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BRCA2
Final classification
Benign
BRCA2 c.5218_5223del · p.Leu1740_Ser1741del
BRCA2

NM_000059.3:c.5218_5223del (p.Leu1740_Ser1741del) is an in-frame deletion of 6 nucleotides in BRCA2 exon 11, removing two amino acids (Leu1740 and Ser1741) from a region between BRC repeats 5 and 6, outside the ENIGMA-defined clinically important functional domains.

Gene
BRCA2
Transcript
NM_000059.3
HGVS · transcript:coding
NM_000059.3:c.5218_5223del
Consequence
N/A
GRCh38
chr13:32339571 ATTTAAG>A
GRCh37
chr13:32913708 ATTTAAG>A
Basis ENIGMA BRCA2 Table 3 combining rules applied to adjudicated criteria. Two Strong Benign criteria are met: BS1_Strong (gnomAD grpmax FAF = 0.0106% exceeds ENIGMA BS1 Strong threshold of >0.01%) and BP1_Strong (in-frame deletion p.Leu1740_Ser1741del outside clinically important functional domains with SpliceAI max delta = 0.00, no splicing impact). The ENIGMA Table 3 benign rule 'Strong (Benign) >= 2' is satisfied. No pathogenic criteria are met, so there is no conflicting evidence to adjudicate.
ENIGMA BRCA2 Table 3 combining rules applied to adjudicated criteria. Two Strong Benign criteria are met: BS1_Strong (gnomAD grpmax FAF = 0.0106% exceeds ENIGMA BS1 Strong threshold of >0.01%) and BP1_Strong (in-frame deletion p.Leu1740_Ser1741del outside clinically important functional domains with SpliceAI max delta = 0.00, no splicing impact). The ENIGMA Table 3 benign rule 'Strong (Benign) >= 2' is satisfied. No pathogenic criteria are met, so there is no conflicting evidence to adjudicate.
Classification rationale
BS1BP1 Benign
BRCA2 c.5218_5223del

NM_000059.3:c.5218_5223del (p.Leu1740_Ser1741del) is an in-frame deletion of 6 nucleotides in BRCA2 exon 11, removing two amino acids (Leu1740 and Ser1741) from a region between BRC repeats 5 and 6, outside the ENIGMA-defined clinically important functional domains.1 The variant is present in gnomAD population databases at a grpmax filter allele frequency of 0.0106% (FAF = 0.000106) in gnomAD v2.1 exomes, exceeding the ENIGMA BS1 Strong threshold of > 0.01% (FAF > 0.0001). Highest subpopulation frequency is in East Asians (AF = 0.030%, 6/19,916 alleles). No homozygotes observed.2 As an in-frame deletion located outside the ENIGMA-defined clinically important functional domains (PALB2 binding aa 10–40; DNA binding aa 2481–3186) with no splicing impact predicted (SpliceAI max delta = 0.00), ENIGMA BP1_Strong is met: in-frame deletion outside a clinically important domain without splicing prediction.3 Clinical-history likelihood ratio from Li et al. 2020 (PMID:31853058) is 0.77 (8 probands), falling in the neutral zone. Neither PP4 nor BP5 is applicable.4 This variant has been reported in ClinVar as Uncertain significance by 9 clinical laboratories and Likely benign by 1 clinical laboratory (ClinVar Variation ID: 51824; review status: criteria provided, single submitter). No expert panel classification exists.5 No functional studies, case-control data, segregation data, or variant-specific publications were identified for this variant. Five publications were reviewed in full text; none mention NM_000059.3:c.5218_5223del. Applying the ENIGMA Table 3 combining rules: two Strong Benign criteria (BS1 + BP1) satisfy the Benign classification threshold (Strong Benign ≥ 2). This variant is classified as BENIGN.6

BS1 + BP1 Benign
4 PMID:31853058 ↗vcep_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 · 2 applied · 13 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
BS1 strong Benign
The gnomAD v2.1 exome grpmax filter allele frequency (FAF) is 0.000106 (0.0106%), which exceeds the ENIGMA BS1 Strong threshold of FAF > 0.01% (FAF > 0.0001) in non-cancer, non-founder populations. This is observed primarily in the East Asian subpopulation (6/19,916 alleles, AF = 0.030%).
gnomAD v2.1 exome grpmax FAF = 0.00010642 (> 0.0001 ENIGMA BS1 Strong threshold)7 total alleles in gnomAD v2.1 (280116 alleles)
BP1 strong Benign
This is an in-frame deletion (p.Leu1740_Ser1741del) located outside the two ENIGMA-defined clinically important functional domains (PALB2 binding aa 10–40; DNA binding aa 2481–3186). SpliceAI predicts no splicing impact (max delta = 0.00, ≤ 0.1). ENIGMA BP1_Strong criteria are satisfied: in-frame deletion outside a clinically important domain with no splicing predicted.
In-frame deletion at aa 1740–1741outside PALB2 binding (aa 10–40) and DNA binding (aa 2481–3186) domainsSpliceAI max delta = 0.00
Assessed · not applied
Pathogenic
PS3 No variant-specific or systematic-range functional data identified for NM_000059.3:c.5218_5223del.
PS4 No case-control study demonstrating significantly increased prevalence of this variant in affected individuals versus controls has been identified.
PM2 ENIGMA PM2 (Supporting) requires absence from gnomAD controls.
PP1 No co-segregation data available for this variant.
PP3 This in-frame deletion (p.Leu1740_Ser1741del) lies outside the two ENIGMA-defined clinically important functional domains (BRCA2 PALB2 binding domain aa 10–40; BRCA2 DNA binding domain aa 2481–3186).
PP4 Clinical-history likelihood ratio (LR) from Li et al.
Benign
BA1 ENIGMA BA1 (Stand Alone) requires filter allele frequency (FAF) > 0.1% (FAF > 0.001) in gnomAD non-cancer populations.
BS2 ENIGMA BS2 requires observation of the variant in trans with a pathogenic variant in the absence of Fanconi Anemia phenotype, scored via a points system (Specifications Table 8).
BS3 No well-established functional studies demonstrate a neutral effect for this variant.
BS4 No lack-of-segregation data available for this variant.
BP4 ENIGMA BP4 applies only to missense or in-frame variants located inside a clinically important functional domain with no predicted impact (BayesDel ≤ 0.18 and SpliceAI ≤ 0.1).
BP5 Clinical-history likelihood ratio (LR) from Li et al.
BP7 ENIGMA BP7 applies to (a) intronic/silent variants with mRNA assay evidence of no splicing impact (BP7_Strong RNA), or (b) silent variants inside a clinically important domain if BP4 is met (BP7_Supporting).
N/A · 12 PVS1 · PS1 · PS2 · PM1 · PM4 · PM5 · PM6 · PP2 · PP5 · BP2 · BP3 · 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= 6.21374e-06; MAF= 0.00062%, 10/1609336 alleles, homozygotes = 0) and has highest observed frequency in the East Asian population (AF= 0.000111562; MAF= 0.01116%, 5/44818 alleles, homozygotes = 0); grpmax FAF= 4.35e-05.
v2.1
This variant is present in gnomAD v2.1 (AF= 2.49896e-05; MAF= 0.00250%, 7/280116 alleles, homozygotes = 0) and has highest observed frequency in the East Asian population (AF= 0.000301265; MAF= 0.03013%, 6/19916 alleles, homozygotes = 0); grpmax FAF= 0.00010642.
🇨🇦 CA
Not available in gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.00062% · 10 / 1,609,336
0 hom · FAF 0.0043%
East Asian
5 / 44,818
0.011%
South Asian
5 / 90,458
0.0055%
+ 8 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, Middle Eastern, Ashkenazi Jewish, African/African American, European (non-Finnish))
gnomAD v2.1
0.0025% · 7 / 280,116
0 hom · FAF 0.011%
East Asian
6 / 19,916
0.03%
South Asian
1 / 29,992
0.0033%
+ 6 not observed (African/African American, Admixed American, Ashkenazi Jewish, European (Finnish), European (non-Finnish), Remaining individuals)
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 (9 clinical laboratories) and as Likely benign (1 clinical laboratory). (ClinVarID = 51824)
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 · 5 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
30702160 ↗ Germline variation in BRCA1/2 is highly ethnic-specific: Evidence from over 30,000 Chinese hereditary breast and ovarian cancer patients. CLINVAR
36627197 ↗ Profiling of the genetic features of Chinese patients with gastric cancer with HRD germline mutations in a large-scale retrospective study. CLINVAR
18779604 ↗ Performance of BRCA1/2 mutation prediction models in Asian Americans. CLINVAR
26187060 ↗ Comprehensive spectrum of BRCA1 and BRCA2 deleterious mutations in breast cancer in Asian countries. CLINVAR