ethical implications of identifying at-risk individuals for hereditary breast and ovarian cancer (HBOC) through cancer risk assessment, with or without genetic susceptibility testing. They were developed by members of the Practice Issues Subcommittee of the National Society of Genetic Counselors' Familial Cancer
      PP5PS4
      18163131 ↗ case observation
      The emerging landscape of breast cancer susceptibility.
      The genetic basis of inherited predisposition to breast cancer has been assiduously investigated for the past two decades and has been the subject of several recent discoveries. Three reasonably well-defined classes of breast cancer susceptibility alleles with different levels of risk and prevalence in the population have become apparent: rare high-penetrance alleles, rare moderate-penetrance alle
      PP5PS4
      19305347 ↗ case observation
      ACOG Practice Bulletin No. 103: Hereditary breast and ovarian cancer syndrome.
      Hereditary breast and ovarian cancer syndrome is an inherited cancer-susceptibility syndrome. The hallmarks of this syndrome are multiple family members with breast cancer or ovarian cancer or both, the presence of both breast cancer and ovarian cancer in a single individual, and early age of breast cancer onset. Clinical genetic testing for gene mutations allows physicians to more precisely ident
      PP5PS4
      20065170 ↗ case observation
      American Society of Clinical Oncology policy statement update: genetic and genomic testing for cancer susceptibility.
      PP5PS4
      28492532 ↗ background review
      Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
      PS3PS4
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots