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
      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 (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.
      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
      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
      20065170 ↗ American Society of Clinical Oncology policy statement update: genetic and genomic testing for cancer susceptibility. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR