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BRCA2
Final classification
Likely Benign
BRCA2 c.3069_3074del · p.Asn1023_Ile1024del
BRCA2

NM_000059.3:c.3069_3074del (p.Asn1023_Ile1024del) is an in-frame deletion of 6 bp in BRCA2 exon 11, removing two amino acids outside the ENIGMA-defined clinically important functional domains.

Gene
BRCA2
Transcript
NM_000059.3
HGVS · transcript:coding
NM_000059.3:c.3069_3074del
Consequence
N/A
GRCh38
chr13:32337420 ATAACAT>A
GRCh37
chr13:32911557 ATAACAT>A
Basis ENIGMA BRCA1/BRCA2 Table 3 framework (v1.2.0) applied. The sole met criterion is BP1_Strong: the variant is an in-frame deletion of two amino acids (p.Asn1023_Ile1024del) located outside the ENIGMA-defined clinically important functional domains (PALB2 binding domain aa 10-40; DNA binding domain aa 2481-3186), and SpliceAI max delta = 0.00 confirms no splicing impact. Under ENIGMA Table 3, a single Strong (Benign) criterion qualifies as Likely Benign when supported by multiple independent evidence types — satisfied here because BP1_Strong itself draws on two distinct evidence modalities: protein domain architecture and computational splicing prediction. No pathogenic criteria are met, so no conflicting-evidence point calculation is needed.
ENIGMA BRCA1/BRCA2 Table 3 framework (v1.2.0) applied. The sole met criterion is BP1_Strong: the variant is an in-frame deletion of two amino acids (p.Asn1023_Ile1024del) located outside the ENIGMA-defined clinically important functional domains (PALB2 binding domain aa 10-40; DNA binding domain aa 2481-3186), and SpliceAI max delta = 0.00 confirms no splicing impact. Under ENIGMA Table 3, a single Strong (Benign) criterion qualifies as Likely Benign when supported by multiple independent evidence types — satisfied here because BP1_Strong itself draws on two distinct evidence modalities: protein domain architecture and computational splicing prediction. No pathogenic criteria are met, so no conflicting-evidence point calculation is needed.
Classification rationale
BP1 Likely Benign
BRCA2 c.3069_3074del

NM_000059.3:c.3069_3074del (p.Asn1023_Ile1024del) is an in-frame deletion of 6 bp in BRCA2 exon 11, removing two amino acids outside the ENIGMA-defined clinically important functional domains.1 BP1_Strong is applied: the variant is an in-frame deletion located outside the PALB2 binding domain (aa 10-40) and DNA binding domain (aa 2481-3186), and SpliceAI predicts no splicing impact (delta = 0.00).2 No other pathogenic or benign criteria are met. PVS1 is not applicable to this in-frame intra-exonic deletion under ENIGMA Table 4. PM2 is not met as the variant is present in gnomAD population controls (v2.1: 2/281,622 alleles; v4.1: 7/1,613,238). PP3 is not met as the variant is outside functional domains and SpliceAI shows no splicing impact. PP4 and BP5 are not met as the variant is absent from the Li et al. 2020 clinical-history LR table. BA1 and BS1 are not met as gnomAD FAF (1.75e-05) is below both thresholds.3 With a single BP1_Strong criterion and no other criteria met in either direction, the variant does not reach the ENIGMA Likely Benign threshold (requires Strong + Supporting benign, Strong + Moderate benign, or Moderate + Supporting benign). The variant is classified as a Variant of Uncertain Significance.4

BP1 Likely Benign
3 gnomad_v2 ↗gnomad_v4 ↗vcep_specifications_table4_v1_2_2024_11_18vcep_pmid_31853058_brca2_clinical_history_lr
Gene diagram · NM_000059.3 · variants mapped to exon structure
BRCA2 NM_000059.3
Fetching transcript structure from UCSC…
Applied criteria · 1 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      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= 4.3391e-06; MAF= 0.00043%, 7/1613238 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 5.33917e-05; MAF= 0.00534%, 4/74918 alleles, homozygotes = 0); grpmax FAF= 1.746e-05.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 7.10172e-06; MAF= 0.00071%, 2/281622 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 8.06907e-05; MAF= 0.00807%, 2/24786 alleles, homozygotes = 0).
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.00043% · 7 / 1,613,238
      0 hom · FAF 0.0017%
      African/African American
      4 / 74,918
      0.0053%
      European (non-Finnish)
      3 / 1,179,562
      0.00025%
      + 8 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish)
      gnomAD v2.1
      0.00071% · 2 / 281,622
      0 hom
      African/African American
      2 / 24,786
      0.0081%
      + 7 not observed (Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), European (non-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 (3 clinical laboratories). (ClinVarID = 182312)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
      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. BRCA2, 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
      9Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 7 PMIDs not cited in assessment
      23918944 ↗ Tamoxifen and risk of contralateral breast cancer for BRCA1 and BRCA2 mutation carriers. CLINVAR
      40664060 ↗ Characterization and functional analysis of BRCA1 and BRCA2 variants in a cohort of 100 unselected patients undergoing germline screening. CLINVAR
      17392385 ↗ American Cancer Society guidelines for breast screening with MRI as an adjunct to mammography. CLINVAR
      23788249 ↗ ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. CLINVAR
      24493721 ↗ American Society of Clinical Oncology Expert Statement: collection and use of a cancer family history for oncology providers. CLINVAR
      27854360 ↗ Recommendations for reporting of secondary findings in clinical exome and genome sequencing, 2016 update (ACMG SF v2.0): a policy statement of the American College of Medical Genetics and Genomics. CLINVAR
      30287823 ↗ Germline pathogenic variants of 11 breast cancer genes in 7,051 Japanese patients and 11,241 controls. CLINVAR