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BRCA1
Final classification
VUS
BRCA1 c.3170G>A · p.Ser1057Asn
BRCA1

c.3170G>A (p.Ser1057Asn) is a missense variant in BRCA1 exon 10 (legacy exon 11) located at amino acid position 1057, outside the established clinically important functional domains (RING aa 2-101, coiled-coil aa 1391-1424, BRCT aa 1650-1857).

Gene
BRCA1
Transcript
NM_007294.4
HGVS · transcript:coding
NM_007294.4:c.3170G>A
Consequence
N/A
GRCh38
chr17:43092361 C>T
GRCh37
chr17:41244378 C>T
Basis ENIGMA BRCA1 v1.2 Table 3 categorical rules applied. Only BP1_Strong is met (missense variant outside clinically important functional domains, no splicing predicted). ENIGMA Likely Benign rule for a single Strong Benign criterion requires multiple independent evidence types; BP1 alone constitutes a single evidence type (coldspot/domain location). No other benign criteria are met. The variant does not satisfy any pathogenic, likely pathogenic, benign, or likely benign combination rule, and therefore defaults to Uncertain Significance.
ENIGMA BRCA1 v1.2 Table 3 categorical rules applied. Only BP1_Strong is met (missense variant outside clinically important functional domains, no splicing predicted). ENIGMA Likely Benign rule for a single Strong Benign criterion requires multiple independent evidence types; BP1 alone constitutes a single evidence type (coldspot/domain location). No other benign criteria are met. The variant does not satisfy any pathogenic, likely pathogenic, benign, or likely benign combination rule, and therefore defaults to Uncertain Significance.
Classification rationale
BP1 VUS
BRCA1 c.3170G>A

c.3170G>A (p.Ser1057Asn) is a missense variant in BRCA1 exon 10 (legacy exon 11) located at amino acid position 1057, outside the established clinically important functional domains (RING aa 2-101, coiled-coil aa 1391-1424, BRCT aa 1650-1857).1 SpliceAI predicts no splicing impact (max delta score 0.00), and BayesDel no-AF score is -0.0291, consistent with a benign computational prediction.2 BP1_Strong is met: the variant is a missense substitution outside clinically important functional domains with no predicted splicing impact (SpliceAI ≤0.1). This is the only applicable ACMG/AMP criterion supported by current evidence.3 BRCA1 exon 11 (aa 224-1366), where p.Ser1057Asn resides, has been characterized as a coldspot with zero pathogenic or likely pathogenic missense variants among 1,117 exon 11 missense variants reported to ClinVar.4 The variant is present at extremely low frequency in population databases (gnomAD v2.1: 1/250,824 alleles, AF=0.0004%; gnomAD v4.1: 3/1,613,924 alleles, grpmax FAF=6.8e-7), below thresholds for both benign (BS1) and pathogenic (PM2) population criteria.5 No functional data, case-control studies, segregation analysis, clinical history likelihood ratios, or variant-specific publications were identified for this variant. It is reported in ClinVar as Uncertain Significance (5 clinical laboratories, single submitter criteria only, no expert panel review).6 Under the ENIGMA BRCA1 v1.2 point-based classification system, the evidence totals -4 points (BP1_Strong alone), placing the variant in the Likely Benign range (-6 to -2). However, ENIGMA Table 3 requires multiple evidence types to support Likely Benign when based on a single Strong Benign criterion. With only BP1_Strong met and no additional benign criteria satisfied from independent evidence types, the classification defaults to Uncertain Significance per the ENIGMA adapted ACMG/AMP framework.7

BP1 VUS
1 cspec ↗vcep_appendices_v1_2_2024_11_18
2 spliceai ↗bayesdel
7 cspec ↗vcep_specifications_v1_2_2024_11_18
Gene diagram · NM_007294.4 · variants mapped to exon structure
BRCA1 NM_007294.4
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 15 assessed
Applied · 1
Strength Supporting Moderate Strong Very strong
BP1 strong Benign
ENIGMA BP1_Strong applies to missense variants located outside the clinically important functional domains of BRCA1 when no splicing is predicted. p.Ser1057Asn is at amino acid position 1057, which lies in the exon 11 spacer region (aa 224-1366), well outside the RING domain (aa 2-101), coiled-coil domain (aa 1391-1424), and BRCT repeats (aa 1650-1857). SpliceAI max delta score is 0.0, confirming no predicted splicing impact. This region has been characterized as a coldspot with zero pathogenic/likely pathogenic missense variants among 1,117 exon 11 missense variants in ClinVar (Dines et al. 2020, PMID:31911673).
Missense variant at aa 1057outside RING (2-101)coiled-coil (1391-1424)
Assessed · not applied
Pathogenic
PS1 No previously classified pathogenic or likely pathogenic missense variant was identified at the same amino acid residue (Ser1057) in ClinVar or ENIGMA reference datasets.
PS3 c.3170G>A (p.Ser1057Asn) is not listed in ENIGMA Table 9 curated functional assay results and is not present in Supplementary Table 4 functional assay data.
PS4 No case-control data are available for this variant.
PM2 ENIGMA PM2_Supporting requires the variant to be absent from gnomAD v2.1 (non-cancer, exome) and v3.1 (non-cancer) in outbred populations.
PP1 No co-segregation data are available for this variant.
PP3 ENIGMA PP3 for missense variants requires the variant to be located inside a clinically important functional domain with BayesDel ≥0.28, or SpliceAI ≥0.2 for splicing prediction.
PP4 ENIGMA PP4 requires calibrated clinical history likelihood ratio data (LR≥2.08).
Benign
BA1 BA1 requires filter allele frequency (FAF) > 0.1% (0.001) in gnomAD non-cancer, non-founder populations.
BS1 ENIGMA BS1_Strong requires FAF > 0.01% (0.0001) and BS1_Supporting requires FAF > 0.002% (0.00002).
BS2 ENIGMA BS2 requires co-observation data in the absence of Fanconi Anemia phenotype features, with point-based scoring per proband.
BS3 c.3170G>A (p.Ser1057Asn) is not listed in ENIGMA Table 9 with a BS3 assignment and is not present in Supplementary Table 4 functional assay results with an outcome of no functional impact.
BS4 ENIGMA BS4 requires lack of segregation in affected family members, measured by quantitative co-segregation analysis (LR≤0.48).
BP4 ENIGMA BP4 for missense variants requires the variant to be located inside a clinically important functional domain AND have no predicted impact (BayesDel ≤0.15 AND SpliceAI ≤0.1).
BP5 ENIGMA BP5 requires calibrated clinical history likelihood ratio data toward benignity (LR≤0.48).
BP7 ENIGMA BP7_Strong (RNA) for missense variants outside functional domains requires well-established mRNA assay data demonstrating no splicing impact.
N/A · 9 PVS1 · PS2 · PM1 · PM5 · PM6 · PP2 · PP5 · BP2 · BP6
Research & evidence
Population frequency
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= 1.85882e-06; MAF= 0.00019%, 3/1613924 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 2.54242e-06; MAF= 0.00025%, 3/1179976 alleles, homozygotes = 0); grpmax FAF= 6.8e-07.
v2.1
This variant is present in gnomAD v2.1 (AF= 3.98686e-06; MAF= 0.00040%, 1/250824 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.83455e-06; MAF= 0.00088%, 1/113192 alleles, homozygotes = 0).
🇨🇦 CA
Not available in gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.00019% · 3 / 1,613,924
0 hom · FAF 6.8e-05%
European (non-Finnish)
3 / 1,179,976
0.00025%
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
gnomAD v2.1
0.0004% · 1 / 250,824
0 hom
European (non-Finnish)
1 / 113,192
0.00088%
+ 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian)
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 (5 clinical laboratories) and as Uncertain Significance (1 clinical laboratory). (ClinVarID = 156191)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.543. BayesDel score = -0.0291003.
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 previously been reported in somatic cancers (COSMIC; COSV58797942, n = 1 times).
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. 6 further PMIDs triaged but not cited — see Sources & References.
Systematic misclassification of missense variants in BRCA1 and BRCA2 "coldspots".
Searched
c.3170G>Ap.Ser1057AsnS1057NSer10571057
Found
Identifies BRCA1 exon 11 (aa 224-1366) as a coldspot with zero pathogenic or likely pathogenic missense variants among 1,117 exon 11 missense variants submitted to ClinVar. Proposes using coldspot regions as benign evidence for variant classification. p.Ser1057Asn falls within this coldspot region.
Variant
◇ Residue / gene-level — variant not named
Applied to
BP1 supports · met
Why
Provides domain-level coldspot evidence supporting BP1_Strong; variant not named individually but falls within the characterized coldspot region.
Exon 11 in BRCA1... 0 (0%) P or LP [pathogenic or likely pathogenic] out of 1,117 total missense variants.
Location Results, Table 1; entire discussion of exon 11 coldspot (aa 224-1366)  ·  full text
Sources & reference links
9Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 6 PMIDs not cited in assessment
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
17392385 ↗ American Cancer Society guidelines for breast screening with MRI as an adjunct to mammography. CLINVAR
23188549 ↗ NSGC practice guideline: risk assessment and genetic counseling for hereditary breast and ovarian cancer. CLINVAR
24366376 ↗ Risk assessment, genetic counseling, and genetic testing for BRCA-related cancer in women: U.S. Preventive Services Task Force recommendation statement. CLINVAR
24366402 ↗ Summaries for patients. Assessing the genetic risk for BRCA-related breast or ovarian cancer in women: recommendations from the U.S. Preventive Services Task Force. CLINVAR
24493721 ↗ American Society of Clinical Oncology Expert Statement: collection and use of a cancer family history for oncology providers. CLINVAR