The BRCA2 NM_000059.4:c.8167G>C (NP_000050.3:p.(Asp2723His)) missense variant has not previously been reported in somatic cancers (COSMIC). Experimental evidence: ENIGMA Table 9 pre-assigns PS3 Strong from three calibrated studies showing protein function similar to pathogenic controls. Based on available guidelines, this variant is considered to be Pathogenic. This variant is considered to be Pathogenic by the VCEP (Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA); ClinVar ID 52515).
Five-step scale from benign to pathogenic. This variant is pathogenic. Select a step to read what it means.
This variantScenario
BenignPathogenic
Pathogenic.A pathogenic classification under the recorded framework.
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.
ACMG/AMP criteria under ClinGen BRCA2 VCEP v1.2, with the data and sources behind each one.
28 criteria with recorded statuses: 5 met · 10 not met · 2 not assessed · 11 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
Only PS1 was potentially applicable; PM1, PM5, PP2, and BP1 are excluded or not applicable under ENIGMA BRCA2 v1.2.
The variant is p.Asp2723His in the BRCA2 DNA-binding domain, but domain location cannot generate PM1 or BP1 under the VCEP rules.
The exact ENIGMA Specifications Table 9 row governs the functional adjudication: PS3 Strong is pre-assigned for c.8167G>C / p.(Asp2723His), and no benign functional code is assigned.
The five requested criteria were evaluated independently under ENIGMA BRCA2 v1.2 rules.
PP4 Strong is supported by the exact Li et al. clinical-history LR of 79.25653766180034; PS4 is not met because no qualifying case-control p-value and OR/CI were verified.
PP5 is counted at Supporting strength from the three-star ENIGMA expert-panel ClinVar Pathogenic assertion; BP5 and BP6 are not met.
PP3 Supporting is met through the governing protein-impact path: p.Asp2723His is in the BRCA2 DNA-binding domain and BayesDel no-AF is 0.579612, above the BRCA2 threshold of 0.30.
BP4 is not met because its missense-domain path requires BayesDel no-AF ≤0.18 and SpliceAI ≤0.1; only the SpliceAI component is satisfied.
BP7 is not applicable because this is a missense variant inside the clinically important domain, not a qualifying outside-domain missense or a silent/intronic variant.
No criteria match.
Met · 5
PS3StrongVCEPMet at Strong: ENIGMA Table 9 pre-assigns PS3 Strong from three calibrated studies showing protein function similar to pathogenic controls.
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Reasoning
The ENIGMA BRCA2 Version 1.2 Specifications Table 9 contains the exact row for BRCA2 c.8167G>C, p.(Asp2723His), and pre-assigns PS3 Strong. The row states that three calibrated studies reported protein function similar to pathogenic control variants: Mesman 2019 (PMID:29988080), Richardson 2021 (PMID:33609447), and Ikegami 2020 (PMID:32444794). It also records no aberration in the cited splicing assessment (PMID:22505045), so the calibrated protein-function result is not displaced by a reported splicing effect. The ENIGMA rule requires well-established functional studies supportive of a damaging effect when the assay measures protein only or mRNA and protein combined; the pre-assigned Table 9 code is therefore governing and PS3 Strong is met. Independent extracted evidence is concordant: PMID:15290653 reports disrupted DNA-repair capacity and aberrant cellular localization for D2723H, and PMID:18451181 reports reduced HDR activity and increased centrosome amplification, classifying D2723H as inactivating.
VCEP rule
Well-established in vitro or in vivo functional studies supportive of a damaging effect
Assay measures effect via protein only OR mRNA and protein combined.
Evidence considered
ENIGMA Specifications Table 9, row BRCA2 c.8167G>C / p.(Asp2723His): PS3 Strong; reported by three calibrated studies to exhibit protein function similar to pathogenic control variants; PMIDs 29988080, 33609447, and 32444794; splicing column records no aberration (PMID:22505045).
ENIGMA Specifications v1.2 functional-assay rule: well-established in vitro or in vivo functional studies supportive of a damaging effect, with assays measuring effect via protein only or mRNA and protein combined.
PMID:15290653, Results, BRCA2 D2723H paragraph and Table 2: D2723H showed disrupted DNA-repair capacity after gamma irradiation and mitomycin-C exposure and aberrant cellular localization compared with wild-type BRCA2.
PMID:18451181, Tables 1-2 and functional-assay results: D2723H showed reduced homology-directed recombination activity, increased centrosome amplification, and was classified as inactivated in OB2.
Still missing
No exact variant-notation entry was found in Specifications_V1.2_2024-11-18.docx.txt for c.8167G>C, p.Asp2723His, or p.D2723H; the exact governing entry is present in Specifications_Table9_V1.2_2024-11-18.xlsx.txt.
No exact variant-notation entry was found in HUMU-40-1557-s001.xlsx.txt for c.8167G>C, p.Asp2723His, or p.D2723H.
PP1Very strongVCEPMet, Very Strong: complete co-segregation in 10 pedigrees produced odds of 13,731:1, exceeding the VCEP PP1 Very Strong threshold of 350:1.
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Reasoning
The VCEP requires quantitative co-segregation evidence and assigns PP1 Very Strong at LR >=350:1. The variant-specific extraction for BRCA2 D2723H reports complete co-segregation with breast and ovarian cancer in all 10 pedigrees with multiple individuals tested, yielding overall odds of 13,731:1 in favor of causality. This exceeds the VCEP Very Strong threshold. The same source reports a damaging functional effect, satisfying the VCEP stipulation for PP1 Very Strong; the available evidence also spans multiple pedigrees rather than a single family.
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_Very Strong – LR≥350:1 ... Stipulation: to apply code as Pathogenic Very Strong, VUS should have bioinformatically predicted (or experimentally proven) effect on protein or mRNA splicing.
Evidence considered
Specifications V1.2, PP1: quantitative co-segregation with disease in multiple affected family members is weighted by Bayes score, with PP1 Very Strong at LR >=350:1.
Appendix I: the Bayes score combines family evidence quantitatively, and the VCEP stipulates a demonstrated protein or mRNA effect for PP1 Very Strong and assessment of alternative causative variants when evidence is from a single family or isolated population.
Integrated evaluation of DNA sequence variants of unknown clinical significance, Results, BRCA2 D2723H paragraph; Table 2: D2723H was observed 24 times, never with a proven deleterious mutation, and all 10 pedigrees with multiple individuals tested showed complete co-segregation with breast and ovarian cancer, yielding overall odds of 13,731:1 in favor of causality.
Still missing
HUMU-40-1557-s001.xlsx was searched under c.8167G>C, p.Asp2723His, and p.D2723H; no matching row was found.
PP3SupportingVCEPMet: BayesDel no-AF is 0.579612, exceeding the ENIGMA BRCA2 PP3 protein-impact threshold of 0.30 for missense variants in the DNA-binding domain.
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Reasoning
The variant is missense p.(Asp2723His) and the ENIGMA BRCA2 Appendix J domain table lists D2723H (c.8167G>C (p.Asp2723His)) in the BRCA2 DNA-binding domain, aa 2481-3186. The governing PP3 protein-impact path applies to missense variants inside a clinically important functional domain and uses BayesDel no-AF. The BayesDel no-AF score is 0.579612, exceeding the BRCA2 cutoff of 0.30, so PP3 Supporting is met. SpliceAI maximum delta is 0.011, below the separate PP3 splice threshold of 0.2; it is not used to add a second PP3 finding or double-count the protein prediction.
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). ... Missense Predictions (BayesDel no AF)
BRCA2:
Impact ≥0.30
Evidence considered
ENIGMA Specifications v1.2, Appendix J domain table: D2723H (c.8167G>C (p.Asp2723His)) is listed in the BRCA2 DNA-binding domain, aa 2481-3186.
Case BayesDel no-AF score: 0.579612; the VCEP BRCA2 PP3 protein-impact cutoff is 0.30.
Case SpliceAI scores: DS_AG 0.001, DS_AL 0.007, DS_DG 0.000, DS_DL 0.011; maximum delta 0.011, below the VCEP PP3 splice threshold of 0.2.
Still missing
No exact c.8167G>C, p.Asp2723His, or p.D2723H entry was found in Specifications_V1.2_2024-11-18.docx; the governing PP3 rule itself was found there.
No exact c.8167G>C, p.Asp2723His, or p.D2723H entry was found in PMID_22505045_Houdayer_2012_HumMutat.pdf; this paper is not needed for the protein-impact PP3 path.
ENIGMA restricts PP4 to combined multifactorial clinical likelihood data and assigns Strong evidence at LR >=18.7:1. Li et al. Supplementary Table 4 gives BRCA2 c.8167G>C a LOG(LR) of 1.899035096168518 and LR = 79.25653766180034 from 21 probands. Explicit comparison: 79.25653766180034 >= 18.7? yes; therefore PP4 Strong is met. The value is also below the Very Strong threshold of 350, so Strong is the applicable weight.
VCEP rule
Breast cancer is very common and has a high degree of genetic heterogeneity (caused by pathogenic variants in numerous genes). Use ONLY to capture combined LR towards pathogenicity, based on multifactorial likelihood clinical data. ... PP4_Strong – LR≥18.7:1
Evidence considered
ENIGMA Specifications V1.2 PP4 rule: use only combined LR towards pathogenicity based on multifactorial likelihood clinical data; PP4 Strong is LR >=18.7:1 and PP4 Very Strong is LR >=350:1.
Li et al. 2020 BRCA2 clinical-history LR table, Sheet1 exact match: Gene BRCA2, HGVS_Nucleotide c.8167G>C, LOG(LR)=1.899035096168518, N_Probands=21, LR=79.25653766180034.
PP5SupportingVCEPMet, Supporting: ClinVar records an ENIGMA expert-panel Pathogenic assertion with three review stars.
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Reasoning
Expert panel Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) classified as Pathogenic.
VCEP rule
Reputable source recently reports variant as pathogenic but the evidence is not available to the laboratory to perform an independent evaluation.
Evidence considered
ClinVar variation 52515 for NM_000059.4(BRCA2):c.8167G>C (p.Asp2723His): classification Pathogenic, review status reviewed by expert panel, review_stars=3, expert panel ENIGMA.
ENIGMA Specifications V1.2 PP5 entry states: reputable source recently reports variant as pathogenic but the evidence is not available to the laboratory to perform an independent evaluation; the VCEP text itself says Do not use, while the case-level ClinVar expert-panel override is applied at Supporting strength.
PS1VCEPNot met: the only VCEP-listed likely pathogenic alternate, p.Asp2723Gly, has documented exon 18 splicing and cannot serve as a protein-change PS1 reference.
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Reasoning
PS1 is not met. ENIGMA permits PS1 for the same missense substitution as a previously classified pathogenic or likely pathogenic variant acting through protein change without confirmed or predicted mRNA-splicing impact. The VCEP Supplementary Tables identify p.Asp2723Gly (c.8168A>G) as likely pathogenic, but the same VCEP materials document six studies showing exon 18 splicing alteration for p.Asp2723Gly; it is therefore not an eligible protein-change-only reference. The other same-residue variants p.Asp2723Ala and p.Asp2723Val have functional-assay entries but no VCEP pathogenic or likely pathogenic classification establishing them as PS1 reference variants.
VCEP rule
Same amino acid change as a previously established pathogenic variant regardless of 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)). ... Apply PS1_Moderate, for predicted missense substitutions, where previously established likely 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 requires a previously classified pathogenic or likely pathogenic same-missense variant acting via protein change without confirmed or predicted mRNA-splicing impact (SpliceAI <=0.1).
Supplementary Tables ST7 lists c.8167G>C p.(Asp2723His) as (Likely) Pathogenic, posterior probability 1 and IARC class 5, and c.8168A>G p.(Asp2723Gly) as (Likely) Pathogenic, posterior probability 0.998 and IARC class 5.
Supplementary Tables ST3 and Appendix E document exon 18 splicing alteration for p.Asp2723Gly in six studies, including a 164 nt exon 18 deletion.
Specifications Table 9 lists p.Asp2723Ala and p.Asp2723Val as PS3 Strong functional-assay entries but does not provide a pathogenic or likely pathogenic classification for them.
The assessed p.Asp2723His has SpliceAI max delta 0.011, but that does not create a qualifying different-nucleotide reference variant.
PMID:15290653 and PMID:18451181 were reviewed for exact p.D2723H same-residue evidence; both discuss the assessed variant rather than establishing a separate qualifying reference substitution.
PS4VCEPNot met: no verified variant-specific case-control p-value, OR >=4, or confidence interval excluding 2.0 was available.
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Reasoning
The ENIGMA rule requires case-control evidence with p-value <=0.05 and OR >=4, with the lower confidence interval excluding 2.0. The governing Supplementary Table 7 does contain this variant as c.8167G>C/p.(Asp2723His), with posterior probability 1 and IARC class 5, but it does not provide case and control counts or a case-control OR/CI. PMID:15290653 reports 24 observations and complete cosegregation in 10 pedigrees, and PMID:18451181 reports 25 pedigrees and very high causality odds, but neither provides a qualifying affected-versus-unaffected/population case-control comparison for this variant. The literature_pass PS4 index was checked; its listed papers were not available as full-text publications in this case, and no verified variant-specific case-control counts were available.
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 Specifications V1.2, PS4 rule: case-control studies require p-value <=0.05 and OR >=4, with the lower confidence interval excluding 2.0.
ENIGMA Supplementary Tables ST7 row 4151: BRCA2 c.8167G>C, p.(Asp2723His), (Likely) Pathogenic, posterior probability 1, IARC class 5, absent from the control-frequency field; this is not a case-control OR/CI result.
PMID:15290653, Results BRCA2 D2723H paragraph: observed 24 times; all 10 pedigrees with multiple individuals tested showed complete cosegregation, yielding odds of 13,731:1; this is familial/co-segregation evidence, not case-control evidence.
PMID:18451181, Table 1/Table 2 and results: D2723H was evaluated across 25 pedigrees with combined odds of 5.6 x 10^11 and posterior probability 1.000; this is multifactorial/family evidence, not a qualifying case-control comparison.
Still missing
No case-control counts, p-value, OR, or confidence interval for c.8167G>C/p.Asp2723His were found in SupplementaryTables_V1.2_2024-11-18.xlsx.txt.
No exact variant row was found in HUMU-40-1557-s001.xlsx.txt under c.8167G>C, p.Asp2723His, or p.D2723H.
The literature_pass PS4-indexed papers PMID:17508274, PMID:20065170, PMID:23961350, PMID:26681312, PMID:29922827, and PMID:31479213 were not present as full-text publication files in this case, so their variant-level case-control data could not be independently verified.
PM2VCEPNot met: the variant occurs once in gnomAD v3.1 non-cancer, so it is not absent from the VCEP-required control datasets.
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Reasoning
The VCEP permits PM2 Supporting only when the variant is absent from controls in both the specified gnomAD v2.1 non-cancer exome and gnomAD v3.1 non-cancer genome datasets, with adequate depth. The variant is absent from gnomAD v2.1 non-cancer but is present once in gnomAD v3.1 non-cancer (1/147,924 alleles; 0 homozygotes). The VCEP states that a single observation is not informative and no code is applied, so the absence requirement for PM2 is not satisfied.
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
ENIGMA Specifications v1.2, Table 1/CSPEC PM2 rule: absence from controls in gnomAD v2.1 non-cancer exome and gnomAD v3.1 non-cancer genome datasets, with average read depth ≥25.
ENIGMA SupplementaryTables_V1.2_2024-11-18.xlsx, ST7 Reference Set row c.8167G>C / p.(Asp2723His): (Likely) Pathogenic, prior probability 0.81, posterior probability 1, population category Absent in that reference set; this is historical reference-set data and does not override the current gnomAD v3.1 observation.
GNOMAD_V2_1_NON_CANCER: exact variant absent.
GNOMAD_V3_1_NON_CANCER: exact variant present at 1/147924 alleles, AF 6.76023e-06, 0 homozygotes; the VCEP specifically states that observation only once in a gnomAD outbred population is not informative and no code is applied.
gnomAD v4.1 all-comers: 21/1614046 alleles, 0 homozygotes; this is not used as the governing PM2 dataset because the VCEP specifies non-cancer v2.1/v3.1 data.
Still missing
HUMU-40-1557-s001.xlsx was searched for c.8167G>C, p.Asp2723His, and p.D2723H; no exact variant row was found.
PM3VCEPNot met: D2723H was never observed with a proven deleterious mutation, and no qualifying Fanconi Anemia phenotype or chromosome-breakage result is reported.
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Reasoning
Not met. The ENIGMA BRCA2 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 for BRCA2 D2723H states that it was observed 24 times and never appeared with a proven deleterious mutation; it reports breast/ovarian-cancer pedigrees, not Fanconi Anemia chromosome-breakage or qualifying clinical features. Therefore the required same-gene co-occurrence and FA phenotype conditions are not satisfied, and no PM3 points can be assigned.
VCEP rule
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.
Evidence considered
ENIGMA BRCA2 PM3 rule: PM3 applies only for a patient with phenotype consistent with BRCA1- or BRCA2-related Fanconi Anemia and co-occurrent variants in the same gene; the phenotype requires either increased chromosome breakage plus at least one qualifying clinical feature, or unknown chromosome-breakage status plus at least two qualifying clinical features from at least two categories.
Easton et al. 2004, PMID:15290653, Results, BRCA2 D2723H paragraph: D2723H was observed in the Myriad Genetics Laboratories database 24 times and never appeared with a proven deleterious mutation; all 10 pedigrees with multiple individuals tested showed complete cosegregation with breast and ovarian cancer.
The reported observations concern BRCA2-related breast/ovarian-cancer pedigrees and do not document the VCEP's required Fanconi Anemia phenotype or chromosome-breakage findings.
Still missing
The reviewed evidence does not provide a Fanconi Anemia phenotype assessment, chromosome-breakage result, or qualifying same-gene pathogenic/likely pathogenic co-occurrence in trans or homozygosity.
BA1VCEPNot met: gnomAD v3.1 non-cancer grpmax FAF is 0, below the VCEP BA1 threshold of >0.001.
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Reasoning
The ENIGMA BRCA2 VCEP requires FAF >0.001 in gnomAD v2.1 non-cancer exomes and/or gnomAD v3.1 non-cancer genomes. The variant is absent from the collected gnomAD v2.1 non-cancer record; in the gnomAD v3.1 non-cancer record it has 1/147,924 alleles, 0 homozygotes, and grpmax FAF 0, with the highest subpopulation allele frequency 1.54283e-05, all below the BA1 threshold. The current gnomAD v4 all-comers record is also far below the threshold (grpmax FAF 1.144e-05) but is not the governing dataset where the VCEP specifies non-cancer data.
VCEP rule
Filter allele frequency (FAF) is above 0.1% (FAF > 0.001) in gnomAD v2.1 (non-cancer, exome only subset) and/or gnomAD v3.1 (non-cancer), non-founder population(s). See Appendix G for details.
GNOMAD_V2_1_NON_CANCER: exact variant query c.8167G>C/p.(Asp2723His) was absent.
GNOMAD_V3_1_NON_CANCER: exact variant present at 1/147924 alleles, AF 6.76023e-06, 0 homozygotes; highest subpopulation AF 1.54283e-05 and grpmax FAF 0.
gnomAD v4.1 all-comers: 21/1614046 alleles, 0 homozygotes, grpmax FAF 1.144e-05; this is corroborative only because the VCEP specifies non-cancer datasets.
BS1VCEPNot met: gnomAD v3.1 non-cancer grpmax FAF is 0, below the BS1 Supporting threshold of >0.00002.
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Reasoning
The VCEP assigns BS1 Strong only when FAF >0.0001 and BS1 Supporting when FAF >0.00002 and ≤0.0001 in the specified non-cancer gnomAD datasets. The variant is absent from gnomAD v2.1 non-cancer; gnomAD v3.1 non-cancer shows 1/147,924 alleles, 0 homozygotes, and grpmax FAF 0, so neither BS1 threshold is reached. The highest observed subpopulation allele frequency is 1.54283e-05, also below the Supporting threshold, and gnomAD v4 all-comers is non-governing corroboration only.
VCEP rule
Filter allele frequency (FAF) is above 0.01% (FAF > 0.0001) in gnomAD v2.1 (non-cancer, exome only subset) and/or gnomAD v3.1 (non-cancer), non-founder population(s). See Appendix G for details. ... Filter allele frequency (FAF) is above 0.002% (FAF > 0.00002) and less than or equal to 0.01% (FAF ≤ 0.0001) in gnomAD v2.1 (non-cancer, exome only subset) and/or gnomAD v3.1 (non-cancer), non-founder population(s). See Appendix G for details.
GNOMAD_V2_1_NON_CANCER: exact variant query c.8167G>C/p.(Asp2723His) was absent.
GNOMAD_V3_1_NON_CANCER: exact variant present at 1/147924 alleles, AF 6.76023e-06, 0 homozygotes; highest subpopulation AF 1.54283e-05 and grpmax FAF 0.
gnomAD v4.1 all-comers: grpmax FAF 1.144e-05, below BS1 Supporting and not the governing non-cancer dataset.
BS3VCEPNot met: ENIGMA Table 9 assigns PS3 Strong because three calibrated studies show damaging function, not the no-damage result required for BS3.
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Reasoning
BS3 requires well-established functional studies showing no damaging effect on protein function. The governing ENIGMA Specifications Table 9 row for BRCA2 c.8167G>C, p.(Asp2723His), instead pre-assigns PS3 Strong based on three calibrated studies showing function similar to pathogenic controls, with study-level results of Mesman 2019 complementation No, Richardson 2021 Damaging, and Ikegami 2020 fClass 4 or 5. The available extracted functional studies are concordant with damage rather than neutrality. Therefore the evidence does not satisfy the BS3 rule and BS3 is not met; no separate BS3 code is assigned.
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.
Evidence considered
ENIGMA Specifications Table 9, row BRCA2 c.8167G>C / p.(Asp2723His): PS3 Strong, not BS3; three calibrated studies report function similar to pathogenic controls: Mesman 2019 complementation No, Richardson 2021 Damaging, and Ikegami 2020 fClass 4 or 5.
ENIGMA Specifications v1.2 BS3 rule: well-established in vitro or in vivo functional studies must show no damaging effect on protein function, with assays measuring effect via protein only or mRNA and protein combined.
PMID:15290653 and PMID:18451181 provide concordant extracted functional evidence of impaired BRCA2 activity for D2723H rather than a neutral protein-function result.
Still missing
No BS3-specific row was found for c.8167G>C, p.Asp2723His, or p.D2723H in Specifications_Table9_V1.2_2024-11-18.xlsx.txt; its exact row assigns PS3 Strong instead.
No exact variant-notation entry was found in Specifications_V1.2_2024-11-18.docx.txt for c.8167G>C, p.Asp2723His, or p.D2723H; the exact governing entry is present in Specifications_Table9_V1.2_2024-11-18.xlsx.txt.
No exact variant-notation entry was found in HUMU-40-1557-s001.xlsx.txt for c.8167G>C, p.Asp2723His, or p.D2723H.
BP4VCEPNot met: SpliceAI maximum delta is 0.011, but BayesDel no-AF is 0.579612, above the ENIGMA BRCA2 BP4 no-impact cutoff of 0.18.
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Reasoning
The variant is a missense substitution inside the ENIGMA-defined BRCA2 DNA-binding domain, so the governing BP4 missense-domain path requires no predicted impact through both protein change and splicing. The BRCA2 BayesDel no-AF no-impact cutoff is ≤0.18 and the SpliceAI cutoff is ≤0.1. SpliceAI maximum delta is 0.011 and satisfies the splice component, but BayesDel no-AF is 0.579612 and fails the protein component. Therefore BP4 Supporting 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, Appendix J: the BRCA2 DNA-binding domain is aa 2481-3186, and D2723H is listed in that domain.
The governing BP4 missense-domain rule requires BayesDel no-AF ≤0.18 AND SpliceAI ≤0.1.
Case BayesDel no-AF score is 0.579612, failing the BP4 protein no-impact threshold of ≤0.18.
Case SpliceAI maximum delta is 0.011, satisfying the BP4 splice no-impact threshold of ≤0.1; this alone is insufficient because both components are required.
Still missing
No exact c.8167G>C, p.Asp2723His, or p.D2723H entry was found in Specifications_V1.2_2024-11-18.docx; the governing BP4 rule itself was found there.
No exact c.8167G>C, p.Asp2723His, or p.D2723H entry was found in PMID_22505045_Houdayer_2012_HumMutat.pdf; this paper is not needed for the predictor-based BP4 assessment.
BP5VCEPNot met: clinical-history LR 79.2565 <= 0.48? no, so it does not meet ENIGMA's BP5 Supporting threshold.
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Reasoning
ENIGMA defines BP5 from a combined clinical LR against pathogenicity, with Supporting evidence at LR <=0.48:1. The exact Li et al. row gives LR 79.25653766180034. Explicit comparison: 79.25653766180034 <= 0.48? no; therefore BP5 is not met. The same clinical-history result supports pathogenic rather than benign direction and cannot be reused as BP5.
VCEP rule
N/A for co-observation: cases with pathogenic variants in two (or more) different known breast–ovarian cancer risk genes have no specific phenotype. ... Use ONLY to capture combined LR against pathogenicity, based on multifactorial likelihood clinical data. ... BP5 - LR ≤0.48 to >0.23:1
Evidence considered
ENIGMA Specifications V1.2 BP5 rule: use only combined LR against pathogenicity based on multifactorial likelihood clinical data; BP5 Supporting is LR <=0.48 to >0.23:1.
Li et al. 2020 BRCA2 clinical-history LR table, Sheet1 exact match: c.8167G>C, LOG(LR)=1.899035096168518, N_Probands=21, LR=79.25653766180034.
BP6VCEPNot met: ClinVar's three-star ENIGMA expert-panel assertion is Pathogenic, not benign.
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Reasoning
ClinVar has a three-star ENIGMA expert-panel Pathogenic assertion for this variant, not a benign assertion. No ClinVar expert-panel benign report was identified, so the BP6 Supporting condition is not met; the case-level ClinVar expert-panel override does not convert a pathogenic assertion into BP6.
VCEP rule
Reputable source recently reports variant as benign but the evidence is not available to the laboratory to perform an independent evaluation.
Evidence considered
ClinVar variation 52515: classification Pathogenic, review status reviewed by expert panel, review_stars=3, expert panel ENIGMA; no benign expert-panel assertion was identified.
ENIGMA Specifications V1.2 BP6 entry defines a reputable source reporting the variant as benign but states Do not use; under the case-level ClinVar expert-panel override, the benign direction remains unmet.
BS2VCEPNot assessed: gnomAD reports 0 homozygotes, but no qualifying phenotyped healthy-adult cohort observations or BS2 points are available.
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Reasoning
The VCEP's BS2 rule requires observations in healthy adults and assigns points for phenotype-confirmed clinical or research-cohort observations involving a homozygote or relevant co-occurrence, with final strength based on the summed points. The available gnomAD records show 0 homozygotes, and the VCEP explicitly excludes frequency data from BS2 point assignment; no qualifying phenotyped healthy-adult cohort observations or BS2 point total 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. ... BS2 = ≥ 4 points
Evidence considered
ENIGMA Specifications v1.2, Table 1/CSPEC BS2 rule: BS2 is applied in the absence of features of recessive disease, namely Fanconi Anemia phenotype, with final code assignment based on summed BS2-related points.
Appendix H, Table 13: BS2 points require a phenotyped individual with the relevant co-occurrence or homozygote presentation; the appendix states that frequency-based data are not to be used for BS2 point assignment.
GNOMAD_V2_1_NON_CANCER: variant absent; no homozygote observation.
GNOMAD_V3_1_NON_CANCER: 1 allele and 0 homozygotes; this frequency observation is not a BS2 point assignment.
gnomAD v4.1 all-comers: 0 homozygotes; frequency data are not used for BS2 under the VCEP rule.
Still missing
No qualifying phenotyped healthy-adult clinical or research-cohort observations with BS2 point assignments were available.
Appendices_V1.2_2024-11-18.docx was searched for c.8167G>C, p.Asp2723His, and p.D2723H; no variant-specific BS2 observation was found.
BS4VCEPNot assessed: no quantitative benign-direction LR or affected-relative non-segregation evidence is available, while the reported LR supports complete co-segregation.
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Reasoning
The ENIGMA BRCA2 VCEP requires a quantitative co-segregation likelihood ratio for lack of segregation to assess BS4. The available variant-specific evidence reports complete co-segregation and a pathogenic-direction LR, not non-segregation; no quantitative LR toward benignity or affected-relative non-segregation was provided.
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 ≤0.48:1 ... BS4_Moderate - LR ≤0.23:1 ... BS4 - LR ≤0.05:1 ... BS4_Very strong – LR ≤0.00285:1
Evidence considered
Specifications V1.2, BS4: lack of segregation must be measured by a quantitative co-segregation method and weighted by Bayes score; BS4 Supporting requires LR <=0.48:1, BS4 Moderate LR <=0.23:1, and BS4 Strong LR <=0.05:1.
Integrated evaluation of DNA sequence variants of unknown clinical significance, Results, BRCA2 D2723H paragraph; Table 2: all 10 pedigrees with multiple individuals tested showed complete co-segregation, yielding overall odds of 13,731:1 in favor of causality; this does not provide a benign-direction BS4 LR.
Still missing
SupplementaryTables_V1.2_2024-11-18.xlsx was searched under c.8167G>C, p.Asp2723His, and p.D2723H; no BS4 segregation assignment was found.
HUMU-40-1557-s001.xlsx was searched under c.8167G>C, p.Asp2723His, and p.D2723H; no matching row was found.
No quantitative co-segregation LR toward lack of segregation was available in the case evidence.
Not applicable · 11· recorded as not applicableShow reasons ▾Hide reasons ▴PVS1N/ANot applicable: c.8167G>C causes p.Asp2723His, a missense substitution, whereas ENIGMA PVS1 applies to null variants such as nonsense, frameshift, deletion, duplication, or canonical splice-site variants.
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Reasoning
The variant is NM_000059.4:c.8167G>C, NP_000050.3:p.(Asp2723His), a missense substitution in exon 18, not a null variant. The ENIGMA PVS1 rule is restricted to null variants and its decision-tree examples are initiation, nonsense/frameshift, deletion, duplication, and canonical splice-site variants; therefore PVS1 is not applicable. The searched Specifications_Table4_V1.2_2024-11-18.xlsx contains exon 18 PVS1 rows for splice-site/null-variant decisions but no row for this missense variant. The other searched VCEP files contain variant-level records for p.Asp2723His in functional or other tables, but no PVS1 assignment for this missense change.
VCEP rule
Null variant in a gene where loss of function is a known mechanism of disease. ... In alignment with SVI recommendations for PVS1 code application, evidence strength and description has been separated for different variant types. Apply according to PVS1 flowchart, which considers knowledge of clinically important functional domains.
Evidence considered
Case normalization: NM_000059.4:c.8167G>C; NP_000050.3:p.(Asp2723His); NP_000050.3:p.(D2723H); consequence class missense; exon 18.
ENIGMA Specifications v1.2, Table 1, PVS1_VariableWeight: 'Null variant in a gene where loss of function is a known mechanism of disease.'
ENIGMA Specifications v1.2, Table 1, PVS1_VariableWeight: 'In alignment with SVI recommendations for PVS1 code application, evidence strength and description has been separated for different variant types. Apply according to PVS1 flowchart, which considers knowledge of clinically important functional domains.'
ENIGMA Specifications v1.2, Table 4, BRCA2 exon 18 rows: PVS1 decisions are listed for splice-site/null-variant positions; no c.8167G>C or p.Asp2723His row is present.
Still missing
No PVS1-specific variant row for c.8167G>C, p.Asp2723His, or p.D2723H in Specifications_Table4_V1.2_2024-11-18.xlsx; the exon 18 entries are for null/splice-site decisions.
No PVS1 assignment for this missense variant in Specifications_V1.2_2024-11-18.docx, Appendices_V1.2_2024-11-18.docx, or PMID_22505045_Houdayer_2012_HumMutat.pdf.
PS2VCEPNot applicable: the ENIGMA BRCA2 VCEP prohibits PS2 because de novo occurrences lack calibrated predictive capacity for relatively common BRCA1/2-related cancers.
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Reasoning
The ENIGMA BRCA2 VCEP marks PS2 as not applicable because BRCA1/2-related cancers are relatively common and there is no information to calibrate the predictive capacity of de novo occurrences.
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
Specifications V1.2, Table 1, PS2: the criterion is marked Do not use because BRCA1/2-related cancers occur relatively commonly and no information calibrates the predictive capacity of de novo occurrences.
PM1VCEPNot applicable: residue 2723 is in the DNA-binding domain, but ENIGMA explicitly directs that PM1 is not used and domain evidence belongs under PP3/BP4.
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Reasoning
PM1 is not applicable under ENIGMA BRCA2 v1.2. Although p.Asp2723His lies in the BRCA2 DNA-binding domain at aa 2481-3186, the VCEP explicitly says PM1 is not used and that this information is considered as part of PP3/BP4.
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 rule states: Do not use; considered as a component of bioinformatic analysis (PP3/BP4).
Specifications v1.2 defines the BRCA2 DNA-binding domain as aa 2481-3186, placing residue 2723 inside it.
Appendix C Table 4 lists D2723H within the BRCA2 DBD at aa 2481-3186.
vcep_materials.json domain_tables is empty for BRCA2; the VCEP text supplies the applicable domain information, but its explicit PM1 prohibition remains controlling.
PM4VCEPNot applicable: p.Asp2723His is a missense substitution, not an in-frame deletion, in-frame insertion, or stop-loss protein-length change, and ENIGMA marks PM4 'Do not use.'
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Reasoning
The variant is a missense substitution, p.(Asp2723His), and does not change protein length through an in-frame deletion, in-frame insertion, or stop-loss event. ENIGMA explicitly states that PM4 is not used and that the described protein-length-change scenario is considered through bioinformatic analysis instead. PM4 is therefore not applicable to this variant.
VCEP rule
Protein length changes due to in-frame deletions/insertions in a non-repeat region or stop-loss variants. ... Do not use
Evidence considered
Case normalization: NM_000059.4:c.8167G>C; NP_000050.3:p.(Asp2723His); consequence class missense.
ENIGMA Specifications v1.2, Table 1, PM4 row: 'Protein length changes due to in-frame deletions/insertions in a non-repeat region or stop-loss variants.'
ENIGMA Specifications v1.2, Table 1, PM4 row: 'Do not use' and 'Considered as component of bioinformatic analysis (PP3/BP4).'
Still missing
No variant-specific PM4 entry for c.8167G>C, p.Asp2723His, or p.D2723H in Specifications_V1.2_2024-11-18.docx; the governing table marks PM4 'Do not use.'
PM5N/ANot applicable: c.8167G>C is missense, while ENIGMA reserves PM5 for exon-specific protein-termination-codon variants.
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Reasoning
PM5 is not applicable. ENIGMA explicitly says classic missense PM5 is not used and repurposes PM5 only for protein-termination-codon variants in an exon where a different proven pathogenic PTC has been seen; c.8167G>C is missense in exon 18, not a PTC variant.
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 states for classic missense PM5: Do not use; considered as a component of bioinformatic analysis (PP3/BP4).
The repurposed PM5_VariableWeight (PTC) route applies to a protein-termination-codon variant in an exon where a different proven pathogenic PTC has been seen and provides additional weight for PVS1.
The case identifies c.8167G>C as a missense variant in exon 18; Table 4 exon 18 entries do not assign a classic missense PM5 code.
PM6VCEPNot applicable: the ENIGMA BRCA2 VCEP prohibits PM6 because de novo occurrences lack calibrated predictive capacity for relatively common BRCA1/2-related cancers.
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Reasoning
The ENIGMA BRCA2 VCEP marks PM6 as not applicable because BRCA1/2-related cancers are relatively common and there is no information to calibrate the predictive capacity of de novo occurrences.
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
Specifications V1.2, Table 1, PM6: the criterion is marked Do not use because BRCA1/2-related cancers occur relatively commonly and no information calibrates the predictive capacity of de novo occurrences.
PP2VCEPNot applicable: ENIGMA says not to use PP2 for BRCA2 because the gene has a high frequency of benign missense variants.
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Reasoning
PP2 is not applicable. The ENIGMA BRCA2 specification explicitly says not to use PP2 because BRCA2 has a high frequency of benign missense variants.
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 entry says: Do not use; High frequency of benign missense variants.
BP1N/ANot applicable: residue 2723 is inside the ENIGMA DNA-binding domain, although SpliceAI max delta is 0.011 and below 0.1.
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Reasoning
BP1 is not applicable because the governing rule requires a missense variant to be outside a potentially clinically important functional domain. p.Asp2723His is inside the VCEP-defined BRCA2 DNA-binding domain at aa 2481-3186. Its SpliceAI max delta is 0.011, but the required outside-domain condition is not met.
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).
Evidence considered
Specifications v1.2 BP1 requires missense variants outside a potentially clinically important functional domain and no predicted splicing with SpliceAI ≤0.1.
Specifications v1.2 defines the BRCA2 DNA-binding domain as aa 2481-3186; residue 2723 is inside it.
Appendix C Table 4 lists D2723H within the BRCA2 DBD.
The case evidence reports SpliceAI max delta 0.011, which is ≤0.1, but the outside-domain requirement is not met.
BP2VCEPNot applicable: the ENIGMA VCEP says BP2 is not applicable and may be applied only in the context of BS2.
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Reasoning
Not applicable. The ENIGMA BRCA2 VCEP pre-assigns BP2 as not applicable and states that it should not be used; it is applied only in the context of BS2. The VCEP rule therefore excludes BP2 from this assessment regardless of whether phase or co-observation information is available.
VCEP rule
Do not use ... Applied only in the context of BS2.
Evidence considered
ENIGMA BRCA2 CSPEC entry for BP2: applicability is Not applicable and the instruction is Applied only in the context of BS2.
ENIGMA BRCA2 Specifications v1.2 Table 1, BP2 row: the criterion is marked Do not use and Applied only in the context of BS2.
BP3VCEPNot applicable: c.8167G>C is a missense substitution, not an in-frame deletion or insertion in a repetitive region, and ENIGMA marks BP3 'Do not use.'
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Reasoning
The variant is a missense substitution and is not an in-frame deletion or insertion. It therefore cannot meet the ENIGMA BP3 variant-type requirement for an in-frame deletion or insertion in a repetitive region without a known function. ENIGMA also marks BP3 'Do not use' and states that this consideration is captured by bioinformatic tool prediction and domain analysis; BP3 is not applicable.
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
Case normalization: NM_000059.4:c.8167G>C; NP_000050.3:p.(Asp2723His); consequence class missense.
ENIGMA Specifications v1.2, Table 1, BP3 row: 'In-frame deletions/insertions in a repetitive region without a known function.'
ENIGMA Specifications v1.2, Table 1, BP3 row: 'Do not use' and 'Captured by bioinformatic tool prediction, and domain analysis. See Appendix J.'
Still missing
No variant-specific BP3 entry for c.8167G>C, p.Asp2723His, or p.D2723H in Specifications_V1.2_2024-11-18.docx; the governing table marks BP3 'Do not use.'
The variant is missense and lies inside the ENIGMA-defined BRCA2 DNA-binding domain. The VCEP's BP7 RNA repurposing rule applies missense/in-frame variants only when located outside a clinically important functional domain; the ordinary BP7 Supporting paths are limited to silent or qualifying intronic variants. This missense variant is inside the domain, so BP7 is outside its own scope before evidence sufficiency is considered.
VCEP rule
Apply as BP7_Strong (RNA) for intronic, silent, and missense/in-frame variants located outside a (potentially) clinically important functional domain. ... 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
Evidence considered
ENIGMA Specifications v1.2, Appendix J domain table: D2723H (c.8167G>C (p.Asp2723His)) is listed in the BRCA2 DNA-binding domain, aa 2481-3186.
ENIGMA Specifications v1.2 BP7 RNA rule: BP7_Strong applies to intronic, silent, and missense/in-frame variants located outside a clinically important functional domain; BP7 Supporting applies to silent variants inside a domain or qualifying intronic variants if BP4 is met.
The variant is missense and inside the domain, not silent or intronic; therefore BP7 is not applicable.
Still missing
No exact c.8167G>C, p.Asp2723His, or p.D2723H entry was found in Specifications_V1.2_2024-11-18.docx; the governing BP7 scope rule itself was found there.
No exact c.8167G>C, p.Asp2723His, or p.D2723H entry was found in PMID_22505045_Houdayer_2012_HumMutat.pdf.
An exact c.8167G>C, p.Asp2723His entry was found in SupplementaryTables_V1.2_2024-11-18.xlsx (row 4151), but it is a functional-impact row, not an mRNA-only BP7 RNA result.
AF 1.3e-05 · 21 / 1,614,046 alleles · 0 hom · FAF 1.1e-05
European (non-Finnish)21 / 1,180,042
1.8e-05
0 alternate alleles recorded in 9 other groups: Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American.
Statements
gnomAD v4.1
This variant is present in gnomAD v4.1 (AF= 1.30108e-05; MAF= 0.00130%, 21/1614046 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 1.7796e-05; MAF= 0.00178%, 21/1180042 alleles, homozygotes = 0); grpmax FAF= 1.144e-05.
gnomAD v2.1
Absent from gnomAD v2.1.
gnomAD-Canada
Not available in gnomAD-Canada v1.0.
SpliceAI and Pangolin
SpliceAI acceptor lossat +1 bp
0.007
SpliceAI acceptor gainat +46 bp
0.001
SpliceAI donor lossat +164 bp
0.011
SpliceAI donor gainat +4 bp
0.000
Pangolin splice lossmagnitude shown
-0.035
Pangolin splice gain
0.004
Other predictors
REVEL
0.932
BayesDel
0.580
How the predictions were used
PP3SupportingVCEPMet: BayesDel no-AF is 0.579612, exceeding the ENIGMA BRCA2 PP3 protein-impact threshold of 0.30 for missense variants in the DNA-binding domain.
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Reasoning
The variant is missense p.(Asp2723His) and the ENIGMA BRCA2 Appendix J domain table lists D2723H (c.8167G>C (p.Asp2723His)) in the BRCA2 DNA-binding domain, aa 2481-3186. The governing PP3 protein-impact path applies to missense variants inside a clinically important functional domain and uses BayesDel no-AF. The BayesDel no-AF score is 0.579612, exceeding the BRCA2 cutoff of 0.30, so PP3 Supporting is met. SpliceAI maximum delta is 0.011, below the separate PP3 splice threshold of 0.2; it is not used to add a second PP3 finding or double-count the protein prediction.
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). ... Missense Predictions (BayesDel no AF)
BRCA2:
Impact ≥0.30
Evidence considered
ENIGMA Specifications v1.2, Appendix J domain table: D2723H (c.8167G>C (p.Asp2723His)) is listed in the BRCA2 DNA-binding domain, aa 2481-3186.
Case BayesDel no-AF score: 0.579612; the VCEP BRCA2 PP3 protein-impact cutoff is 0.30.
Case SpliceAI scores: DS_AG 0.001, DS_AL 0.007, DS_DG 0.000, DS_DL 0.011; maximum delta 0.011, below the VCEP PP3 splice threshold of 0.2.
Still missing
No exact c.8167G>C, p.Asp2723His, or p.D2723H entry was found in Specifications_V1.2_2024-11-18.docx; the governing PP3 rule itself was found there.
No exact c.8167G>C, p.Asp2723His, or p.D2723H entry was found in PMID_22505045_Houdayer_2012_HumMutat.pdf; this paper is not needed for the protein-impact PP3 path.
BP4VCEPNot met: SpliceAI maximum delta is 0.011, but BayesDel no-AF is 0.579612, above the ENIGMA BRCA2 BP4 no-impact cutoff of 0.18.
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Reasoning
The variant is a missense substitution inside the ENIGMA-defined BRCA2 DNA-binding domain, so the governing BP4 missense-domain path requires no predicted impact through both protein change and splicing. The BRCA2 BayesDel no-AF no-impact cutoff is ≤0.18 and the SpliceAI cutoff is ≤0.1. SpliceAI maximum delta is 0.011 and satisfies the splice component, but BayesDel no-AF is 0.579612 and fails the protein component. Therefore BP4 Supporting 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, Appendix J: the BRCA2 DNA-binding domain is aa 2481-3186, and D2723H is listed in that domain.
The governing BP4 missense-domain rule requires BayesDel no-AF ≤0.18 AND SpliceAI ≤0.1.
Case BayesDel no-AF score is 0.579612, failing the BP4 protein no-impact threshold of ≤0.18.
Case SpliceAI maximum delta is 0.011, satisfying the BP4 splice no-impact threshold of ≤0.1; this alone is insufficient because both components are required.
Still missing
No exact c.8167G>C, p.Asp2723His, or p.D2723H entry was found in Specifications_V1.2_2024-11-18.docx; the governing BP4 rule itself was found there.
No exact c.8167G>C, p.Asp2723His, or p.D2723H entry was found in PMID_22505045_Houdayer_2012_HumMutat.pdf; this paper is not needed for the predictor-based BP4 assessment.
The variant is missense and lies inside the ENIGMA-defined BRCA2 DNA-binding domain. The VCEP's BP7 RNA repurposing rule applies missense/in-frame variants only when located outside a clinically important functional domain; the ordinary BP7 Supporting paths are limited to silent or qualifying intronic variants. This missense variant is inside the domain, so BP7 is outside its own scope before evidence sufficiency is considered.
VCEP rule
Apply as BP7_Strong (RNA) for intronic, silent, and missense/in-frame variants located outside a (potentially) clinically important functional domain. ... 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
Evidence considered
ENIGMA Specifications v1.2, Appendix J domain table: D2723H (c.8167G>C (p.Asp2723His)) is listed in the BRCA2 DNA-binding domain, aa 2481-3186.
ENIGMA Specifications v1.2 BP7 RNA rule: BP7_Strong applies to intronic, silent, and missense/in-frame variants located outside a clinically important functional domain; BP7 Supporting applies to silent variants inside a domain or qualifying intronic variants if BP4 is met.
The variant is missense and inside the domain, not silent or intronic; therefore BP7 is not applicable.
Still missing
No exact c.8167G>C, p.Asp2723His, or p.D2723H entry was found in Specifications_V1.2_2024-11-18.docx; the governing BP7 scope rule itself was found there.
No exact c.8167G>C, p.Asp2723His, or p.D2723H entry was found in PMID_22505045_Houdayer_2012_HumMutat.pdf.
An exact c.8167G>C, p.Asp2723His entry was found in SupplementaryTables_V1.2_2024-11-18.xlsx (row 4151), but it is a functional-impact row, not an mRNA-only BP7 RNA result.
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.932. BayesDel score = 0.579612.
4 paper records listed. 2 cited in the classification.
Cited in the classification
Integrated evaluation of DNA sequence variants of unknown clinical significance: application to BRCA1 and BRCA2.
Goldgar DE et al. · 2004 Oct
The paper explicitly discusses BRCA2 D2723H, corresponding to p.(D2723H); D2723H was observed 24 times, showed complete cosegregation in 10 pedigrees with multiple tested individuals, and had functional and cellular-localization findings.
→ PS3 · strong→ PP1 · very strongNames this variant
D2723H.—This variant has been observed in the Myriad Genetics Laboratories database 24 times and has never appeared with a proven deleterious mutation. The variant yields odds in favor of causality under the BRCA2 co-occurrence model of 2.0:1. All 10 pedigrees with multiple individuals tested for this variant showed complete cosegregation with breast and ovarian cancer, yielding overall odds of 13,731:1 in favor of causality.
Location Results, BRCA2 D2723H paragraph; Table 2
Context Myriad Genetics database; 10 pedigrees; BRCA2 functional assays after gamma irradiation and mitomycin-C exposure; cellular localization in 293T cells.
Functional assays for classification of BRCA2 variants of uncertain significance.
Farrugia DJ et al. · 2008 May 1
The paper explicitly describes p.D2723H and reports combined odds of 5.6 × 10^11, posterior probability 1.000, reduced homology-directed recombination activity, increased centrosome amplification, and localization in the BRCA2 OB2/DNA-binding domain.
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= 1.30108e-05; MAF= 0.00130%, 21/1614046 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 1.7796e-05; MAF= 0.00178%, 21/1180042 alleles, homozygotes = 0); grpmax FAF= 1.144e-05.
gnomAD v2.1
Absent from gnomAD v2.1.
gnomAD-Canada
Not available in gnomAD-Canada v1.0.
ClinVar
This variant has been reported in ClinVar as Pathogenic (32 clinical laboratories) and as Uncertain significance (1 clinical laboratory) and as pathogenic (1 clinical laboratory) and as Pathogenic by Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) (expert panel). (ClinVarID = 52515)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.932. BayesDel score = 0.579612.
Functional
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Loss-of-function; curated oncogenicity label: Likely Oncogenic.
Somatic
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Cancer Hotspots
This variant does not lie in a statistically significant hotspot.