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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 applied · 14 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
The variant is absent from gnomAD v2.1 (non-cancer, exome only) and gnomAD v4.1 (non-cancer) in outbred populations, meeting ENIGMA PM2_Supporting criteria for absent from controls.
Absent from gnomAD v2.1 (exome)Absent from gnomAD v4.1
BP1 strong Benign
ENIGMA BP1_Strong applies to missense variants located outside all clinically important functional domains with no predicted splicing impact (SpliceAI ≤0.1). p.Asp1574Tyr lies at amino acid 1574, outside the RING (aa 2-101), coiled-coil (aa 1391-1424), and BRCT (aa 1650-1857) domains. SpliceAI max delta score is 0.02 (≤0.1), confirming no predicted splice impact.
Missense variant at aa 1574 outside all three BRCA1 functional domainsSpliceAI 0.02 (≤0.1 threshold)BayesDel 0.109 (confirmatory)
Assessed · not applied
Pathogenic
PS1 No known pathogenic or likely pathogenic missense variant has been identified at the same amino acid residue (Asp1574) to serve as a comparator.
PS3 ENIGMA PS3 rule directs to Specifications Table 9 for calibrated functional assay code assignment.
PS4 ENIGMA PS4 requires case-control data with p≤0.05 and OR≥4 (lower CI excludes 2.0).
PP1 ENIGMA PP1 requires quantitative cosegregation analysis demonstrating co-segregation with disease in multiple affected family members (LR≥2.08 for supporting).
PP3 ENIGMA PP3 applies to missense variants inside a clinically important functional domain with BayesDel ≥0.28, or variants with SpliceAI ≥0.2 irrespective of domain location.
PP4 ENIGMA PP4 uses calibrated clinical-history likelihood ratios from Li et al.
Benign
BA1 ENIGMA BA1 requires filter allele frequency (FAF) above 0.1% (FAF > 0.001) in gnomAD v2.1 (non-cancer, exome) and/or gnomAD v3.1 (non-cancer).
BS1 ENIGMA BS1 requires FAF > 0.01% (strong) or FAF > 0.002% and ≤ 0.01% (supporting) in gnomAD non-founder populations.
BS2 ENIGMA BS2 requires observation in healthy adults without features of Fanconi anemia.
BS3 ENIGMA BS3 requires well-established functional studies showing no damaging effect on protein function.
BS4 ENIGMA BS4 requires quantitative lack-of-segregation data (LR ≤0.48 for supporting, ≤0.23 for moderate, ≤0.05 for strong).
BP4 ENIGMA BP4 (supporting benign from computational evidence) applies to missense variants inside a clinically important functional domain with BayesDel ≤0.15 AND SpliceAI ≤0.1.
BP5 ENIGMA BP5 uses calibrated clinical-history likelihood ratios from Li et al.
BP7 ENIGMA BP7_Strong (RNA) requires well-established mRNA assay data demonstrating no splicing aberration.
N/A · 9 PVS1 · PS2 · PM1 · PM5 · PM6 · PP2 · PP5 · BP2 · BP6
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