Analysis in progress
Initialising…
0%
complete
This report is still being assembled — sections appear as each stage finishes. It isn't final yet.
BRCA1
Final classification
Likely Benign
BRCA1 c.1568T>G · p.Leu523Trp
BRCA1

NM_007294.3:c.1568T>G (p.Leu523Trp) is a missense variant in BRCA1 exon 10, located outside the clinically important functional domains (RING aa 2-101, coiled-coil aa 1391-1424, BRCT aa 1650-1857).

Gene
BRCA1
Transcript
NM_007294.3
HGVS · transcript:coding
NM_007294.3:c.1568T>G
Consequence
N/A
GRCh38
chr17:43093963 A>C
GRCh37
chr17:41245980 A>C
Basis Conflicting evidence: PM2_Supporting (+1 pathogenic) and BP1_Strong (-4 benign) both met. Applied ENIGMA BRCA1 v1.2.0 conflicting-evidence point system. Total = -3, which falls in the Likely Benign range (-6 to -2).
Conflicting evidence: PM2_Supporting (+1 pathogenic) and BP1_Strong (-4 benign) both met. Applied ENIGMA BRCA1 v1.2.0 conflicting-evidence point system. Total = -3, which falls in the Likely Benign range (-6 to -2).
Classification rationale
PM2 BP1 Likely Benign
BRCA1 c.1568T>G

NM_007294.3:c.1568T>G (p.Leu523Trp) is a missense variant in BRCA1 exon 10, located outside the clinically important functional domains (RING aa 2-101, coiled-coil aa 1391-1424, BRCT aa 1650-1857).1 This variant is absent from gnomAD v2.1 (non-cancer exome subset) and present at extremely low frequency in gnomAD v4.1 (1/1,613,758 alleles; AF = 6.20e-7). The absence from the v2.1 outbred population controls meets ENIGMA PM2_Supporting.2 The variant falls within the BRCA1 exon 11 coldspot region (aa 224-1366), where no pathogenic missense variants have been observed in ClinVar. Combined with its location outside clinically important functional domains and absence of predicted splicing impact (SpliceAI = 0.00), this meets ENIGMA BP1_Strong.3 In silico predictors are discordant: BayesDel (0.322, ≥0.28 threshold) predicts a damaging protein change but PP3 is not triggered because the variant lies outside clinically important functional domains per ENIGMA rules. REVEL score is 0.613.4 No functional data (PS3/BS3), segregation data (PP1/BS4), clinical-history likelihood ratios (PP4/BP5), or case-control studies (PS4) are available for this variant. It is absent from the ENIGMA Table 9 curated functional assay results and from the ST4 functional assay dataset.5 The variant is reported in ClinVar as Uncertain significance by 6 clinical laboratories and Likely benign by 1 laboratory (ClinVar ID 54295). No expert panel classification is available.6 With PM2_Supporting on the pathogenic side and BP1_Strong on the benign side, the evidence is conflicting and does not meet ENIGMA Table 3 thresholds for Likely Pathogenic, Likely Benign, or Benign classification. The variant remains classified as Uncertain Significance.7

PM2 + BP1 Likely Benign
Gene diagram · NM_007294.3 · variants mapped to exon structure
BRCA1 NM_007294.3
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 subset), meeting the ENIGMA PM2_Supporting criterion for absence from controls in an outbred population. In gnomAD v4.1, a single allele is observed (AF = 6.2e-7, 1/1,613,758 alleles, no homozygotes).
Absent from gnomAD v2.1 (non-cancer exome subset).One allele in gnomAD v4.1 (AF = 6.20e-7).
BP1 strong Benign
This missense variant lies outside ENIGMA-defined clinically important functional domains (RING aa 2-101, coiled-coil aa 1391-1424, BRCT aa 1650-1857) and no splicing impact is predicted (SpliceAI max delta = 0.00, ≤0.1). The variant falls within the BRCA1 exon 11 coldspot region (aa 224-1366), where no pathogenic missense variants have been reported. Per ENIGMA rules, BP1_Strong applies.
Position 523 is outside functional domains (RING 2-101coiled-coil 1391-1424BRCT 1650-1857).
Assessed · not applied
Pathogenic
PS1 No previously classified pathogenic or likely pathogenic missense variant at the same amino acid position (Leu523) with a different substitution has been identified in the ENIGMA specification tables, ClinVar, or the reviewed literature.
PS3 No variant-specific or systematic-range functional data is available for NM_007294.3:c.1568T>G.
PS4 No case-control study demonstrating statistically significant enrichment of this variant in affected individuals versus controls has been identified.
PP1 No co-segregation data are available for this variant.
PP3 Although BayesDel (0.322, ≥0.28 threshold) predicts a damaging protein change, the variant lies outside ENIGMA-defined clinically important functional domains (RING aa 2-101, coiled-coil aa 1391-1424, BRCT aa 1650-1857).
PP4 The variant is not listed in the Li et al.
Benign
BA1 The variant does not meet ENIGMA BA1 threshold (filter allele frequency >0.1% in gnomAD v2.1 or v3.1).
BS1 The variant does not meet ENIGMA BS1 thresholds.
BS2 No observation of this variant in a healthy adult individual without features of Fanconi anemia has been identified in the available evidence.
BS3 No well-established functional study demonstrates absence of a damaging effect for this variant.
BS4 No lack-of-segregation data are available for this variant.
BP4 The ENIGMA BP4 rule applies only to missense variants inside a clinically important functional domain with no predicted impact (BayesDel ≤0.15 AND SpliceAI ≤0.1), or to intronic variants outside donor/acceptor sites.
BP5 The variant is not listed in the Li et al.
BP7 BP7_Strong (RNA) requires well-established mRNA assay data showing no damaging effect on splicing.
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
This variant is present in gnomAD v4.1 (AF= 6.19672e-07; MAF= 0.00006%, 1/1613758 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.47521e-07; MAF= 0.00008%, 1/1179912 alleles, homozygotes = 0).
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
6.2e-05% · 1 / 1,613,758
0 hom
European (non-Finnish)
1 / 1,179,912
8.5e-05%
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
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 (6 clinical laboratories) and as Likely benign (1 clinical laboratory). (ClinVarID = 54295)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.613. BayesDel score = 0.322592.
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 · 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. 8 further PMIDs triaged but not cited — see Sources & References.
Systematic misclassification of missense variants in BRCA1 and BRCA2 "coldspots".
Searched
c.1568T>Gp.Leu523TrpL523W1568
Found
Identifies coldspot regions in BRCA1 and BRCA2 where missense variation is tolerated. Reports BRCA1 exon 11 (codons 224-1366) as a coldspot with 0 pathogenic or likely pathogenic missense variants and 93.8% VUS. NM_007294.3:c.1568T>G was not individually mentioned, but the variant falls within this coldspot region.
Variant
◇ Residue / gene-level — variant not named
Applied to
BP1 supports · met
Why
Supports BP1_Strong by confirming that position 523 falls within the exon 11 coldspot where no pathogenic missense variants are observed.
Exon 11 in BRCA1 and exons 10 and 11 in BRCA2 were considered potential coldspots, consistent with literature describing the lack of pathogenic missense variants outside of known critical domains.
Location Table 1; Results, paragraph on BRCA1 coldspots  ·  full text
Sources & reference links
9Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 8 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
37937776 ↗ Actionable Genotypes and Their Association with Life Span in Iceland. CLINVAR
23788249 ↗ ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. CLINVAR
24366376 ↗ Risk assessment, genetic counseling, and genetic testing for BRCA-related cancer in women: U.S. Preventive Services Task Force recommendation statement. CLINVAR
25085752 ↗ Development and validation of a new algorithm for the reclassification of genetic variants identified in the BRCA1 and BRCA2 genes. CLINVAR
25356965 ↗ ACMG policy statement: updated recommendations regarding analysis and reporting of secondary findings in clinical genome-scale sequencing. CLINVAR
28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR