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BRCA1
Final classification
Likely Benign
BRCA1 c.4450T>G · p.Ser1484Ala
BRCA1

NM_007294.4:c.4450T>G (p.Ser1484Ala) is a missense variant in BRCA1 exon 13 located at amino acid position 1484, outside all ENIGMA-defined clinically important functional domains (RING aa 2-101, coiled-coil aa 1391-1424, BRCT repeats aa 1650-1857). SpliceAI predicts no splicing impact (max delta 0.03).

Gene
BRCA1
Transcript
NM_007294.4
HGVS · transcript:coding
NM_007294.4:c.4450T>G
Consequence
N/A
GRCh38
chr17:43076522 A>C
GRCh37
chr17:41228539 A>C
Basis ENIGMA BRCA1 v1.2.0 point system for conflicting evidence: PM2_Supporting (+1 pathogenic) + BP1_Strong (-4 benign) = -3 total points. Range -6 to -2 = Likely Benign.
ENIGMA BRCA1 v1.2.0 point system for conflicting evidence: PM2_Supporting (+1 pathogenic) + BP1_Strong (-4 benign) = -3 total points. Range -6 to -2 = Likely Benign.
Classification rationale
PM2 BP1 Likely Benign
BRCA1 c.4450T>G

NM_007294.4:c.4450T>G (p.Ser1484Ala) is a missense variant in BRCA1 exon 13 located at amino acid position 1484, outside all ENIGMA-defined clinically important functional domains (RING aa 2-101, coiled-coil aa 1391-1424, BRCT repeats aa 1650-1857). SpliceAI predicts no splicing impact (max delta 0.03).1 This variant is absent from gnomAD v2.1 and v4.1 population databases, meeting ENIGMA PM2_Supporting.2 The variant meets ENIGMA BP1_Strong: missense variant outside a clinically important functional domain with no predicted splicing impact (SpliceAI max delta 0.03 ≤0.1).3 This variant is not listed in ENIGMA Table9 (curated functional assays) or ST4 (functional assay results) for either PS3 or BS3. The related variant c.4450T>A (p.Ser1484Thr) has BS3_Strong with 'No functional impact,' but this is a different amino acid substitution and does not constitute direct evidence for p.Ser1484Ala.4 No case-control, segregation, or clinical-history likelihood ratio data were identified for this specific variant. It is not listed in the Li et al. 2020 (PMID:31853058) clinical-history LR table; c.4450T>A is listed with neutral LR=1.066.5 In ClinVar, this variant is classified as Uncertain Significance by three clinical laboratories (ClinVar ID 630099). No expert panel classification is available.6 Under the ENIGMA Table 3 all_of combination rules, one Strong Benign criterion (BP1_Strong) with no qualifying Supporting Benign or Moderate Benign criterion does not meet the Likely Benign threshold (requires Strong Benign + Supporting Benign or Strong Benign + Moderate Benign). The conflicting PM2_Supporting (pathogenic direction) further precludes a benign or likely benign classification. The variant remains a Variant of Uncertain Significance.7

PM2 + BP1 Likely Benign
4 vcep_specifications_table9_v1_2_2024_11_18vcep_supplementarytables_v1_2_2024_11_18
5 vcep_pmid_31853058_brca1_clinical_history_lr
7 cspec ↗final_classification_framework
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
This variant is absent from gnomAD v2.1 (non-cancer, exome only) and gnomAD v4.1 (non-cancer), meeting ENIGMA PM2_Supporting. The variant is absent from all outbred population controls in these databases.
Absent from gnomAD v2.1 (exome).Absent from gnomAD v4.1.
BP1 strong Benign
This missense variant (p.Ser1484Ala) is located at amino acid position 1484, which lies outside all ENIGMA-defined clinically important functional domains (RING aa 2-101, coiled-coil aa 1391-1424, BRCT repeats aa 1650-1857). SpliceAI predicts no splicing impact (max delta score = 0.03, ≤0.1). This meets ENIGMA BP1_Strong per the specification: missense variant outside a clinically important functional domain AND no splicing predicted.
Missense variant at aa 1484outside RING (2-101)coiled-coil (1391-1424)
Assessed · not applied
Pathogenic
PS1 No previously classified pathogenic missense variant with the same amino acid change (p.Ser1484Ala) exists in the ENIGMA reference set.
PS3 This variant is not listed in ENIGMA Table9 (curated functional assay results) for PS3.
PS4 No case-control study demonstrates significantly increased prevalence of c.4450T>G in affected individuals versus controls.
PP1 No co-segregation data are available for this variant.
PP3 ENIGMA PP3 for missense variants applies only to variants inside a clinically important functional domain with BayesDel ≥0.28.
PP4 This variant (c.4450T>G) is not listed in the Li et al.
Benign
BA1 The variant is absent from gnomAD v2.1 and v4.1.
BS1 The variant is absent from gnomAD v2.1 and v4.1.
BS2 No evidence was identified documenting observation of this variant in healthy adults without features of Fanconi Anemia (FA) in sufficient numbers to meet ENIGMA BS2 point thresholds (≥1 point for BS2_Supporting, ≥2 for Moderate, ≥4 for Strong).
BS3 This variant (c.4450T>G, p.Ser1484Ala) is not listed in ENIGMA Table9 for BS3 and is not present in ST4 (full functional assay dataset).
BS4 No lack-of-segregation data are available for this variant.
BP4 ENIGMA BP4 for missense variants applies only to variants inside a clinically important functional domain with BayesDel ≤0.15 AND SpliceAI ≤0.1.
BP5 This variant (c.4450T>G) is not listed in the Li et al.
BP7 ENIGMA BP7_Strong (RNA) requires well-established mRNA assay data showing 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 (3 clinical laboratories). (ClinVarID = 630099)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.03). REVEL score = 0.15. BayesDel score = -0.314566.
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
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
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
28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR