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BRCA2
Final classification
VUS
BRCA2 c.10027G>T · p.Glu3343Ter
BRCA2

NM_000059.4:c.10027G>T (p.Glu3343Ter) is a nonsense variant in BRCA2 exon 27 that introduces a premature termination codon at position 3343 of 3418 amino acids.

Gene
BRCA2
Transcript
NM_000059.4
HGVS · transcript:coding
NM_000059.4:c.10027G>T
Consequence
N/A
GRCh38
chr13:32398540 G>T
GRCh37
chr13:32972677 G>T
Basis ENIGMA BRCA1/BRCA2 Table 3 combination rules applied. Only PM2_Supporting is met (absence from gnomAD outbred populations). PVS1 is not applicable per ENIGMA Table 4 (PTC beyond p.E3309 in exon 27). No benign criteria are met. A single pathogenic Supporting criterion does not satisfy any Pathogenic, Likely Pathogenic, Benign, or Likely Benign combination rule in ENIGMA Table 3. Under the ENIGMA point system (1 point from PM2_Supporting, 0 from benign), the total of 1 falls in the Uncertain Significance range (-1 to 5).
ENIGMA BRCA1/BRCA2 Table 3 combination rules applied. Only PM2_Supporting is met (absence from gnomAD outbred populations). PVS1 is not applicable per ENIGMA Table 4 (PTC beyond p.E3309 in exon 27). No benign criteria are met. A single pathogenic Supporting criterion does not satisfy any Pathogenic, Likely Pathogenic, Benign, or Likely Benign combination rule in ENIGMA Table 3. Under the ENIGMA point system (1 point from PM2_Supporting, 0 from benign), the total of 1 falls in the Uncertain Significance range (-1 to 5).
Classification rationale
PM2 VUS
BRCA2 c.10027G>T

NM_000059.4:c.10027G>T (p.Glu3343Ter) is a nonsense variant in BRCA2 exon 27 that introduces a premature termination codon at position 3343 of 3418 amino acids. PVS1 is not applicable per ENIGMA BRCA2 Table 4: nonsense variants in exon 27 beyond codon p.E3309 are assigned PVS1_N/A, as truncation of the extreme C-terminus is not considered sufficient evidence for pathogenicity under the ENIGMA decision framework.1 PM2_Supporting is met: the variant is absent from gnomAD v2.1 (non-cancer, exome), gnomAD v4.1 (non-cancer), and gnomAD-Canada v1.0 outbred populations.2 PP3 is not met: although BayesDel no-AF score is 0.65 (≥0.30), the variant lies at position 3343, outside the BRCA2 clinically important functional domains (DNA binding domain aa 2481-3186; PALB2 binding domain aa 10-40). SpliceAI max delta is 0.17 (<0.20 threshold).3 BA1 and BS1 are not met: the variant is absent from gnomAD; filter allele frequency does not exceed benign population thresholds.4 PS3 and BS3 are not assessed: no variant-specific functional assay data were identified in ENIGMA Table 9 or in any of the six reviewed publications.5 PP4 and BP5 are not assessed: the variant was not present in the Li et al. 2020 (PMID:31853058) BRCA2 clinical-history likelihood-ratio table; no multifactorial likelihood data are available.6 ClinVar reports this variant as Likely benign (1 clinical laboratory, criteria provided, single submitter; variation ID 1770751). PP5 is not applicable under ENIGMA specifications, and no expert panel classification exists to warrant an override.7 With only PM2_Supporting met and PVS1 not applicable per ENIGMA Table 4, the available evidence is insufficient to classify this variant as pathogenic or likely pathogenic. Multiple evidence categories (functional, segregation, clinical history, case-control) lack data. The variant remains a variant of uncertain significance (VUS).

PM2 VUS
1 vcep_specifications_table4_v1_2_2024_11_18
3 bayesdelspliceai ↗
5 vcep_specifications_table9_v1_2_2024_11_18
6 vcep_pmid_31853058_brca2_clinical_history_lr
Gene diagram · NM_000059.4 · variants mapped to exon structure
BRCA2 NM_000059.4
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 11 assessed
Applied · 1
Strength Supporting Moderate Strong Very strong
PM2 supporting review Pathogenic
This variant is absent from gnomAD v2.1 (non-cancer, exome) and gnomAD v4.1 (non-cancer) outbred populations. Per ENIGMA PM2 rule, absence from controls in outbred populations qualifies for PM2_Supporting. Read depth at the variant region has not been independently verified but BRCA2 exon 27 is well-covered in exome sequencing.
Absent from gnomAD v2.1 exomesabsent from gnomAD v4.1absent from gnomAD-Canada v1.0
Assessed · not applied
Pathogenic
PS3 No variant-specific functional assay data found in ENIGMA Table 9 for c.10027G>T.
PS4 No case-control data available for this variant.
PP1 No co-segregation data available for this variant.
PP3 Per ENIGMA PP3 rules: (a) For protein change impact, requires BayesDel no-AF score ≥ 0.30 AND location inside a clinically important functional domain (BRCA2 DNA binding domain aa 2481-3186 or PALB2 binding domain aa 10-40).
PP4 The variant was not found in the Li et al.
Benign
BA1 Per ENIGMA BA1, filter allele frequency must be above 0.1% (FAF > 0.001) in gnomAD non-founder populations.
BS1 Per ENIGMA BS1, BS1_Strong requires FAF > 0.0001 and BS1_Supporting requires FAF > 0.00002 in gnomAD non-founder populations.
BS2 No data on observation of this variant in healthy adults without features of Fanconi Anemia.
BS3 No variant-specific functional assay data showing no damaging effect were found in ENIGMA Table 9 or in any publication.
BS4 No segregation data available for this variant.
BP5 The variant was not found in the Li et al.
N/A · 16 PVS1 · PS1 · PS2 · PM1 · PM3 · PM4 · PM5 · PM6 · PP2 · PP5 · BP1 · BP2 · BP3 · BP4 · BP6 · BP7
Research & evidence
Population frequency
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
Absent from gnomAD-Canada v1.0.
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 Likely benign (1 clinical laboratory). (ClinVarID = 1770751)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.17). BayesDel score = 0.652534.
Functional / OncoKB screenshot
Functional Likely Oncogenic
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.
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
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
10570174 ↗ Truncated BRCA2 is cytoplasmic: implications for cancer-linked mutations. ONCOKB
11239455 ↗ BRCA2 is required for homology-directed repair of chromosomal breaks. ONCOKB
20878484 ↗ A new mutation of BRCA2 gene in an Italian healthy woman with familial breast cancer history. ONCOKB
22193408 ↗ BRCA1 and BRCA2: different roles in a common pathway of genome protection. ONCOKB
24312913 ↗ A comprehensive focus on global spectrum of BRCA1 and BRCA2 mutations in breast cancer. ONCOKB
25394175 ↗ A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment. CLINVAR