The BRCA2 NM_000059.4:c.8524C>T (NP_000050.3:p.(Arg2842Cys)) missense variant has previously been reported in somatic cancers (COSMIC; COSV66450665, n = 21 times). Based on available guidelines, this variant is considered to be a Variant of Uncertain Significance (VUS).
Five-step scale from benign to pathogenic. This variant is uncertain. Select a step to read what it means.
This variantScenario
BenignPathogenic
Uncertain.The recorded classification is uncertain significance.
In plain language
Gene-level background from the recorded interpretation.
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About BRCA2
BRCA2 encodes a DNA repair protein that maintains genome stability by repairing double-strand breaks through homologous recombination and by protecting DNA replication forks. It acts as a tumor suppressor, and inherited loss-of-function changes cause hereditary breast and ovarian cancer syndrome, with elevated lifetime risks of breast, ovarian, prostate, and pancreatic cancers; biallelic changes cause Fanconi anemia complementation group D1. Reduced or altered BRCA2 activity is implicated in multiple tumor types, and PARP inhibitors are an approved treatment for BRCA2-associated ovarian and breast cancers.
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01The reasoning
How it was classified
The recorded framework is ClinGen BRCA2 VCEP v1.2. 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.
Met at Supporting: BayesDel no-AF 0.371621 meets the ENIGMA BRCA2 PP3 protein-impact threshold of >=0.30 in the DNA-binding domain.
Benign criteria applied · 0
No benign criterion marked as applied in the recorded assessment.
Recorded classification: Uncertain significance
VUS: PP3 (supporting) is the only met criterion and does not satisfy an ENIGMA BRCA2 V1.2 classification combination.
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
64 / 1,613,762 alleles
gnomAD v4.1: 64 / 1,613,762 alleles. Recorded AF 3.96589e-05. Recorded homozygote count 0.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 1.06237e-05; MAF= 0.00106%, 3/282388 alleles, homozygotes = 0) and has highest observed frequency in the European (Finnish) population (AF= 7.96305e-05; MAF= 0.00796%, 2/25116 alleles, homozygotes = 0).
ACMG/AMP criteria under ClinGen BRCA2 VCEP v1.2, with the data and sources behind each one.
28 criteria with recorded statuses: 1 met · 9 not met · 4 not assessed · 14 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
All three requested criteria are not applicable under the ENIGMA BRCA2 V1.2 rules: the variant is missense, PM4 and BP3 are explicitly marked Do not use, and PVS1 is restricted to specified null-variant classes.
Under ENIGMA BRCA2 V1.2, PM1, PM5, and PP2 are explicitly not used; PS1 is not met because no VCEP-established pathogenic same-amino-acid reference variant was identified; BP1 is not met because Arg2842 lies inside the defined DNA-binding domain despite SpliceAI max delta 0.051.
For both functional criteria, the explicit ENIGMA BRCA2 Table 9 pre-assignment of None/N/A governs the adjudication and outranks independent threshold calculations.
The available assay evidence is discordant, and the VCEP reserves PS3 and BS3 for protein-function evidence rather than RNA-only splicing results.
The phenotype/prevalence group yields no applicable positive or negative code: PS4 lacks the required matched case-control statistics, PP4 and BP5 are not applicable for the exact Li et al. LR of 0.6383007708778127, and PP5/BP6 are prohibited by the ENIGMA specification.
PP3 is met at Supporting strength through the VCEP's BayesDel protein-impact path; BP4 is not met because its required BayesDel no-impact condition fails; BP7 is not applicable to this missense variant inside the DNA-binding domain.
The variant is rare but present in both governing non-cancer gnomAD datasets, so PM2 is not met.
Available frequencies do not meet ENIGMA BA1 or BS1 FAF thresholds; raw subgroup AF is not substituted for missing FAF.
BS2 is not assessed because gnomAD homozygote counts do not replace the VCEP-required phenotyped individual-level Table 8 evidence.
No criteria match.
Met · 1
PP3SupportingVCEPMet at Supporting: BayesDel no-AF 0.371621 meets the ENIGMA BRCA2 PP3 protein-impact threshold of >=0.30 in the DNA-binding domain.
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Reasoning
The variant is missense p.Arg2842Cys and lies in the BRCA2 DNA-binding domain (aa 2481-3186), a VCEP-defined potentially clinically important functional domain. The governing ENIGMA rule permits PP3 for a missense variant in this domain when BayesDel no-AF is at least 0.30. The variant-specific BayesDel no-AF score is 0.371621, so the protein-impact path meets PP3 at Supporting strength. The SpliceAI max delta score is 0.051, below the VCEP PP3 splice threshold of 0.2; therefore the splice-prediction path does not contribute, and the same prediction is not double-counted. The VCEP Table 9 entry for c.8524C>T assigns no PS3/BS3 code and is not used as a substitute for the named BayesDel rule.
VCEP rule
Apply PP3 for missense or in-frame insertion, deletion or delins variants inside a (potentially) clinically important functional domain and predicted impact via protein change (BayesDel predicted Impact). ... Apply PP3 for predicted splicing (SpliceAI ≥0.2) for silent, missense/in-frame (irrespective of location in clinically important functional domain) and for intronic variants outside of the donor and acceptor ±1,2 positions. ... Missense Predictions (BayesDel no AF) ... BRCA2: ... Impact ≥0.30
Evidence considered
ENIGMA Specifications v1.2, PP3 rule: missense variants inside the BRCA2 DNA-binding domain aa 2481-3186 qualify through the protein path when BayesDel no-AF is >=0.30, or through the splice path when SpliceAI is >=0.2.
ENIGMA Supplementary Tables v1.2, DNA Binding row for BRCA2 c.8524C>T / p.(Arg2842Cys): BayesDel score 0.371621; the row identifies the variant as having conflicting functional impact.
PS1VCEPNot met: no VCEP-established pathogenic or likely pathogenic alternate change at Arg2842 is available, although c.8524C>T itself shows no routine splicing aberration.
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Reasoning
PS1 is not met. The ENIGMA rule requires the same missense substitution as a previously classified pathogenic or likely pathogenic variant caused by a different nucleotide change, with no confirmed or predicted mRNA-splicing effect. The VCEP files identify c.8524C>T/p.Arg2842Cys as a missense variant, but the same-residue alternate changes p.Arg2842His and p.Arg2842Leu are reported with indeterminate or neutral/conflicting functional classifications, not as established pathogenic reference variants. The exact c.8524C>T entry in Specifications Table 9 is assigned no PS3 or BS3 code, and the available paper extraction for PMID:23108138 describes p.R2842C/L as intermediate-activity VUS rather than pathogenic. PMID:24123850 reports no splicing aberration in the routine assay, but that satisfies only the no-splicing prerequisite and does not supply a pathogenic same-amino-acid reference variant.
VCEP rule
Same amino acid change as a previously established pathogenic variant regardless of nucleotide change. ... PS1 may be applied for a variant predicted to lead to the same missense substitution as a known pathogenic/likely pathogenic variant that is due to a different nucleotide change. ... Apply PS1, for predicted missense substitutions, where a previously classified pathogenic variant is considered to act via protein change (no confirmed or predicted effect on mRNA splicing (SpliceAI≤0.1)).
Evidence considered
Specifications V1.2 PS1 rule: PS1 may apply to the same missense substitution as a known pathogenic/likely pathogenic variant caused by a different nucleotide change, with no confirmed or predicted mRNA-splicing effect; the reference classification must use VCEP specifications.
Specifications Table 9, BRCA2 c.8524C>T / p.(Arg2842Cys): no code assigned; the row states that calibrated studies were discordant and PS3 and BS3 were not met.
SupplementaryTables V1.2, ST4 row 4182: c.8524C>T / p.(Arg2842Cys) has partial or conflicting functional impact and an indeterminate classification; same-residue p.Arg2842His is indeterminate and p.Arg2842Leu is neutral.
PMID:23108138: p.R2842C/L are described as intermediate-activity VUS and remained unclassified in the HDR-based model, not established pathogenic reference variants.
PMID:24123850 Table 1: c.8524C>T/p.Ar2842Cys had no effect in the routine splicing assay and was classified analytical Class 2.
Still missing
No exact c.8524C>T, p.Arg2842Cys, or p.R2842C entry was found in Specifications_V1.2_2024-11-18.docx.txt.
No exact c.8524C>T, p.Arg2842Cys, or p.R2842C entry was found in Appendices_V1.2_2024-11-18.docx.txt.
No exact c.8524C>T, p.Arg2842Cys, or p.R2842C entry was found in Specifications_Table4_V1.2_2024-11-18.xlsx.txt.
PS3VCEPNot met: ENIGMA Table 9 assigns no PS3 (N/A) after discordant calibrated functional results across three studies.
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Reasoning
The governing ENIGMA BRCA2 Table 9 row for NM_000059.4:c.8524C>T / p.(Arg2842Cys) assigns no PS3 code and states that the variant was evaluated in two or more calibrated studies with discordant results: functional effect similar to pathogenic controls in PMID:32444794, but intermediate between benign and pathogenic controls in PMID:29988080 and PMID:29884841. The row also records no aberration in PMID:24123850, but the VCEP specification explicitly reserves PS3/BS3 for protein-function assays and excludes splicing assays from these codes. Therefore PS3 is not met at any strength; the pre-assigned Table 9 result governs over any independent threshold calculation.
VCEP rule
Well-established in vitro or in vivo functional studies supportive of a damaging effect. Apply PS3 for assays measuring effect via protein only OR mRNA and protein combined. See Specifications Table 9 for code recommendations from calibrated published assays. Also see Figure1C and Appendix E for details. ... In consultation with members of the ClinGen SVI Group, and the ClinGen SVI Splicing Subgroup, evidence from splicing assays will be not be assigned PS3 and BS3 codes, but rather noted as additional annotation under the PVS1 or BP7 code. PS3 and BS3 codes are reserved for assigning variant impact on protein function
Evidence considered
ENIGMA BRCA2 Specifications Table 9, row c.8524C>T / p.(Arg2842Cys): assigned code None and strength N/A; the row states that two or more calibrated studies were discordant, with functional effect similar to pathogenic controls in PMID:32444794 and intermediate between benign and pathogenic controls in PMID:29988080 and PMID:29884841.
ENIGMA BRCA2 Specifications Table 9, same row: no aberration (PMID:24123850), functional assay summary 0.05, classification N/no aberration, three studies.
ENIGMA Specifications v1.2, PS3 functional-assay rule: PS3 applies to well-established in vitro or in vivo studies supportive of a damaging effect when the assay measures protein only or mRNA and protein combined, with Table 9 providing calibrated code recommendations.
ENIGMA Appendices v1.2, Appendix E: splicing-assay evidence is not assigned PS3 or BS3 and those codes are reserved for assigning variant impact on protein function.
Guidugli et al. 2013 (PMID:23108138) reports p.R2842C in an HDR assay as part of an intermediate-activity R2842C/L VUS group; this does not override the explicit Table 9 N/A assignment.
de Garibay et al. 2014 (PMID:24123850), Table 1, reports c.8524C>T with no effect in a Class-2 routine splicing assay; under the VCEP this RNA-only result is not PS3 evidence.
Still missing
Specifications_V1.2_2024-11-18.docx contains the governing general PS3 rule but no variant-specific PS3 assignment.
Appendices_V1.2_2024-11-18.docx contains the governing assay-use framework but no variant-specific PS3 assignment.
HUMU-40-1557-s001.xlsx contains no searchable entry for c.8524C>T, p.Arg2842Cys, or p.R2842C.
The Table 9 row cites PMID:29988080, PMID:29884841, and PMID:32444794, but those PMIDs are not present as source_registry keys or paper_extracts entries in this case; the governing Table 9 pre-assignment is nevertheless explicit.
PM2VCEPNot met: the variant is observed in both specified non-cancer controls datasets, at 2/236574 and 1/147686 alleles, rather than absent.
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Reasoning
PM2 is not met. ENIGMA BRCA2 VCEP v1.2 requires absence from controls in the specified gnomAD v2.1 non-cancer exome and gnomAD v3.1 non-cancer genome datasets, with regional average read depth at least 25. The variant is present in both specified non-cancer datasets: 2/236574 alleles in gnomAD v2.1 non-cancer exomes and 1/147686 alleles in gnomAD v3.1 non-cancer genomes. Because it is observed in controls, PM2 cannot be applied; the missing depth value does not change that conclusion.
VCEP rule
Absent from controls in an outbred population, from gnomAD v2.1 (non-cancer, exome only subset) and gnomAD v3.1 (non-cancer). Region around the variant must have an average read depth ≥25. See Appendix G for details.
Evidence considered
Specifications_V1.2_2024-11-18.docx, PM2: PM2 Supporting requires absence from gnomAD v2.1 non-cancer exomes and gnomAD v3.1 non-cancer genomes, with average regional read depth at least 25; a single observation in a gnomAD outbred population is not informative.
GNOMAD_V2_1_NON_CANCER: the variant is present at 2/236574 alleles (AF 8.45401e-06), with zero homozygotes.
GNOMAD_V3_1_NON_CANCER: the variant is present at 1/147686 alleles (AF 6.77112e-06), with zero homozygotes.
Still missing
The bundle does not report local average read depth or QC-filter status, but these missing values cannot restore PM2 because the variant is present in controls.
PM3VCEPNot met: the variant was homozygous, but the reported patient had isolated primary ovarian insufficiency without the VCEP-required Fanconi anemia phenotype.
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Reasoning
The ENIGMA BRCA2 PM3 rule requires a patient with a phenotype consistent with BRCA1- or BRCA2-related Fanconi anemia and co-occurrent variants in the same gene. The available exact-variant report describes homozygous c.8524C>T/p.R2842C in a consanguineous family with isolated primary ovarian insufficiency without a Fanconi anemia trait, so the required FA phenotype is not met. The VCEP Table 6 permits a homozygote as the allelic configuration, but only for a Fanconi anemia patient; therefore PM3 is not met.
VCEP rule
For recessive disorders, detected in trans with a pathogenic variant. ... Apply for patient with phenotype consistent with BRCA1- or BRCA2-related Fanconi Anemia (FA), and co-occurrent variants in the same gene. ... Phenotype is considered consistent with BRCA1- or BRCA2-related FA if: ... (i) Increased chromosome breakage (DEB, MMC, or spontaneous) and at least one clinical feature indicative of BRCA1/2-related FA, categorized under: physical features, pathology and laboratory findings, cancer diagnosis ≤5yr. ... (ii) Result unknown for chromosome breakage, and at least two clinical features indicative of BRCA1/2-related FA under at least two of the three categories: physical features, pathology and laboratory findings, cancer diagnosis ≤5yr. ... See Table 6 for approach to assign points per proband, and final PM3 code assignment based on the sum of PM3-related points.
Evidence considered
The case literature pass identifies the exact variant as homozygous c.8524C>T/p.R2842C in a consanguineous Turkish family with isolated primary ovarian insufficiency and explicitly describes the report as being without a cancer or Fanconi anaemia trait (PMID 32482800 record).
Specifications_V1.2_2024-11-18.docx.txt, Table 6: a P or LP variant in trans or homozygote receives points only in a BRCA2-related Fanconi Anemia patient; the final PM3 code is based on the summed points.
The exact variant was searched in the governing BRCA2 full-text files under c.8524C>T, p.Arg2842Cys, and p.R2842C; the governing Specifications file had no variant-specific PM3 row.
Still missing
No variant-specific PM3 entry for c.8524C>T, p.Arg2842Cys, or p.R2842C was found in Specifications_V1.2_2024-11-18.docx.txt; the decision therefore uses the governing general PM3 rule and available case evidence.
BA1VCEPNot met: maximum reported non-cancer subgroup AF is 7.96813e-05, below the ENIGMA BA1 threshold of 0.001.
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Reasoning
BA1 is not met. ENIGMA BRCA2 VCEP v1.2 requires FAF above 0.001 in a specified non-founder gnomAD population. The available gnomAD v2.1 non-cancer exome record reports AF 8.45401e-06 overall and highest subgroup AF 7.96813e-05; the gnomAD v3.1 non-cancer genome record reports highest subgroup AF 6.64099e-05 and grpmax FAF 0. Neither available value reaches 0.001. The case bundle does not report gnomAD v2.1 FAF, but the observed frequencies are far below the BA1 threshold.
VCEP rule
Above 0.001 (0.1%) ... Preferred datasets to use: ... gnomAD v2.1 non-cancer, exomes ... gnomAD v3.1 non-cancer, genomes ... Apply based on maximum filter allele frequency observed in a gnomAD non-founder population, considering exome and genome data separately.
Evidence considered
Specifications_V1.2_2024-11-18.docx, BA1: the VCEP specifies a threshold above 0.001 and prefers gnomAD v2.1 non-cancer exomes and gnomAD v3.1 non-cancer genomes.
GNOMAD_V2_1_NON_CANCER: NM_000059.4:c.8524C>T is present at 2/236574 alleles (AF 8.45401e-06), with highest reported subgroup AF 2/25100 (7.96813e-05) in European (Finnish) individuals and zero homozygotes; FAF is not reported.
GNOMAD_V3_1_NON_CANCER: the variant is present at AF 6.77112e-06, with highest reported subgroup AF 1/15058 (6.64099e-05) in Admixed American individuals and grpmax FAF 0.
Still missing
The gnomAD v2.1 non-cancer exome record does not report a FAF value or local read depth; no available frequency approaches the BA1 threshold.
BS1VCEPNot met: gnomAD v3.1 non-cancer grpmax FAF is 0, while gnomAD v2.1 reports no FAF for its highest raw subgroup AF of 7.96813e-05.
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Reasoning
BS1 is not met. ENIGMA BRCA2 VCEP v1.2 requires FAF above 0.0001 for BS1 Strong or above 0.00002 through 0.0001 for BS1 Supporting. The gnomAD v3.1 non-cancer record reports grpmax FAF 0, while the gnomAD v2.1 non-cancer record reports no FAF; its highest raw subgroup AF is 7.96813e-05, which cannot substitute for the VCEP FAF metric. Therefore no qualifying reported FAF establishes BS1, and the available frequencies do not establish a strong benign-frequency code.
VCEP rule
BS1 - above 0.0001 (0.01%) BS1_Supporting - >0.00002 (0.002%) to ≤ 0.0001 (0.01%). ... Apply based on maximum filter allele frequency in a gnomAD non-founder population, considering exome and genome data separately.
Evidence considered
Specifications_V1.2_2024-11-18.docx, BS1: BS1 Strong requires FAF above 0.0001 and BS1 Supporting requires FAF above 0.00002 and at most 0.0001 in the specified non-founder gnomAD populations.
GNOMAD_V2_1_NON_CANCER: the variant is present at 2/236574 alleles overall and the highest reported subgroup AF is 7.96813e-05; no FAF is reported, so this raw AF does not establish BS1 Supporting.
GNOMAD_V3_1_NON_CANCER: the highest reported subgroup AF is 6.64099e-05, but grpmax FAF is 0, below the BS1 Supporting threshold.
Still missing
The gnomAD v2.1 non-cancer exome record does not report FAF, local read depth, or QC-filter status; raw AF cannot be substituted for FAF.
BS3VCEPNot met: ENIGMA Table 9 assigns no BS3 (N/A) because calibrated functional studies produced discordant results rather than consistent benign function.
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Reasoning
The governing ENIGMA BRCA2 Table 9 row for NM_000059.4:c.8524C>T / p.(Arg2842Cys) assigns no BS3 code and states that the calibrated functional results were discordant across three studies, including pathogenic-control-like, intermediate, and no-aberration findings. The row's explicit None/N/A assignment is the governing answer. The VCEP rule requires well-established evidence of no damaging effect measured through protein only or mRNA plus protein; the cited RNA-only no-aberration result cannot independently establish BS3 under Appendix E.
VCEP rule
Well-established in vitro or in vivo functional studies shows no damaging effect on protein function. Assay measures effect via protein only OR mRNA and protein combined. See Specifications Table 9 for code recommendations from calibrated published assays. Also see Figure1C and Appendix E for details. ... In consultation with members of the ClinGen SVI Group, and the ClinGen SVI Splicing Subgroup, evidence from splicing assays will be not be assigned PS3 and BS3 codes, but rather noted as additional annotation under the PVS1 or BP7 code. PS3 and BS3 codes are reserved for assigning variant impact on protein function
Evidence considered
ENIGMA BRCA2 Specifications Table 9, row c.8524C>T / p.(Arg2842Cys): assigned code None and strength N/A; the row states that functional effect was similar to pathogenic controls in PMID:32444794 and intermediate between benign and pathogenic controls in PMID:29988080 and PMID:29884841.
ENIGMA BRCA2 Specifications Table 9, same row: no aberration (PMID:24123850), functional assay summary 0.05, classification N/no aberration, three studies; this is discordant with the other calibrated protein-function results.
ENIGMA Specifications v1.2, BS3 functional-assay rule: BS3 requires well-established in vitro or in vivo studies showing no damaging effect on protein function, with assays measuring protein only or mRNA and protein combined, and Table 9 providing calibrated code recommendations.
ENIGMA Appendices v1.2, Appendix E: splicing-assay evidence is not assigned PS3 or BS3 and those codes are reserved for assigning variant impact on protein function.
Guidugli et al. 2013 (PMID:23108138) reports p.R2842C in an HDR assay as an intermediate-activity VUS, not consistent benign function; this does not override the explicit Table 9 N/A assignment.
de Garibay et al. 2014 (PMID:24123850), Table 1, reports c.8524C>T with no effect in a Class-2 routine splicing assay; under the VCEP this RNA-only result is not BS3 evidence.
Still missing
Specifications_V1.2_2024-11-18.docx contains the governing general BS3 rule but no variant-specific BS3 assignment.
Appendices_V1.2_2024-11-18.docx contains the governing assay-use framework but no variant-specific BS3 assignment.
HUMU-40-1557-s001.xlsx contains no searchable entry for c.8524C>T, p.Arg2842Cys, or p.R2842C.
The Table 9 row cites PMID:29988080, PMID:29884841, and PMID:32444794, but those PMIDs are not present as source_registry keys or paper_extracts entries in this case; the governing Table 9 pre-assignment is nevertheless explicit.
BP1VCEPNot met: SpliceAI max delta 0.051 is within the ≤0.1 limit, but Arg2842 lies inside the ENIGMA DNA-binding domain aa 2481-3186.
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Reasoning
BP1 is not met. The VCEP requires a missense or specified in-frame variant to be outside a clinically important functional domain and to have no predicted splicing effect (SpliceAI ≤0.1). NM_000059.4:c.8524C>T produces p.Arg2842Cys at residue 2842, which is inside the ENIGMA-defined BRCA2 DNA-binding domain aa 2481-3186. The available SpliceAI max delta is 0.051, satisfying the no-splicing condition, but the required outside-domain condition is false.
VCEP rule
Apply BP1_Strong for silent substitution, missense or in-frame insertion, deletion or delins variants outside a (potentially) clinically important functional domain AND no splicing predicted (SpliceAI ≤0.1). ... (potentially) clinically important functional domains are defined as: BRCA2 PALB2 binding domain aa 10-40; BRCA2 DNA binding aa 2481-3186.
Evidence considered
Specifications V1.2 BP1 rule: BP1_Strong applies to silent, missense, or in-frame insertion/deletion/delins variants outside a clinically important functional domain and with no predicted splicing (SpliceAI ≤0.1); missense prediction is not applicable.
Specifications V1.2 defines the BRCA2 DNA-binding domain as aa 2481-3186; Arg2842 is inside the domain.
Case normalization and SupplementaryTables V1.2 identify the variant as c.8524C>T / p.Arg2842Cys at residue 2842 and label it DNA Binding.
The case SpliceAI result is max delta 0.051, below the VCEP no-splicing threshold of 0.1; PMID:24123850 also reports no effect in its routine splicing assay.
Still missing
No exact c.8524C>T, p.Arg2842Cys, or p.R2842C entry was found in Specifications_V1.2_2024-11-18.docx.txt.
No exact c.8524C>T, p.Arg2842Cys, or p.R2842C entry was found in Appendices_V1.2_2024-11-18.docx.txt.
BP4VCEPNot met: SpliceAI 0.051 is <=0.1, but BayesDel no-AF 0.371621 exceeds the ENIGMA BRCA2 BP4 no-impact cutoff of 0.18.
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Reasoning
The variant is a missense change inside the BRCA2 DNA-binding domain, so BP4 requires both no predicted protein impact and no predicted splice impact: BayesDel no-AF <=0.18 AND SpliceAI <=0.1. SpliceAI meets its benign-side threshold at 0.051, but BayesDel no-AF is 0.371621, above the BRCA2 no-impact cutoff of 0.18. Because the required conjunction fails, BP4 is not met.
VCEP rule
Apply BP4 for: ... Missense or in-frame insertion, deletion or delins variants inside a (potentially) clinically important functional domain, and no predicted impact via protein change or splicing (BayesDel predicted No Impact AND SpliceAI ≤0.1). ... Missense Predictions (BayesDel no AF) ... BRCA2: ... No impact ≤ 0.18
Evidence considered
ENIGMA Specifications v1.2, BP4 rule for missense variants inside a potentially clinically important functional domain: BayesDel no-AF <=0.18 AND SpliceAI <=0.1.
ENIGMA Supplementary Tables v1.2, DNA Binding row for BRCA2 c.8524C>T / p.(Arg2842Cys): BayesDel score 0.371621.
Variant-specific SpliceAI lookup: maximum delta score 0.051.
PS4VCEPNot assessed: no matched case-control counts, p-value, OR, or confidence interval are available to test the ENIGMA PS4 requirements.
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Reasoning
PS4 requires a matched case-control comparison with p-value ≤0.05, OR ≥4, and a lower confidence interval excluding 2.0. The ENIGMA sources were searched for c.8524C>T, p.Arg2842Cys, and p.R2842C. SupplementaryTables_V1.2_2024-11-18.xlsx lists c.8524C>T/p.Arg2842Cys in its functional/posterior tables, but it does not provide the required affected-versus-control counts, odds ratio, p-value, or confidence interval. PMID:23108138 reports p.R2842C in an intermediate HDR-activity VUS group, not a case-control comparison. PMID:24123850 reports the variant in affected hereditary breast/ovarian cancer index cases with frequency 0.0004 (N=2558 chromosomes), but no matched unaffected or population control count suitable for the required PS4 calculation. The literature_pass packet has no ai_classified_papers entry assigned PS4; its PS4 criterion index is a lead list, not verified evidence. Therefore PS4 cannot be evaluated from the available case-control data.
VCEP rule
The prevalence of the variant in affected individuals is significantly increased compared with the prevalence in controls. ... Case-control studies; p-value ≤0.05 and OR ≥4 (lower confidence interval excludes 2.0).
Evidence considered
ENIGMA BRCA2 PS4 rule: case-control studies require p-value ≤0.05 and OR ≥4, with the lower confidence interval excluding 2.0; the case dataset should be ethnicity- and country-matched to the control dataset.
SupplementaryTables_V1.2_2024-11-18.xlsx, matching c.8524C>T / p.(Arg2842Cys) rows: the variant appears in ST7/reference and posterior/functional tables, but no affected-control contingency table or PS4 statistics are supplied.
PMID:23108138, Discussion: p.R2842C/L is listed among intermediate-activity VUS; this is functional/HDR evidence, not a matched case-control comparison.
PMID:24123850, Table 1, Exon 20: c.8524C>T (p.Ar2842Cys) is listed with minor allele frequency 0.0004 among 2558 chromosomes from hereditary breast and ovarian cancer index cases; no matched control count is reported in the extracted record.
Still missing
No affected-versus-matched-control counts, case-control p-value, odds ratio, or 95% confidence interval are available for c.8524C>T/p.Arg2842Cys.
Specifications_V1.2_2024-11-18.docx.txt was searched for c.8524C>T, p.Arg2842Cys, and p.R2842C; no variant-specific PS4 case-control result was found.
SupplementaryTables_V1.2_2024-11-18.xlsx.txt was searched for c.8524C>T, p.Arg2842Cys, and p.R2842C; the matching rows do not contain the PS4 case-control statistics.
HUMU-40-1557-s001.xlsx.txt was searched for c.8524C>T, p.Arg2842Cys, and p.R2842C; no matching variant row was found.
The literature_pass.json ai_classified_papers array contains no paper classified as PS4; the separate PS4 criterion-index leads were not accompanied by extracted full-text evidence in this case.
PP1VCEPNot assessed: no quantitative co-segregation likelihood ratio, affected-relative meioses, or variant-specific PP1 segregation entry is available for applying the 2.08:1 threshold.
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Reasoning
PP1 requires multiple affected family members and a quantitative co-segregation analysis with a Bayes-score likelihood ratio. The case evidence does not provide a quantitative PP1 co-segregation LR, meioses, or a pedigree-level segregation result. Searches for c.8524C>T, p.Arg2842Cys, and p.R2842C in SupplementaryTables_V1.2_2024-11-18.xlsx.txt, Specifications_V1.2_2024-11-18.docx.txt, and HUMU-40-1557-s001.xlsx.txt found no PP1 segregation entry for this variant; the HUMU file's relevant multifactorial table has no matching row.
VCEP rule
Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease, as measured by a quantitative co-segregation analysis method. See Appendix I for details. ... Apply weight as per Bayes Score: ... PP1 - LR ≥2.08:1
Evidence considered
ENIGMA BRCA2 specification, PP1 rule: co-segregation with disease in multiple affected family members must be measured by a quantitative co-segregation analysis method; PP1 Supporting requires LR ≥2.08:1.
HUMU-40-1557-s001.xlsx, SuppT1 All Data: no matching BRCA2 c.8524C>T/p.Arg2842Cys/p.R2842C row was found; the file's SuppT2 Data Sources table was also searched for the variant notations.
SupplementaryTables_V1.2_2024-11-18.xlsx and Specifications_V1.2_2024-11-18.docx: no matching segregation/de novo entry was found for the three requested variant notations.
Still missing
No quantitative co-segregation LR or pedigree-level segregation result is provided in the case evidence.
No matching PP1 segregation entry was found in SupplementaryTables_V1.2_2024-11-18.xlsx.txt after searching c.8524C>T, p.Arg2842Cys, and p.R2842C.
No matching PP1 segregation entry was found in Specifications_V1.2_2024-11-18.docx.txt after searching c.8524C>T, p.Arg2842Cys, and p.R2842C.
No matching PP1 segregation entry was found in HUMU-40-1557-s001.xlsx.txt after searching c.8524C>T, p.Arg2842Cys, and p.R2842C.
BS2VCEPNot assessed: zero gnomAD homozygotes do not provide the phenotyped individual-level observations required for ENIGMA BS2 point assignment.
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Reasoning
BS2 is not assessed. ENIGMA BRCA2 VCEP v1.2 requires qualifying individual-level clinical or research observations and point assignment under Specification Table 8, including absence of a Fanconi anemia phenotype and age or cancer-status information. gnomAD reports zero homozygotes, but the VCEP explicitly states that frequency-database observations are not to be used for BS2 point assignment. No qualifying phenotyped individuals or Table 8 points are available.
VCEP rule
Applied in absence of features of recessive disease, namely Fanconi Anemia phenotype. See Specifications Table 8 for additional stipulations, and approach to assign points per proband, and final BS2 code assignment based on the sum of BS2-related points. See Appendix H for additional details. ... ** Apply only for phenotyped individuals from clinical or research cohorts. NOT to be applied for data used to assign frequency-based codes; we have observed that variants observed as ≥2 homozygotes in GnomAD data (assumed unaffected adults of unspecified age) are already captured by the BA1 or BS1 frequency codes.
Evidence considered
Specifications_V1.2_2024-11-18.docx, BS2 and Table 8: the code is assigned from qualifying proband-level observations and summed points, with BS2 Supporting at 1 point, Moderate at 2 points, and Strong at 4 or more points.
Specifications_V1.2_2024-11-18.docx, Table 8 footnote: homozygote points apply only for phenotyped individuals from clinical or research cohorts and are not to be applied to frequency-based database data.
GNOMAD_V2_1_NON_CANCER and GNOMAD_V3_1_NON_CANCER report zero homozygotes, but neither provides individual phenotype, age, cancer-status, phase, or Fanconi anemia information.
Still missing
No documented phenotyped clinical or research individuals with qualifying homozygosity or co-occurrence, age or cancer-status data, and absence of Fanconi anemia features.
No ENIGMA Table 8 BS2-related point total is available.
BS4VCEPNot assessed: no quantitative non-segregation likelihood ratio, affected-relative meioses, or variant-specific BS4 entry is available for applying the 0.48:1 threshold.
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Reasoning
BS4 requires lack of segregation in affected family members measured by a quantitative co-segregation analysis and an LR at or below a specified threshold. The case evidence provides no quantitative BS4 LR, pedigree-level non-segregation result, or affected-relative meioses. Searches for c.8524C>T, p.Arg2842Cys, and p.R2842C in SupplementaryTables_V1.2_2024-11-18.xlsx.txt, Specifications_V1.2_2024-11-18.docx.txt, and HUMU-40-1557-s001.xlsx.txt found no BS4 segregation entry for this variant; the HUMU file's relevant multifactorial table has no matching row.
VCEP rule
Lack of segregation in affected members of a family, as measured by a quantitative co-segregation analysis method. See Appendix I for details. ... Apply weight as per Bayes Score: ... BS4_Supporting - LR ≤0.48 to >0.23:1 ... BS4_Moderate - LR ≤0.23:1 ... BS4 - LR ≤0.05:1 ... BS4_Very strong – LR ≤0.00285:1
Evidence considered
ENIGMA BRCA2 specification, BS4 rule: lack of segregation in affected family members must be measured by a quantitative co-segregation analysis method; BS4 Supporting requires LR ≤0.48:1.
HUMU-40-1557-s001.xlsx, SuppT1 All Data: no matching BRCA2 c.8524C>T/p.Arg2842Cys/p.R2842C row was found; the file's SuppT2 Data Sources table was also searched for the variant notations.
SupplementaryTables_V1.2_2024-11-18.xlsx and Specifications_V1.2_2024-11-18.docx: no matching segregation/de novo entry was found for the three requested variant notations.
Still missing
No quantitative non-segregation LR or pedigree-level BS4 result is provided in the case evidence.
No matching BS4 segregation entry was found in SupplementaryTables_V1.2_2024-11-18.xlsx.txt after searching c.8524C>T, p.Arg2842Cys, and p.R2842C.
No matching BS4 segregation entry was found in Specifications_V1.2_2024-11-18.docx.txt after searching c.8524C>T, p.Arg2842Cys, and p.R2842C.
No matching BS4 segregation entry was found in HUMU-40-1557-s001.xlsx.txt after searching c.8524C>T, p.Arg2842Cys, and p.R2842C.
Not applicable · 14· recorded as not applicableShow reasons ▾Hide reasons ▴PVS1N/ANot applicable: c.8524C>T produces missense p.Arg2842Cys, whereas ENIGMA PVS1 applies to specified null variants such as nonsense, frameshift, splice-site, initiation-codon, or exon-deletion variants.
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Reasoning
PVS1 is not applicable because NM_000059.4:c.8524C>T is a missense variant, p.(Arg2842Cys), not a nonsense, frameshift, canonical splice-site, initiation-codon, or exon-deletion null variant. The ENIGMA rule limits PVS1 to the specified null-variant classes. The variant is recorded in the VCEP functional-assay table as c.8524C>T, p.(Arg2842Cys), confirming the missense consequence and that it is not a PVS1-type protein-terminating change.
VCEP rule
Null variant in a gene where loss of function is a known mechanism of disease.
Evidence considered
Case normalization: NM_000059.4:c.8524C>T -> NP_000050.3:p.(Arg2842Cys), a missense substitution.
Specifications Table 9, BRCA2 c.8524C>T / p.(Arg2842Cys): the variant is listed as a missense functional-assay entry, with no PS3 or BS3 code assigned.
The three requested variant notations were searched across the governing BRCA2 full-text files; exact matches were found in Specifications_Table9_V1.2_2024-11-18.xlsx.txt and SupplementaryTables_V1.2_2024-11-18.xlsx.txt, not in the PVS1 exon decision table.
Still missing
No exact c.8524C>T, p.Arg2842Cys, or p.R2842C entry was found in Specifications_V1.2_2024-11-18.docx.txt; the governing PVS1 rule was nevertheless directly available there.
No exact c.8524C>T, p.Arg2842Cys, or p.R2842C entry was found in Appendices_V1.2_2024-11-18.docx.txt.
No exact c.8524C>T, p.Arg2842Cys, or p.R2842C entry was found in Specifications_Table4_V1.2_2024-11-18.xlsx.txt.
PS2VCEPNot applicable: the ENIGMA VCEP explicitly prohibits PS2 because BRCA1/2-related cancers are relatively common and de novo predictive capacity is uncalibrated.
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Reasoning
The ENIGMA BRCA2 VCEP explicitly marks PS2 as not to be used for BRCA1/2-related cancers because those cancers occur relatively commonly and the predictive capacity of de novo occurrences has not been calibrated.
VCEP rule
De novo (paternity confirmed) in a patient with the disease and no family history. ... Do not use ... BRCA1/2-related cancers occur relatively commonly. No information to calibrate the predictive capacity of de novo occurrences.
Evidence considered
ENIGMA BRCA2 specification Table 1 marks PS2 as Do not use; the same rule is represented in the CSPEC criterion entry as applicability Not Applicable.
PM1VCEPNot applicable: residue 2842 lies in the DNA-binding domain, but ENIGMA explicitly marks PM1 Do not use and captures domain information under PP3/BP4.
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Reasoning
PM1 is not applicable because the ENIGMA BRCA2 specification explicitly marks PM1 Do not use and states that it is considered within bioinformatic analysis under PP3/BP4. Although residue 2842 lies within the VCEP-defined BRCA2 DNA-binding domain aa 2481-3186, that domain location cannot independently generate PM1 under this VCEP rule.
VCEP rule
Located in a mutational hot spot and/or critical and well-established functional domain. ... Do not use ... Considered as component of bioinformatic analysis (PP3/BP4).
Evidence considered
Specifications V1.2 PM1 row: PM1 is marked Do not use and is considered as a component of bioinformatic analysis under PP3/BP4.
Specifications V1.2 defines the BRCA2 DNA-binding domain as aa 2481-3186; Arg2842 is within this interval.
SupplementaryTables V1.2 ST4 row 4182 labels p.(Arg2842Cys) as DNA Binding.
PMID:24323938 describes the BRCA2 C-terminal DNA-binding domain as amino acids 2459-3190, consistent with the variant's domain location, but does not provide a separate PM1 route under the VCEP.
Still missing
No exact c.8524C>T, p.Arg2842Cys, or p.R2842C entry was found in Specifications_V1.2_2024-11-18.docx.txt.
No exact c.8524C>T, p.Arg2842Cys, or p.R2842C entry was found in Appendices_V1.2_2024-11-18.docx.txt.
PM4VCEPNot applicable: p.Arg2842Cys is a missense substitution with no protein-length change, and the ENIGMA specification explicitly says PM4 is not used.
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Reasoning
PM4 is not applicable under the ENIGMA BRCA2 specification: the rule addresses protein-length changes from in-frame insertions/deletions in non-repeat regions or stop-loss variants, and the specification explicitly says not to use PM4. This variant is a missense substitution, p.(Arg2842Cys), with no protein-length change.
VCEP rule
Protein length changes due to in-frame deletions/insertions in a non-repeat region or stop-loss variants. ... Do not use ... Considered as component of bioinformatic analysis (PP3/BP4).
Evidence considered
Specifications V1.2, Table 1 PM4 row: PM4 is defined for protein-length changes due to in-frame deletions/insertions in a non-repeat region or stop-loss variants, and is marked Do not use.
Case normalization identifies p.(Arg2842Cys), a missense substitution that neither inserts nor deletes protein residues and does not alter the termination codon.
Still missing
No exact c.8524C>T, p.Arg2842Cys, or p.R2842C entry was found in Specifications_V1.2_2024-11-18.docx.txt for PM4.
No exact c.8524C>T, p.Arg2842Cys, or p.R2842C entry was found in Appendices_V1.2_2024-11-18.docx.txt for PM4.
PM5N/ANot applicable: ENIGMA marks missense PM5 Do not use, and the separate PM5 route is restricted to PVS1 protein-termination-codon variants.
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Reasoning
PM5 is not applicable for this missense variant because the ENIGMA BRCA2 specification explicitly marks the missense PM5 criterion Do not use and directs this evidence to PP3/BP4. The VCEP Supplementary Tables contain same-residue alternate variants p.Arg2842His and p.Arg2842Leu, but their indeterminate or neutral/conflicting classifications do not change the VCEP prohibition on missense PM5. The separate PM5 variable-weight route is limited to protein-termination-codon variants annotated as PVS1, which this missense variant is not.
VCEP rule
Missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before. ... Do not use ... Considered as component of bioinformatic analysis (PP3/BP4). ... Protein termination codon (PTC) variant in an exon where a different proven pathogenic PTC variant has been seen before ... Use to justify additional weight for PTC variants annotated as PVS1.
Evidence considered
Specifications V1.2 PM5 row: missense change at a residue where a different pathogenic missense change has been seen before is marked Do not use and considered under PP3/BP4.
Specifications V1.2 PM5 variable-weight row: the repurposed route is for a protein termination codon variant in an exon with a different proven pathogenic PTC and is additional weight for PVS1.
SupplementaryTables V1.2 contains p.Arg2842His and p.Arg2842Leu at the same residue, with indeterminate and neutral/conflicting functional classifications, respectively; this missense evidence cannot be assigned PM5 under the VCEP.
PMID:23108138 describes the same-residue p.R2842C/L variants as intermediate-activity VUS rather than proven pathogenic variants.
Still missing
No exact c.8524C>T, p.Arg2842Cys, or p.R2842C entry was found in Specifications_V1.2_2024-11-18.docx.txt.
No exact c.8524C>T, p.Arg2842Cys, or p.R2842C entry was found in Appendices_V1.2_2024-11-18.docx.txt.
No exact c.8524C>T, p.Arg2842Cys, or p.R2842C entry was found in Specifications_Table4_V1.2_2024-11-18.xlsx.txt.
PM6VCEPNot applicable: the ENIGMA VCEP explicitly prohibits PM6 because BRCA1/2-related cancers are relatively common and de novo predictive capacity is uncalibrated.
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Reasoning
The ENIGMA BRCA2 VCEP explicitly marks PM6 as not to be used for BRCA1/2-related cancers because those cancers occur relatively commonly and the predictive capacity of de novo occurrences has not been calibrated.
VCEP rule
Confirmed de novo without confirmation of paternity and maternity. ... Do not use ... BRCA1/2-related cancers occur relatively commonly. No information to calibrate the predictive capacity of de novo occurrences.
Evidence considered
ENIGMA BRCA2 specification Table 1 marks PM6 as Do not use; the same rule is represented in the CSPEC criterion entry as applicability Not Applicable.
PP2VCEPNot applicable: ENIGMA explicitly marks PP2 Do not use because missense variants are not a common BRCA1/BRCA2 pathogenicity mechanism.
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Reasoning
PP2 is not applicable because the ENIGMA BRCA2 specification explicitly marks PP2 Do not use and states that missense variants are not a common mechanism of pathogenicity for BRCA1 and BRCA2.
VCEP rule
Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease. ... Do not use ... High frequency of benign missense variants.
Evidence considered
Specifications V1.2 PP2 row: PP2 is marked Do not use because there is a high frequency of benign missense variants and missense variants are not a common mechanism of pathogenicity for BRCA1 and BRCA2.
Still missing
No exact c.8524C>T, p.Arg2842Cys, or p.R2842C entry was found in Specifications_V1.2_2024-11-18.docx.txt.
No exact c.8524C>T, p.Arg2842Cys, or p.R2842C entry was found in Appendices_V1.2_2024-11-18.docx.txt.
PP4N/ANot applicable: Li et al. clinical-history LR 0.6383 fails the ENIGMA PP4 requirement, 0.6383007708778127 ≥ 2.08? no.
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Reasoning
ENIGMA PP4 is restricted to combined multifactorial clinical likelihood ratios. The exact BRCA2 c.8524C>T row in Li et al. 2020 Supplementary Table 4 reports LOG(LR)=-0.1949746310710907, N=5, and LR=0.6383007708778127. The governing PP4 rule requires LR ≥2.08:1 for supporting evidence, while the specification states that combined LR 1.00 to <2.08 is not informative and PP4 is not applicable. The explicit inequality is 0.6383007708778127 ≥ 2.08? no. The value is also within the benign-neutral interval described by the VCEP, but it does not meet PP4's pathogenic-direction threshold.
VCEP rule
Use ONLY to capture combined LR towards pathogenicity, based on multifactorial likelihood clinical data. ... PP4 - LR ≥2.08:1 ... Combined LR 1.00 to <2.08 is not informative (PP4 not applicable).
Evidence considered
Li et al. 2020 Supplementary Table 4, BRCA2 c.8524C>T: LOG(LR)=-0.1949746310710907, N=5, LR=0.6383007708778127.
The Li et al. paper describes a logistic-regression model using personal and family history from a large multigene-panel cohort; the VCEP permits such calibrated clinical data under PP4/BP5 only as a combined LR.
PP5VCEPNot applicable: the ENIGMA BRCA2 specification explicitly says PP5 is not used.
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Reasoning
The ENIGMA BRCA2 specification says not to use PP5. No independent PP5 assertion is made from ClinVar or another reputable source.
VCEP rule
Reputable source recently reports variant as pathogenic but the evidence is not available to the laboratory to perform an independent evaluation. ... Do not use
Evidence considered
ENIGMA BRCA2 specification Table 1 marks PP5 as Do not use.
BP2VCEPNot applicable: the ENIGMA BRCA2 specification says BP2 is not used and is applied only in the context of BS2.
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Reasoning
The ENIGMA BRCA2 specification explicitly marks BP2 as not for use and limits any application to the context of BS2. BP2 is therefore not applicable regardless of the available homozygous/co-occurrence information.
VCEP rule
Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder, or observed in cis with a pathogenic variant in any inheritance pattern ... Do not use ... Applied only in the context of BS2.
Evidence considered
Specifications_V1.2_2024-11-18.docx.txt, BP2 row: observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder, or observed in cis with a pathogenic variant in any inheritance pattern; Do not use; Applied only in the context of BS2.
BP3VCEPNot applicable: p.Arg2842Cys is not an in-frame insertion or deletion, and ENIGMA explicitly marks BP3 as not to use for BRCA2.
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Reasoning
BP3 is not applicable under the ENIGMA BRCA2 specification: it concerns in-frame deletions or insertions in a repetitive region without a known function, and the specification explicitly says not to use BP3. This variant is a missense substitution, p.(Arg2842Cys), not an in-frame insertion or deletion.
VCEP rule
In-frame deletions/insertions in a repetitive region without a known function ... Do not use ... Captured by bioinformatic tool prediction, and domain analysis.
See Appendix J.
Evidence considered
Specifications V1.2, Table 1 BP3 row: BP3 is defined for in-frame deletions/insertions in a repetitive region without a known function, and is marked Do not use.
Case normalization identifies p.(Arg2842Cys), a missense substitution rather than an in-frame insertion or deletion.
Still missing
No exact c.8524C>T, p.Arg2842Cys, or p.R2842C entry was found in Specifications_V1.2_2024-11-18.docx.txt for BP3.
No exact c.8524C>T, p.Arg2842Cys, or p.R2842C entry was found in Appendices_V1.2_2024-11-18.docx.txt for BP3.
No exact c.8524C>T, p.Arg2842Cys, or p.R2842C entry was found in PMID_22505045_Houdayer_2012_HumMutat.pdf.txt.
BP5N/ANot applicable: Li et al. clinical-history LR 0.6383 fails BP5's ≤0.48 threshold, 0.6383007708778127 ≤ 0.48? no.
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Reasoning
ENIGMA BP5 is restricted to combined multifactorial clinical likelihood ratios against pathogenicity. The exact BRCA2 c.8524C>T row in Li et al. 2020 Supplementary Table 4 reports LR=0.6383007708778127. The governing BP5 supporting rule is LR ≤0.48 to >0.23:1, while the specification states that combined LR >0.48-1.00 is not informative and BP5 is not applicable. The explicit inequality is 0.6383007708778127 ≤ 0.48? no. Therefore the value does not meet BP5.
VCEP rule
Use ONLY to capture combined LR against pathogenicity, based on multifactorial likelihood clinical data. ... BP5 - LR ≤0.48 to >0.23:1 ... Combined LR >0.48-1.00 is not informative (BP5 not applicable)
Evidence considered
Li et al. 2020 Supplementary Table 4, BRCA2 c.8524C>T: LOG(LR)=-0.1949746310710907, N=5, LR=0.6383007708778127.
ENIGMA BP5 supporting threshold: LR ≤0.48 to >0.23:1; explicit comparison: 0.6383007708778127 ≤ 0.48? no.
The VCEP states that combined LR >0.48-1.00 is not informative and BP5 is not applicable.
BP6VCEPNot applicable: the ENIGMA BRCA2 specification explicitly says BP6 is not used.
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Reasoning
The ENIGMA BRCA2 specification says not to use BP6. No independent BP6 assertion is made from ClinVar or another reputable source.
VCEP rule
Reputable source recently reports variant as benign but the evidence is not available to the laboratory to perform an independent evaluation. ... Do not use
Evidence considered
ENIGMA BRCA2 specification Table 1 marks BP6 as Do not use.
BP7N/ANot applicable: p.Arg2842Cys is a missense variant inside the BRCA2 DNA-binding domain, whereas BP7 covers silent/intronic variants or missense variants outside that domain.
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Reasoning
BP7 is not applicable because this variant is missense and lies inside the BRCA2 DNA-binding domain. The VCEP's ordinary BP7 scope covers silent variants inside a clinically important functional domain or intronic variants outside conserved donor/acceptor motif positions, and its BP7_Strong (RNA) alternative covers missense/in-frame variants only when they are located outside a potentially clinically important functional domain. This variant is p.Arg2842Cys within aa 2481-3186, so neither BP7 path applies.
VCEP rule
Apply BP7 for ... Silent variant inside a (potentially) clinically important functional domain, IF BP4 met. ... Intronic variants located outside conserved donor or acceptor motif positions (at or beyond positions +7/-21) IF BP4 met ... Apply as BP7_Strong (RNA) for intronic, silent, and missense/in-frame variants located outside a (potentially) clinically important functional domain. ... As justified in the appendices, (potentially) clinically important functional domains are defined as: BRCA2 PALB2 binding domain aa 10-40; BRCA2 DNA binding aa 2481-3186.
Evidence considered
ENIGMA Specifications v1.2, BP7 scope: silent variants inside the functional domain if BP4 is met, and intronic variants outside conserved donor/acceptor motif positions if BP4 is met.
ENIGMA Specifications v1.2, BP7_Strong (RNA) scope: mRNA-only evidence for intronic, silent, and missense/in-frame variants located outside a potentially clinically important functional domain.
Variant normalization: NM_000059.4:c.8524C>T, p.Arg2842Cys; the VCEP defines the BRCA2 DNA-binding domain as aa 2481-3186.
AF 4e-05 · 64 / 1,613,762 alleles · 0 hom · FAF 3.9e-05
Middle Eastern1 / 6,082
0.00016
European (non-Finnish)58 / 1,179,988
4.9e-05
Admixed American1 / 59,970
1.7e-05
Remaining individuals1 / 62,478
1.6e-05
European (Finnish)1 / 63,940
1.6e-05
African/African American1 / 74,854
1.3e-05
South Asian1 / 91,056
1.1e-05
0 alternate alleles recorded in 3 other groups: Amish, East Asian, Ashkenazi Jewish.
gnomAD v2.1
AF 1.1e-05 · 3 / 282,388 alleles · 0 hom
European (Finnish)2 / 25,116
8e-05
European (non-Finnish)1 / 128,764
7.8e-06
0 alternate alleles recorded in 6 other groups: African/African American, Admixed American, Ashkenazi Jewish, East Asian, Remaining individuals, South Asian.
Statements
gnomAD v4.1
This variant is present in gnomAD v4.1 (AF= 3.96589e-05; MAF= 0.00397%, 64/1613762 alleles, homozygotes = 0) and has highest observed frequency in the Middle Eastern population (AF= 0.00016442; MAF= 0.01644%, 1/6082 alleles, homozygotes = 0); grpmax FAF= 3.856e-05.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 1.06237e-05; MAF= 0.00106%, 3/282388 alleles, homozygotes = 0) and has highest observed frequency in the European (Finnish) population (AF= 7.96305e-05; MAF= 0.00796%, 2/25116 alleles, homozygotes = 0).
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
SpliceAI and Pangolin
SpliceAI acceptor lossat -36 bp
0.051
SpliceAI acceptor gainat -339 bp
0.005
SpliceAI donor lossat +108 bp
0.015
SpliceAI donor gainat +297 bp
0.000
Pangolin splice lossmagnitude shown
-0.092
Pangolin splice gain
0.011
Other predictors
REVEL
0.843
BayesDel
0.372
How the predictions were used
PP3SupportingVCEPMet at Supporting: BayesDel no-AF 0.371621 meets the ENIGMA BRCA2 PP3 protein-impact threshold of >=0.30 in the DNA-binding domain.
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Reasoning
The variant is missense p.Arg2842Cys and lies in the BRCA2 DNA-binding domain (aa 2481-3186), a VCEP-defined potentially clinically important functional domain. The governing ENIGMA rule permits PP3 for a missense variant in this domain when BayesDel no-AF is at least 0.30. The variant-specific BayesDel no-AF score is 0.371621, so the protein-impact path meets PP3 at Supporting strength. The SpliceAI max delta score is 0.051, below the VCEP PP3 splice threshold of 0.2; therefore the splice-prediction path does not contribute, and the same prediction is not double-counted. The VCEP Table 9 entry for c.8524C>T assigns no PS3/BS3 code and is not used as a substitute for the named BayesDel rule.
VCEP rule
Apply PP3 for missense or in-frame insertion, deletion or delins variants inside a (potentially) clinically important functional domain and predicted impact via protein change (BayesDel predicted Impact). ... Apply PP3 for predicted splicing (SpliceAI ≥0.2) for silent, missense/in-frame (irrespective of location in clinically important functional domain) and for intronic variants outside of the donor and acceptor ±1,2 positions. ... Missense Predictions (BayesDel no AF) ... BRCA2: ... Impact ≥0.30
Evidence considered
ENIGMA Specifications v1.2, PP3 rule: missense variants inside the BRCA2 DNA-binding domain aa 2481-3186 qualify through the protein path when BayesDel no-AF is >=0.30, or through the splice path when SpliceAI is >=0.2.
ENIGMA Supplementary Tables v1.2, DNA Binding row for BRCA2 c.8524C>T / p.(Arg2842Cys): BayesDel score 0.371621; the row identifies the variant as having conflicting functional impact.
BP4VCEPNot met: SpliceAI 0.051 is <=0.1, but BayesDel no-AF 0.371621 exceeds the ENIGMA BRCA2 BP4 no-impact cutoff of 0.18.
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Reasoning
The variant is a missense change inside the BRCA2 DNA-binding domain, so BP4 requires both no predicted protein impact and no predicted splice impact: BayesDel no-AF <=0.18 AND SpliceAI <=0.1. SpliceAI meets its benign-side threshold at 0.051, but BayesDel no-AF is 0.371621, above the BRCA2 no-impact cutoff of 0.18. Because the required conjunction fails, BP4 is not met.
VCEP rule
Apply BP4 for: ... Missense or in-frame insertion, deletion or delins variants inside a (potentially) clinically important functional domain, and no predicted impact via protein change or splicing (BayesDel predicted No Impact AND SpliceAI ≤0.1). ... Missense Predictions (BayesDel no AF) ... BRCA2: ... No impact ≤ 0.18
Evidence considered
ENIGMA Specifications v1.2, BP4 rule for missense variants inside a potentially clinically important functional domain: BayesDel no-AF <=0.18 AND SpliceAI <=0.1.
ENIGMA Supplementary Tables v1.2, DNA Binding row for BRCA2 c.8524C>T / p.(Arg2842Cys): BayesDel score 0.371621.
Variant-specific SpliceAI lookup: maximum delta score 0.051.
BP7N/ANot applicable: p.Arg2842Cys is a missense variant inside the BRCA2 DNA-binding domain, whereas BP7 covers silent/intronic variants or missense variants outside that domain.
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Reasoning
BP7 is not applicable because this variant is missense and lies inside the BRCA2 DNA-binding domain. The VCEP's ordinary BP7 scope covers silent variants inside a clinically important functional domain or intronic variants outside conserved donor/acceptor motif positions, and its BP7_Strong (RNA) alternative covers missense/in-frame variants only when they are located outside a potentially clinically important functional domain. This variant is p.Arg2842Cys within aa 2481-3186, so neither BP7 path applies.
VCEP rule
Apply BP7 for ... Silent variant inside a (potentially) clinically important functional domain, IF BP4 met. ... Intronic variants located outside conserved donor or acceptor motif positions (at or beyond positions +7/-21) IF BP4 met ... Apply as BP7_Strong (RNA) for intronic, silent, and missense/in-frame variants located outside a (potentially) clinically important functional domain. ... As justified in the appendices, (potentially) clinically important functional domains are defined as: BRCA2 PALB2 binding domain aa 10-40; BRCA2 DNA binding aa 2481-3186.
Evidence considered
ENIGMA Specifications v1.2, BP7 scope: silent variants inside the functional domain if BP4 is met, and intronic variants outside conserved donor/acceptor motif positions if BP4 is met.
ENIGMA Specifications v1.2, BP7_Strong (RNA) scope: mRNA-only evidence for intronic, silent, and missense/in-frame variants located outside a potentially clinically important functional domain.
Variant normalization: NM_000059.4:c.8524C>T, p.Arg2842Cys; the VCEP defines the BRCA2 DNA-binding domain as aa 2481-3186.
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.05). REVEL score = 0.843. BayesDel score = 0.371621.
7 paper records listed. No publication is explicitly linked to an applied criterion in the recorded metadata.
Recorded publications
A classification model for BRCA2 DNA binding domain missense variants based on homology-directed repair activity.
Guidugli L et al. · 2013
The paper explicitly lists BRCA2 p.R2842C/L as intermediate-activity VUS in an HDR assay; the authors state these variants may influence DNA binding, but the intermediate-activity VUS were not classified as pathogenic.
The remaining intermediate activity VUS R2842C/L (mouse R2763), T3033I (mouse T2952) and Y3092S (mouse Y3011S) are not located at interdomain interfaces but may influence DNA binding.
Discussion, paragraph beginning "To ascertain if a structure-function correlation exists for the pathogenic missense mutations"
Assessment of the Clinical Relevance of BRCA2 Missense Variants by Functional and Computational Approaches.
Capillary electrophoresis analysis of conventional splicing assays: IARC analytical and clinical classification of 31 BRCA2 genetic variants.
de Garibay GR et al. · 2014
The paper explicitly lists BRCA2 c.8524C>T/p.Arg2842Cys in Table 1. Its in-silico results predicted a possible de novo splice site by HSF but no effect by MaxEnt, and the routine in-vitro splicing assay found no effect and assigned analytical Class 2.
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.
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= 3.96589e-05; MAF= 0.00397%, 64/1613762 alleles, homozygotes = 0) and has highest observed frequency in the Middle Eastern population (AF= 0.00016442; MAF= 0.01644%, 1/6082 alleles, homozygotes = 0); grpmax FAF= 3.856e-05.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 1.06237e-05; MAF= 0.00106%, 3/282388 alleles, homozygotes = 0) and has highest observed frequency in the European (Finnish) population (AF= 7.96305e-05; MAF= 0.00796%, 2/25116 alleles, homozygotes = 0).
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
ClinVar
This variant has been reported in ClinVar as Uncertain significance (9 clinical laboratories) and as Likely pathogenic (8 clinical laboratories) and as Pathogenic (1 clinical laboratory) and as Likely benign (1 clinical laboratory) and as Uncertain Significance (1 clinical laboratory). (ClinVarID = 52610)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.05). REVEL score = 0.843. BayesDel score = 0.371621.
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; COSV66450665, n = 21 times).
Cancer Hotspots
This variant does not lie in a statistically significant hotspot.