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Variant interpretation report

BRCA2 c.5350_5351del, p.(Asn1784HisfsTer2)

NM_000059.4:c.5350_5351del NP_000050.3:p.(Asn1784HisfsTer2) View identifiers
Classification
Pathogenic

Variant description:

No variant summary was recorded for this case.

Five-step scale from benign to pathogenic. This variant is pathogenic. Select a step to read what it means.

Pathogenic.A pathogenic classification under the recorded framework.

In plain language

Gene-level background from the recorded interpretation.

About BRCA2

No gene-level summary was recorded for this case.

LYFE Sciences is an AI system, and it can make mistakes. Criteria may be applied incorrectly, sources may be misread, and a confident-looking classification can still be wrong. Double-check every criterion and its underlying evidence before relying on any call.
01The reasoning

How it was classified

The recorded framework is ClinGen BRCA2 VCEP v1.2.0. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.

Recorded applied criteria

The applied criteria and their strengths are shown as assessed under the stated framework.

Pathogenic evidence criteria: 4 Benign evidence criteria: 0
Pathogenic criteria applied · 4
PVS1Very strong
PVS1 · very strong

This variant is a frameshift deletion predicted to produce p.(Asn1784HisfsTer2), truncating BRCA2 shortly after codon 1784. In the ENIGMA BRCA2 specification, loss of function is an established disease mechanism, and exon 11 is designated as PVS1-applicable; therefore full-strength PVS1 is met.

PM5Strong
PM5 · strong

In the BRCA2 ENIGMA framework, PM5 is repurposed for truncating variants. This frameshift creates a premature termination codon in exon 11, and ENIGMA Table 4 assigns exon 11 a PM5_Strong (PTC) designation, so PM5 is met at Strong strength.

PP4Very strong
PP4 · very strong

This variant has a BRCA2 clinical-history likelihood ratio of 812.95 based on 42 probands in the ENIGMA-supported Li et al. dataset. This value is above the Very Strong threshold of 350, so PP4 is met at Very Strong strength.

PP5Supporting
PP5 · supporting

Expert panel Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) classified as Pathogenic.

Benign criteria applied · 0

No benign criterion marked as applied in the recorded assessment.

Recorded classification: Pathogenic

ENIGMA BRCA1 and BRCA2 Specification v1.2.0 Table 3 criteria-combination framework (CSPEC/VCEP official framework override).

02The sources

Evidence at a glance

Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.

gnomAD v4.1
gnomAD v2.1
Population frequency
41 / 1,612,540 alleles

gnomAD v4.1: 41 / 1,612,540 alleles. Recorded AF 2.54257e-05. Recorded homozygote count 0.

gnomAD v2.1

This variant is present in gnomAD v2.1 (AF= 3.20533e-05; MAF= 0.00321%, 1/31198 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 6.52912e-05; MAF= 0.00653%, 1/15316 alleles, homozygotes = 0).

gnomAD-Canada

Absent from gnomAD-Canada v1.0.

SpliceAI score
0.000 maximum delta

Recorded SpliceAI maximum delta score: 0.000. Refer to the recorded PP3/BP4 rationale for interpretation.

No listed criterion applied SpliceAI ↗
Functional evidence
Statement recorded

OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.

No listed criterion applied OncoKB ↗
COSMIC
Cancer Hotspots
Somatic evidence
1 recorded samples

This variant has previously been reported in somatic cancers (COSMIC; COSV104701329, n = 1 times).

Cancer Hotspots

This variant does not lie in a statistically significant hotspot.

For specialists

Technical detail

ACMG/AMP criteria under ClinGen BRCA2 VCEP v1.2.0, with the data and sources behind each one.

28 criteria with recorded statuses: 4 met · 4 not met · 7 not assessed · 13 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.

Met Not met Not assessed Not applicable

The BRCA2 NM_000059.4:c.5350_5351del (NP_000050.3:p.(Asn1784HisfsTer2); p.(N1784Hfs*2)) variant has been reported in ClinVar with an expert-panel Pathogenic classification, and curated somatic review resources describe it as a likely loss-of-function BRCA2 alteration.

This variant is present in population databases at low frequency, including 1/31,198 alleles in gnomAD v2.1 (AF 3.20533e-05) and 41/1,612,540 alleles in gnomAD v4.1 (AF 2.54257e-05; grpmax FAF 2.315e-05), which is too high for PM2 but far below BA1.

The variant is a frameshift deletion predicted to truncate BRCA2 after codon 1784, and the ENIGMA BRCA2 exon-level table designates exon 11 as eligible for full-strength PVS1 and PM5_Strong (PTC).

Clinical-history modeling for BRCA2 reports a likelihood ratio of 812.95 from 42 probands, exceeding the ENIGMA Very Strong PP4 threshold of 350; SpliceAI shows no separate splice signal (max delta 0.00).

Met · 4

PVS1 Very strongThis variant is a frameshift deletion predicted to produce p.(Asn1784HisfsTer2), truncating BRCA2 shortly after codon 1784. In the ENIGMA BRCA2 specification, loss of function is an established disease mechanism, and exon 11 is designated as PVS1-applicable; therefore full-strength PVS1 is met. Details ▾Hide ▴
Rule
ENIGMA BRCA2 PVS1 for null variants in a gene with established loss-of-function mechanism; exon 11 is PVS1-applicable.
Evidence considered
  • NM_000059.4:c.5350_5351del predicts NP_000050.3:p.(Asn1784HisfsTer2)
  • BRCA2 exon 11
  • ENIGMA Table 4 marks exon 11 as PVS1
Sources
cspec ↗vcep_specifications_table4_v1_2_2024_11_18pvs1_gene_contextpvs1_variant_assessment
PM5 StrongIn the BRCA2 ENIGMA framework, PM5 is repurposed for truncating variants. This frameshift creates a premature termination codon in exon 11, and ENIGMA Table 4 assigns exon 11 a PM5_Strong (PTC) designation, so PM5 is met at Strong strength. Details ▾Hide ▴
Rule
ENIGMA BRCA2 PM5_PTC applies to qualifying truncating variants by exon-level assignment in Table 4.
Evidence considered
  • Variant is a PTC-generating frameshift
  • BRCA2 exon 11 is annotated PM5_Strong (PTC)
Sources
cspec ↗vcep_specifications_table4_v1_2_2024_11_18pm5_candidates
PP4 Very strongThis variant has a BRCA2 clinical-history likelihood ratio of 812.95 based on 42 probands in the ENIGMA-supported Li et al. dataset. This value is above the Very Strong threshold of 350, so PP4 is met at Very Strong strength. Details ▾Hide ▴
Rule
ENIGMA PP4_VeryStrong for combined clinical-history LR ≥350.
Evidence considered
  • HGVS_Nucleotide c.5350_5351delAA
  • LR 812.9481905745328
  • N_Probands 42
Sources
vcep_pmid_31853058_brca2_clinical_history_lrPMID:31853058 ↗cspec ↗
PP5 SupportingExpert panel Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) classified as Pathogenic. Details ▾Hide ▴
Rule
Criterion marked not applicable in ENIGMA BRCA2 specification.
Evidence considered
  • Framework marks PP5 not applicable
  • ClinVar expert panel classification
Sources

Not met · 4 · evaluated, threshold not reached

PM2 This variant is not absent from population databases. It is present in gnomAD v2.1 at 1/31,198 alleles (AF 3.20533e-05) and in gnomAD v4.1 at 41/1,612,540 alleles (AF 2.54257e-05), so PM2 is not met. Details ▾Hide ▴
Rule
ENIGMA PM2_Supporting requires absence from controls in gnomAD.
Evidence considered
  • gnomAD v2.1 AF 3.20533e-05
  • gnomAD v4.1 AF 2.54257e-05
Sources
BA1 Population frequency is well below the BA1 threshold. gnomAD v4.1 shows a grpmax FAF of 2.315e-05, which is far below the BRCA2 BA1 threshold of 0.001, and gnomAD v2.1 does not show evidence of a high-frequency founder or non-founder signal. BA1 is not met. Details ▾Hide ▴
Rule
ENIGMA BA1 requires FAF >0.1% in the specified population dataset.
Evidence considered
  • gnomAD v4.1 grpmax FAF 2.315e-05
  • BA1 threshold 0.001
Sources
BS1 Available population data do not support BS1. gnomAD v4.1 shows a grpmax FAF of 2.315e-05, which is below the Strong threshold of 0.0001, and no framework-qualifying benign population signal was identified for this variant. BS1 is not met. Details ▾Hide ▴
Rule
ENIGMA BS1 requires qualifying FAF above benign thresholds.
Evidence considered
  • gnomAD v4.1 grpmax FAF 2.315e-05
  • BS1 Strong threshold 0.0001
Sources
BP5 The available multifactorial clinical-history evidence does not support BP5. The BRCA2 likelihood ratio is 812.95, which is far above the benign BP5 threshold of 0.48 and instead supports pathogenicity. Details ▾Hide ▴
Rule
ENIGMA BP5 applies only when combined clinical likelihood ratios support a benign direction.
Evidence considered
  • LR 812.9481905745328
  • BP5 benign threshold 0.48
Sources
vcep_pmid_31853058_brca2_clinical_history_lrPMID:31853058 ↗cspec ↗

Not assessed · 7 · no assessment recorded

PS3 No variant-specific calibrated functional study assigning PS3 for this variant was identified. General BRCA2 loss-of-function literature supports disease mechanism but does not by itself establish PS3 for this specific variant. Details ▾Hide ▴
Rule
Apply PS3 only from variant-specific well-established functional evidence under ENIGMA Table 9/Figure 1C.
Evidence considered
  • No exact Table 9 entry identified for NM_000059.4:c.5350_5351del
Still missing
  • No variant-specific PS3-calibrated assay result identified.
Sources
vcep_specifications_table9_v1_2_2024_11_18oncokb ↗PMID:10570174 ↗PMID:11239455 ↗PMID:22193408 ↗
PS4 The variant has been reported clinically, but no qualifying case-control study demonstrating a significant enrichment in affected individuals with p-value ≤0.05 and odds ratio ≥4 was identified. PS4 is not assessed from the available evidence. Details ▾Hide ▴
Rule
ENIGMA PS4 requires statistically significant case-control enrichment.
Evidence considered
  • ClinVar reports pathogenic submissions including expert panel review
Still missing
  • No qualifying BRCA2-specific case-control dataset for this exact variant identified.
Sources
PM3 No evidence was identified showing this variant in trans with another BRCA2 variant in an individual with phenotype consistent with BRCA2-related Fanconi anemia. PM3 is not assessed. Details ▾Hide ▴
Rule
ENIGMA PM3 applies only to qualifying recessive Fanconi anemia observations.
Still missing
  • No BRCA2-related Fanconi anemia phase/phenotype data identified.
Sources
PP1 No quantitative co-segregation data were identified for this variant, so PP1 cannot be assessed from the available evidence. Details ▾Hide ▴
Rule
ENIGMA PP1 requires quantitative co-segregation likelihood ratios.
Still missing
  • No segregation likelihood-ratio data identified.
Sources
BS2 No qualifying observations in individuals lacking features of BRCA2-related Fanconi anemia were identified to support BS2. This criterion is not assessed. Details ▾Hide ▴
Rule
ENIGMA BS2 requires specific point-based observations in the absence of recessive disease features.
Still missing
  • No BS2 point-based proband data identified.
Sources
BS3 No variant-specific calibrated functional study showing no damaging effect was identified for this variant. BS3 is not assessed. Details ▾Hide ▴
Rule
Apply BS3 only from variant-specific well-established benign functional evidence under ENIGMA Table 9/Figure 1C.
Evidence considered
  • No exact Table 9 benign functional entry identified
Still missing
  • No exact benign functional assay result identified in Table 9 for this variant.
Sources
vcep_specifications_table9_v1_2_2024_11_18
BS4 No quantitative lack-of-segregation likelihood-ratio data were identified for this variant, so BS4 cannot be assessed. Details ▾Hide ▴
Rule
ENIGMA BS4 requires quantitative lack-of-segregation evidence.
Still missing
  • No BS4 likelihood-ratio segregation dataset identified.
Sources
Not applicable · 13· recorded as not applicable Show reasons ▾Hide reasons ▴
PS1 N/AThis is a frameshift truncating variant, not a missense substitution or alternate variant with the same established splicing effect as a reference pathogenic variant. PS1 is therefore not applicable. Details ▾Hide ▴
Rule
ENIGMA PS1 applies to qualifying missense or same-splice-effect comparisons.
Evidence considered
  • Variant consequence is frameshift
Sources
PS2 VCEPThe BRCA2 specification does not use PS2 for this framework, so this criterion is not applicable. Details ▾Hide ▴
VCEP rule
Criterion marked not applicable in ENIGMA BRCA2 specification.
Evidence considered
  • Framework marks PS2 not applicable
Sources
PM1 VCEPPM1 is not used in the BRCA2 ENIGMA framework for this variant class. Details ▾Hide ▴
VCEP rule
Criterion marked not applicable in ENIGMA BRCA2 specification.
Evidence considered
  • Framework marks PM1 not applicable
Sources
PM4 VCEPPM4 is not used in the BRCA2 ENIGMA framework, so this criterion is not applicable. Details ▾Hide ▴
VCEP rule
Criterion marked not applicable in ENIGMA BRCA2 specification.
Evidence considered
  • Framework marks PM4 not applicable
Sources
PM6 VCEPThe BRCA2 specification does not use PM6 in this framework, so this criterion is not applicable. Details ▾Hide ▴
VCEP rule
Criterion marked not applicable in ENIGMA BRCA2 specification.
Evidence considered
  • Framework marks PM6 not applicable
Sources
PP2 VCEPPP2 is not used in the BRCA2 ENIGMA framework, so this criterion is not applicable. Details ▾Hide ▴
VCEP rule
Criterion marked not applicable in ENIGMA BRCA2 specification.
Evidence considered
  • Framework marks PP2 not applicable
Sources
PP3 N/APP3 in the BRCA2 specification is used for qualifying missense, in-frame, or non-canonical splice-impact variants. This variant is a frameshift deletion, and SpliceAI shows no separate splice signal (max delta 0.00), so PP3 is not applicable. Details ▾Hide ▴
Rule
ENIGMA PP3 applies to specified missense/in-frame/splicing contexts, not to this frameshift truncating variant.
Evidence considered
  • Frameshift variant class
  • SpliceAI max delta score 0.00
Sources
BP1 N/ABP1 in this framework applies to qualifying silent, missense, or in-frame variants outside clinically important domains. This variant is a frameshift truncating variant, so BP1 is not applicable. Details ▾Hide ▴
Rule
ENIGMA BP1 applies only to specified non-truncating variant classes.
Evidence considered
  • Variant consequence is frameshift
Sources
BP2 VCEPBP2 is not used in the BRCA2 ENIGMA framework, so this criterion is not applicable. Details ▾Hide ▴
VCEP rule
Criterion marked not applicable in ENIGMA BRCA2 specification.
Evidence considered
  • Framework marks BP2 not applicable
Sources
BP3 VCEPBP3 is not used in the BRCA2 ENIGMA framework, so this criterion is not applicable. Details ▾Hide ▴
VCEP rule
Criterion marked not applicable in ENIGMA BRCA2 specification.
Evidence considered
  • Framework marks BP3 not applicable
Sources
BP4 N/ABP4 in the BRCA2 specification applies to qualifying missense, in-frame, silent, or intronic variants with no predicted impact. Although SpliceAI predicts no significant splice effect (max delta 0.00), this variant is a frameshift truncating deletion, so BP4 is not applicable. Details ▾Hide ▴
Rule
ENIGMA BP4 applies only to specified non-truncating variant classes.
Evidence considered
  • Frameshift variant class
  • SpliceAI max delta score 0.00
Sources
BP6 VCEPBP6 is not used in the BRCA2 ENIGMA framework, so this criterion is not applicable. Details ▾Hide ▴
VCEP rule
Criterion marked not applicable in ENIGMA BRCA2 specification.
Evidence considered
  • Framework marks BP6 not applicable
Sources
BP7 N/ABP7 applies to qualifying silent or intronic variants, and in some RNA-only contexts, not to a frameshift truncating deletion. BP7 is therefore not applicable. Details ▾Hide ▴
Rule
ENIGMA BP7 applies only to specified silent/intronic or RNA-only contexts.
Evidence considered
  • Variant consequence is frameshift
Sources

Identifiers

Gene
BRCA2
Transcript
NM_000059.4
Coding (HGVS c.)
NM_000059.4:c.5350_5351del
Protein (HGVS p.)
NP_000050.3:p.(Asn1784HisfsTer2)
GRCh38
chr13:32339699 CAA>C
GRCh37
chr13:32913836 CAA>C
ClinVar
37959, 91732
COSMIC
COSV104701329

Gene diagram

Every interpreted variant in BRCA2, mapped onto the exon structure of NM_000059.4. Select a row to find it on the plot.

BRCA2NM_000059.4
Fetching transcript structure from UCSC…
gnomAD v4.1 41 / 1,612,540 alleles AF 2.54e-05 · 0 homozygotes · FAF 2.32e-05
gnomAD v2.1 1 / 31,198 alleles AF 3.21e-05 · 0 homozygotes
gnomAD-Canada v1.0 Allele count data not recorded

By genetic ancestry

gnomAD v4.1

AF 2.5e-05 · 41 / 1,612,540 alleles · 0 hom · FAF 2.3e-05
Remaining individuals3 / 62,434 4.8e-05
European (non-Finnish)37 / 1,179,132 3.1e-05
African/African American1 / 74,774 1.3e-05
0 alternate alleles recorded in 7 other groups: Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish.

gnomAD v2.1

AF 3.2e-05 · 1 / 31,198 alleles · 0 hom
European (non-Finnish)1 / 15,316 6.5e-05
0 alternate alleles recorded in 7 other groups: African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian.

Statements

gnomAD v4.1

This variant is present in gnomAD v4.1 (AF= 2.54257e-05; MAF= 0.00254%, 41/1612540 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 4.80507e-05; MAF= 0.00481%, 3/62434 alleles, homozygotes = 0); grpmax FAF= 2.315e-05.

gnomAD v2.1

This variant is present in gnomAD v2.1 (AF= 3.20533e-05; MAF= 0.00321%, 1/31198 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 6.52912e-05; MAF= 0.00653%, 1/15316 alleles, homozygotes = 0).

gnomAD-Canada

Absent from gnomAD-Canada v1.0.

SpliceAI and Pangolin

SpliceAI acceptor lossat -62 bp
0.000
SpliceAI acceptor gainat -178 bp
0.000
SpliceAI donor lossat +170 bp
0.000
SpliceAI donor gainat -79 bp
0.000
Pangolin splice lossmagnitude shown
-0.050
Pangolin splice gain
0.010

Other predictors

REVEL
Not available
BayesDel
Not available

How the predictions were used

PP3 N/APP3 in the BRCA2 specification is used for qualifying missense, in-frame, or non-canonical splice-impact variants. This variant is a frameshift deletion, and SpliceAI shows no separate splice signal (max delta 0.00), so PP3 is not applicable. Details ▾Hide ▴
Rule
ENIGMA PP3 applies to specified missense/in-frame/splicing contexts, not to this frameshift truncating variant.
Evidence considered
  • Frameshift variant class
  • SpliceAI max delta score 0.00
Sources
BP4 N/ABP4 in the BRCA2 specification applies to qualifying missense, in-frame, silent, or intronic variants with no predicted impact. Although SpliceAI predicts no significant splice effect (max delta 0.00), this variant is a frameshift truncating deletion, so BP4 is not applicable. Details ▾Hide ▴
Rule
ENIGMA BP4 applies only to specified non-truncating variant classes.
Evidence considered
  • Frameshift variant class
  • SpliceAI max delta score 0.00
Sources
BP7 N/ABP7 applies to qualifying silent or intronic variants, and in some RNA-only contexts, not to a frameshift truncating deletion. BP7 is therefore not applicable. Details ▾Hide ▴
Rule
ENIGMA BP7 applies only to specified silent/intronic or RNA-only contexts.
Evidence considered
  • Variant consequence is frameshift
Sources

Statement

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).

9 paper records listed. No publication is explicitly linked to an applied criterion in the recorded metadata. None of the listed paper records explicitly indicates that the variant is named.

Recorded publications

  • Truncated BRCA2 is cytoplasmic: implications for cancer-linked mutations.
    No paper-specific finding is recorded.
    PMID 10570174 ↗
  • BRCA2 is required for homology-directed repair of chromosomal breaks.
    No paper-specific finding is recorded.
    PMID 11239455 ↗
  • A new mutation of BRCA2 gene in an Italian healthy woman with familial breast cancer history.
    No paper-specific finding is recorded.
    PMID 20878484 ↗
  • BRCA1 and BRCA2: different roles in a common pathway of genome protection.
    No paper-specific finding is recorded.
    PMID 22193408 ↗
  • A comprehensive focus on global spectrum of BRCA1 and BRCA2 mutations in breast cancer.
    No paper-specific finding is recorded.
    PMID 24312913 ↗
  • The contribution of germline BRCA1 and BRCA2 mutations to familial ovarian cancer: no evidence for other ovarian cancer-susceptibility genes.
    Gayther SA et al. · 1999
    No paper-specific finding is recorded.
    PMID 10486320 ↗
  • Characterization of BRCA1 and BRCA2 deleterious mutations and variants of unknown clinical significance in unilateral and bilateral breast cancer: the WECARE study.
    No paper-specific finding is recorded.
    PMID 20104584 ↗
  • Mutations in 12 genes for inherited ovarian, fallopian tube, and peritoneal carcinoma identified by massively parallel sequencing.
    Walsh T et al. · 2011
    No paper-specific finding is recorded.
    PMID 22006311 ↗
  • Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
    No paper-specific finding is recorded.
    PMID 28492532 ↗

Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.

All source links

Statements for reports

The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.

gnomAD v4.1

This variant is present in gnomAD v4.1 (AF= 2.54257e-05; MAF= 0.00254%, 41/1612540 alleles, homozygotes = 0) and has highest observed frequency in the Remaining individuals population (AF= 4.80507e-05; MAF= 0.00481%, 3/62434 alleles, homozygotes = 0); grpmax FAF= 2.315e-05.

gnomAD v2.1

This variant is present in gnomAD v2.1 (AF= 3.20533e-05; MAF= 0.00321%, 1/31198 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 6.52912e-05; MAF= 0.00653%, 1/15316 alleles, homozygotes = 0).

gnomAD-Canada

Absent from gnomAD-Canada v1.0.

ClinVar

This variant has been reported in ClinVar as Pathogenic (35 clinical laboratories) and as Uncertain significance (1 clinical laboratory) and as Pathogenic by Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) (expert panel). (ClinVarID = 37959)

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).

Functional

OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.

Somatic

This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV104701329, n = 1 times).

Cancer Hotspots

This variant does not lie in a statistically significant hotspot.