Five-step scale from benign to pathogenic. This variant is benign. Select a step to read what it means.
This variantScenario
BenignPathogenic
Benign.A benign classification under the recorded framework.
In plain language
Gene-level background from the recorded interpretation.
Words with a dotted underline have a short definition. Hover or tap them.
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.
LYFE Sciences is an AI system, and it can make mistakes.
Criteria may be applied incorrectly, sources may be misread, and a
confident-looking classification can still be wrong.
Double-check every criterion and its underlying evidence
before relying on any call.
01The reasoning
How it was classified
The recorded framework is ClinGen BRCA2 VCEP v1.2. 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.
No pathogenic criterion marked as applied in the recorded assessment.
Benign criteria applied · 6
BA1Stand alone
BA1 · stand alone
Met: gnomAD v2.1 non-cancer exome maximum filter allele frequency 0.00142293 exceeds the BRCA2 VCEP BA1 threshold of 0.001.
BS1Strong
BS1 · strong
Met, strong: gnomAD v2.1 non-cancer exome maximum filter allele frequency 0.00142293 exceeds the BRCA2 VCEP BS1 threshold of 0.0001.
BP1Strong
BP1 · strong
Met, Strong: synonymous Ala3246 is outside the aa 2481-3186 DNA-binding domain and SpliceAI max delta 0.013 is below the <=0.1 threshold.
BP4Supporting
BP4 · supporting
Met, Supporting: SpliceAI maximum delta 0.013 meets the ENIGMA BP4 threshold of <=0.1 for no predicted splice impact.
BP6Supporting
BP6 · supporting
Met, Supporting: exact-variant ClinVar expert-panel classification is Benign for c.9738C>T (p.Ala3246=), satisfying the requested BP6 rule.
BP7Supporting
BP7 · supporting
Met, Supporting: synonymous p.Ala3246= has SpliceAI maximum delta 0.013, satisfying BP4 and the ENIGMA BP7 requirement for silent variants.
Recorded classification: Benign
Benign: BA1 stand-alone benign is met by the gnomAD v2.1 non-cancer exome maximum filter allele frequency of 0.00142293, exceeding the ENIGMA threshold of 0.001.
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
89 / 1,613,924 alleles
gnomAD v4.1: 89 / 1,613,924 alleles. Recorded AF 5.51451e-05. Recorded homozygote count 1.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 0.000229932; MAF= 0.02299%, 65/282692 alleles, homozygotes = 1) and has highest observed frequency in the Admixed American population (AF= 0.00177886; MAF= 0.17789%, 63/35416 alleles, homozygotes = 1); grpmax FAF= 0.00140947.
ACMG/AMP criteria under ClinGen BRCA2 VCEP v1.2, with the data and sources behind each one.
28 criteria with recorded statuses: 6 met · 4 not met · 8 not assessed · 10 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
For the three requested consequence/length-change criteria, the governing ENIGMA BRCA1/2 V1.2 framework makes PVS1, PM4, and BP3 inapplicable to this synonymous substitution; no generic fallback is needed.
The variant is NM_000059.4:c.9738C>T, NP_000050.3:p.(Ala3246=), with SpliceAI max delta 0.013 and no documented RNA assay demonstrating a loss-of-function splice consequence.
The governing ENIGMA BRCA2 v1.2 specification was used for all five requested criteria; no generic substitution was needed.
This is a synonymous p.(Ala3246=) variant with SpliceAI max delta 0.013; BP1_Strong is met because residue 3246 is outside the specified critical domains and no splice impact is predicted.
PS1, PM1, PM5, and PP2 are not applicable under the variant type and governing ENIGMA rules.
For this segregation/de novo group, PS2 and PM6 are not applicable under the governing ENIGMA VCEP prohibition, while PP1 and BS4 remain not assessed because no quantitative segregation or non-segregation data are available.
The synonymous variant was searched in the on-record BRCA2 VCEP materials under c.9738C>T, p.Ala3246=, and p.A3246=; the converted HUMU-40-1557-s001.xlsx text had no entry, and SupplementaryTables_V1.2.xlsx full text was unavailable.
The variant is a synonymous BRCA2 change, NM_000059.4:c.9738C>T (NP_000050.3:p.(Ala3246=)); legacy literature uses 9966C>T/C9966T and Ala3246Ala.
PS4 is not met because the available case observations do not provide the ENIGMA-required case-control p-value, OR, and confidence interval.
PP4 and BP5 are not assessed because no exact-variant calibrated combined clinical LR was found in the governing LR tables.
The exact ClinVar expert-panel Benign classification supports BP6 under the requested rule and does not support PP5.
This synonymous variant is adjudicated through the SpliceAI path only: PP3 is not met at maximum delta 0.013, while ENIGMA BP4 Supporting and BP7 Supporting are met under the governing silent-variant rules.
The same SpliceAI result supports the single calibrated splice-impact conclusion; BP7 is assigned because the ENIGMA specification explicitly requires BP4 and applies BP7 in addition for synonymous variants, not as an independent predictor result.
No criteria match.
Met · 6
BA1Stand aloneMet: gnomAD v2.1 non-cancer exome maximum filter allele frequency 0.00142293 exceeds the BRCA2 VCEP BA1 threshold of 0.001.
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Reasoning
The BRCA2 VCEP specifies BA1 when the maximum filter allele frequency in a non-founder population exceeds 0.001, using gnomAD v2.1 non-cancer exomes and/or gnomAD v3.1 non-cancer genomes, with exome and genome data assessed separately. For NM_000059.4:c.9738C>T (p.Ala3246=), the gnomAD v2.1 non-cancer exome maximum filter allele frequency is 0.00142293 (0.142293%), exceeding 0.001; the record contains 63/236766 exome alleles and one homozygote. The gnomAD v3.1 non-cancer genome maximum filter allele frequency is 0.00021507, but the v2.1 non-cancer exome value independently meets BA1. The variant is not identified as a well-established pathogenic founder variant in the available evidence.
Rule
BRCA2 VCEP BA1: maximum filter allele frequency >0.001 in a gnomAD non-founder population; assess gnomAD v2.1 non-cancer exomes and gnomAD v3.1 non-cancer genomes separately; read depth must be >=20; exclude failed-quality data and established pathogenic founder variants.
Evidence considered
The BRCA2 VCEP specification defines BA1 as maximum filter allele frequency above 0.001 in a gnomAD non-founder population, using gnomAD v2.1 non-cancer exomes and gnomAD v3.1 non-cancer genomes with exome and genome data considered separately.
The BRCA2 VCEP appendix states that BA1 was rounded to 0.001 for BRCA2 based on a minimal credible allele frequency of 0.000906, and requires filter allele frequency rather than minor allele frequency.
The case evidence reports gnomAD v2.1 non-cancer exome AF 0.0002660855 from 63/236766 alleles, one homozygote, and maximum filter allele frequency 0.00142293; this exceeds 0.001.
The case evidence reports gnomAD v3.1 non-cancer genome maximum filter allele frequency 0.00021507, below BA1, but the v2.1 non-cancer exome value independently meets BA1.
Still missing
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found when searched in Specifications_V1.2_2024-11-18.docx.txt.
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found when searched in Appendices_V1.2_2024-11-18.docx.txt.
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found when searched in HUMU-40-1557-s001.xlsx.txt.
BS1StrongMet, strong: gnomAD v2.1 non-cancer exome maximum filter allele frequency 0.00142293 exceeds the BRCA2 VCEP BS1 threshold of 0.0001.
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Reasoning
The BRCA2 VCEP specifies BS1 at maximum filter allele frequency above 0.0001 and BS1_Supporting above 0.00002 through 0.0001 in a non-founder population, using gnomAD v2.1 non-cancer exomes and gnomAD v3.1 non-cancer genomes separately. The gnomAD v2.1 non-cancer exome maximum filter allele frequency for NM_000059.4:c.9738C>T (p.Ala3246=) is 0.00142293, which is above 0.0001 and therefore meets BS1 at strong strength. The same observation also meets the higher BA1 threshold; BS1 is consequently redundant for final combination but is met under its own VCEP rule.
Rule
BRCA2 VCEP BS1: maximum filter allele frequency >0.0001; BS1_Supporting applies only when >0.00002 and <=0.0001; use gnomAD v2.1 non-cancer exomes and gnomAD v3.1 non-cancer genomes separately, with read depth >=20.
Evidence considered
The BRCA2 VCEP specification defines BS1 as maximum filter allele frequency above 0.0001 and BS1_Supporting as greater than 0.00002 through 0.0001 in a gnomAD non-founder population, with exome and genome data assessed separately.
The BRCA2 VCEP appendix derives 0.0001 as the rounded BS1 threshold for BRCA2 and recommends the highest filter allele frequency in a non-founder population, excluding TCGA data and established pathogenic founder variants.
The case evidence reports gnomAD v2.1 non-cancer exome maximum filter allele frequency 0.00142293 for this variant, exceeding the strong BS1 threshold of 0.0001.
Still missing
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found when searched in Specifications_V1.2_2024-11-18.docx.txt.
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found when searched in Appendices_V1.2_2024-11-18.docx.txt.
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found when searched in HUMU-40-1557-s001.xlsx.txt.
BP1StrongMet, Strong: synonymous Ala3246 is outside the aa 2481-3186 DNA-binding domain and SpliceAI max delta 0.013 is below the <=0.1 threshold.
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Reasoning
The governing ENIGMA BRCA2 specification assigns BP1_Strong to silent substitutions outside a potentially clinically important functional domain when no splicing is predicted. The variant is synonymous at Ala3246, outside the specified DNA-binding domain aa 2481-3186 and PALB2-binding domain aa 10-40, and its SpliceAI max delta is 0.013, meeting the no-predicted-splice-impact requirement of <=0.1. Searches of Specifications_V1.2_2024-11-18.docx.txt, Appendices_V1.2_2024-11-18.docx.txt, and Specifications_Table4_V1.2_2024-11-18.xlsx.txt found no exact row for c.9738C>T, p.Ala3246=, or p.A3246=; the governing rule is nevertheless directly applicable.
Rule
BP1_Strong applies to a silent substitution outside a potentially clinically important functional domain with no predicted splicing impact (SpliceAI <=0.1).
Evidence considered
ENIGMA BRCA2 v1.2 states: apply BP1_Strong for a silent substitution outside the potentially clinically important domains when no splicing is predicted (SpliceAI <=0.1).
The variant is p.(Ala3246=); Ala3246 is outside the BRCA2 PALB2-binding domain aa 10-40 and DNA-binding domain aa 2481-3186.
SpliceAI max delta is 0.013, which is <=0.1 and therefore satisfies the ENIGMA no-predicted-splicing condition.
Still missing
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in Specifications_V1.2_2024-11-18.docx.txt.
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in Appendices_V1.2_2024-11-18.docx.txt.
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in Specifications_Table4_V1.2_2024-11-18.xlsx.txt.
BP4SupportingMet, Supporting: SpliceAI maximum delta 0.013 meets the ENIGMA BP4 threshold of <=0.1 for no predicted splice impact.
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Reasoning
The variant is synonymous (NM_000059.4:c.9738C>T; p.Ala3246=), so BP4 is evaluated through the SpliceAI path and not through REVEL. The ENIGMA BRCA2 specification assigns BP4 Supporting to silent variants inside a potentially clinically important functional domain when SpliceAI is <=0.1. The case SpliceAI maximum delta is 0.013, meeting that governing threshold. No exact variant-level entry was found when searching Specifications_V1.2_2024-11-18.docx, Appendices_V1.2_2024-11-18.docx, or PMID_22505045_Houdayer_2012_HumMutat.pdf for c.9738C>T, p.Ala3246=, and p.A3246=.
Rule
ENIGMA BRCA2 v1.2: apply BP4 Supporting to a silent variant inside a potentially clinically important functional domain when SpliceAI <=0.1.
Evidence considered
The case normalization identifies NM_000059.4:c.9738C>T as the synonymous protein change NP_000050.3:p.(Ala3246=), so the splice-impact path is applicable and REVEL is not used.
The ENIGMA BRCA2 specification states that BP4 applies to a silent variant inside a potentially clinically important functional domain when SpliceAI <=0.1.
The case SpliceAI result reports DS_AG 0.013, DS_AL 0.004, DS_DG 0.0, and DS_DL 0.0, with maximum delta 0.013; this meets the governing <=0.1 threshold.
The governing VCEP files were searched for c.9738C>T, p.Ala3246=, and p.A3246=; no exact variant-level entry was found in the Specifications, Appendices, or Houdayer full-text files.
Still missing
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in Specifications_V1.2_2024-11-18.docx.
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in Appendices_V1.2_2024-11-18.docx.
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in PMID_22505045_Houdayer_2012_HumMutat.pdf.
The ClinVar record identifies the Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) as the expert panel and reports Benign with reviewed-by-expert-panel status.
The requested exact-variant rule is satisfied: Benign expert-panel classification -> BP6 Supporting.
BP7SupportingMet, Supporting: synonymous p.Ala3246= has SpliceAI maximum delta 0.013, satisfying BP4 and the ENIGMA BP7 requirement for silent variants.
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Reasoning
The variant is synonymous (NM_000059.4:c.9738C>T; p.Ala3246=). The ENIGMA BRCA2 specification states that BP7 Supporting applies to a silent variant inside a potentially clinically important functional domain if BP4 is met, and that BP7 is applied in addition to BP4 to capture the low prior probability of pathogenicity of silent variants. BP4 is met because the SpliceAI maximum delta is 0.013, below the <=0.1 no-impact threshold. No exact variant-level entry was found when searching Specifications_V1.2_2024-11-18.docx, Appendices_V1.2_2024-11-18.docx, or PMID_22505045_Houdayer_2012_HumMutat.pdf for c.9738C>T, p.Ala3246=, and p.A3246=.
Rule
ENIGMA BRCA2 v1.2: apply BP7 Supporting to a silent variant inside a potentially clinically important functional domain if BP4 is met; BP7 is applied in addition to BP4.
Evidence considered
The case normalization identifies NM_000059.4:c.9738C>T as the synonymous protein change NP_000050.3:p.(Ala3246=).
The ENIGMA BRCA2 specification states that BP7 Supporting applies to silent variants inside a potentially clinically important functional domain if BP4 is met, and is applied in addition to BP4.
The case SpliceAI maximum delta is 0.013, which meets the ENIGMA BP4 no-impact threshold of <=0.1 and therefore satisfies the BP7 prerequisite.
The governing VCEP files were searched for c.9738C>T, p.Ala3246=, and p.A3246=; no exact variant-level entry was found in the Specifications, Appendices, or Houdayer full-text files.
Still missing
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in Specifications_V1.2_2024-11-18.docx.
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in Appendices_V1.2_2024-11-18.docx.
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in PMID_22505045_Houdayer_2012_HumMutat.pdf.
PS4Not met: published observations lack the ENIGMA PS4 requirements of p-value <=0.05, OR >=4, and a confidence interval excluding 2.0.
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Reasoning
The ENIGMA BRCA2 specification requires case-control evidence with p-value <=0.05, OR >=4, and a lower confidence interval excluding 2.0; it explicitly does not use simple proband counting. PMID:12442275 reports the synonymous variant under legacy notation 9966C>T in two Mexican breast-cancer patients, and PMID:15889636 reports it as C9966T/Ala3246Ala in one early-onset breast-cancer patient, but neither provides a qualifying case-control OR, p-value, or confidence interval. The governing SupplementaryTables_V1.2.xlsx was searched as directed, but its full text is unavailable, so the ST7 variant-level posterior/case-control lookup cannot be verified. The HUMU-40-1557-s001.xlsx full text was searched for c.9738C>T, p.Ala3246=, p.A3246=, and the legacy 9966C>T/Ala3246Ala notation without an entry. These observations alone do not meet the VCEP PS4 rule.
Rule
ENIGMA PS4 Strong: p-value <=0.05 AND OR >=4 AND lower confidence interval excludes 2.0; proband counting is not used.
Evidence considered
ENIGMA Table 1 states: 'Case-control studies; p-value <=0.05 and OR >=4 (lower confidence interval excludes 2.0).'
The ENIGMA specification states that proband counting is not used as originally described.
PMID:12442275 reports legacy BRCA2 9966C>T in two Mexican breast-cancer patients and notes that no RNA was available.
PMID:15889636 reports legacy BRCA2 C9966T/Ala3246Ala in one early-onset breast-cancer patient.
The exact comparison is not applicable because no qualifying numeric OR and confidence interval were available: OR >=4? not evaluable; p-value <=0.05? not evaluable.
Still missing
SupplementaryTables_V1.2.xlsx full text is unavailable; its ST7 Reference Set variant-level posterior/case-control entry could not be checked.
No qualifying case-control OR, p-value, or confidence interval was identified for this variant in the searchable HUMU-40-1557-s001.xlsx text or the cited papers.
PM2Not met: the variant is present in gnomAD v2.1 non-cancer exomes at AF 0.0002660855 and gnomAD v3.1 non-cancer genomes at AF 0.0000473491.
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Reasoning
The BRCA2 VCEP applies PM2_Supporting only when the variant is absent from controls in gnomAD v2.1 non-cancer exomes and gnomAD v3.1 non-cancer genomes, with regional read depth at least 25; it also states that a single observation in a gnomAD outbred population is not informative. This variant is present in both required non-cancer datasets: gnomAD v2.1 non-cancer exomes show AF 0.0002660855 (63/236766 alleles, one homozygote), and gnomAD v3.1 non-cancer genomes show AF 0.0000473491 (7/147838 alleles, zero homozygotes). Therefore it is not absent from controls and PM2 is not met.
Rule
BRCA2 VCEP PM2_Supporting: variant absent from gnomAD v2.1 non-cancer exomes and gnomAD v3.1 non-cancer genomes, with regional read depth >=25; exclude failed-quality data and do not apply to indels.
Evidence considered
The BRCA2 VCEP defines PM2_Supporting as absence from controls in gnomAD v2.1 non-cancer exomes and gnomAD v3.1 non-cancer genomes, requiring regional read depth at least 25 and excluding failed-quality data; a single outbred observation is not informative.
The case evidence reports gnomAD v2.1 non-cancer exome AF 0.0002660855 from 63/236766 alleles with one homozygote, so the variant is not absent from the specified exome controls.
The case evidence reports gnomAD v3.1 non-cancer genome AF 0.0000473491 from 7/147838 alleles with zero homozygotes, so the variant is also not absent from the specified genome controls.
The BRCA2 VCEP appendix estimates PM2 supporting weight from absence in controls but does not permit PM2 when the variant is observed in the specified control datasets.
Still missing
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found when searched in Specifications_V1.2_2024-11-18.docx.txt.
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found when searched in Appendices_V1.2_2024-11-18.docx.txt.
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found when searched in HUMU-40-1557-s001.xlsx.txt.
PP3Not met: SpliceAI maximum delta 0.013 is below the ENIGMA PP3 threshold of >=0.2 for predicted splicing in silent variants.
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Reasoning
The variant is synonymous (NM_000059.4:c.9738C>T; p.Ala3246=), so the applicable computational path is SpliceAI rather than REVEL. The ENIGMA BRCA2 specification applies PP3 to predicted splicing for silent variants when SpliceAI is >=0.2. The case SpliceAI maximum delta is 0.013, below the VCEP threshold, so PP3 is not met. No exact variant-level entry was found when searching Specifications_V1.2_2024-11-18.docx, Appendices_V1.2_2024-11-18.docx, or PMID_22505045_Houdayer_2012_HumMutat.pdf for c.9738C>T, p.Ala3246=, and p.A3246=.
Rule
ENIGMA BRCA2 v1.2: apply PP3 for predicted splicing in silent variants when SpliceAI >=0.2; do not apply PP3 when the calibrated splice prediction does not reach that threshold.
Evidence considered
The case normalization identifies NM_000059.4:c.9738C>T as the synonymous protein change NP_000050.3:p.(Ala3246=), so REVEL is not the applicable path.
The ENIGMA BRCA2 specification states that PP3 applies to predicted splicing in silent variants at SpliceAI >=0.2.
The ENIGMA Appendix J calibration states that SpliceAI <=0.1 supports BP4, values >0.1 and <0.2 are not informative, and values >=0.2 support PP3; the observed maximum delta is 0.013.
The governing VCEP files were searched for c.9738C>T, p.Ala3246=, and p.A3246=; no exact variant-level entry was found in the Specifications, Appendices, or Houdayer full-text files.
Still missing
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in Specifications_V1.2_2024-11-18.docx.
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in Appendices_V1.2_2024-11-18.docx.
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in PMID_22505045_Houdayer_2012_HumMutat.pdf.
PP5Not met: exact-variant ClinVar expert-panel classification is Benign, not Pathogenic or Likely pathogenic, so PP5 is not triggered.
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Reasoning
ClinVar variation 52896 is an exact match for NM_000059.4(BRCA2):c.9738C>T (p.Ala3246=), but the expert-panel classification is Benign, not Pathogenic or Likely pathogenic. The exact-variant ClinVar expert-panel result therefore does not support PP5. Ordinary laboratory submissions and aggregate labels were not used for this determination. The ENIGMA specification itself lists PP5 as do not use, but under the requested exact-variant expert-panel rule there is still no pathogenic expert-panel classification to trigger PP5.
PS3Not assessed: no calibrated protein-function or combined mRNA-and-protein assay entry was found for c.9738C>T (p.Ala3246=).
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Reasoning
The ENIGMA BRCA1/2 VCEP specification reserves PS3 for well-established protein-function assays or combined mRNA-and-protein assays and directs curators to calibrated Table 9 results. Searches of Specifications_Table9_V1.2_2024-11-18.xlsx, Specifications_V1.2_2024-11-18.docx, Appendices_V1.2_2024-11-18.docx, and HUMU-40-1557-s001.xlsx found no entry for c.9738C>T, p.Ala3246=, or p.A3246=. The case evidence contains no variant-specific protein or combined mRNA-and-protein assay result from which PS3 strength can be assigned; synonymous status and SpliceAI max delta 0.013 do not establish PS3.
Rule
Apply PS3 only for well-established in vitro or in vivo assays showing a damaging effect on protein function, using ENIGMA Table 9 calibrated code recommendations; mRNA-only evidence is handled under the alternative RNA code rather than PS3.
Evidence considered
ENIGMA VCEP Specifications v1.2 states that PS3 functional-assay evidence applies to assays measuring protein function alone or mRNA and protein together, with calibrated recommendations in Table 9.
ENIGMA VCEP Appendices v1.2 states that PS3 and BS3 are reserved for protein-function assays and that calibrated mammalian assay results were used for code-strength assignment.
The exact notations c.9738C>T, p.Ala3246=, and p.A3246= were searched in the declared VCEP functional files; no matching functional-assay row was found.
The case evidence reports a synonymous consequence and SpliceAI maximum delta 0.013, but neither establishes a damaging protein-function result for PS3.
Still missing
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in Specifications_Table9_V1.2_2024-11-18.xlsx.txt.
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in Specifications_V1.2_2024-11-18.docx.txt.
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in Appendices_V1.2_2024-11-18.docx.txt.
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in HUMU-40-1557-s001.xlsx.txt.
No variant-specific protein or combined mRNA-and-protein functional assay result was available in the case evidence bundle.
PM3Not assessed: no documented Fanconi anemia phenotype, pathogenic BRCA2 co-occurring variant, phase, or PM3-scoring affected-proband observation is available.
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Reasoning
The ENIGMA BRCA2 VCEP specification restricts PM3 to a patient with phenotype consistent with BRCA1/2-related Fanconi anemia and a co-occurring pathogenic or likely pathogenic BRCA2 variant; strength is assigned from Table 6 points for documented phase and phenotype. The available case evidence documents the synonymous variant NM_000059.4:c.9738C>T (p.Ala3246=) and population observations, but does not document a Fanconi anemia phenotype, a pathogenic/likely pathogenic BRCA2 co-occurring variant, phase, or affected-proband PM3 observation. The governing Specifications_V1.2_2024-11-18.docx was searched for c.9738C>T, p.Ala3246=, and p.A3246=, with no variant-specific PM3 entry found.
Rule
Apply for a patient with phenotype consistent with BRCA1- or BRCA2-related Fanconi anemia and co-occurring variants in the same gene; assign PM3 strength from the summed Table 6 points.
Evidence considered
ENIGMA BRCA2 VCEP Specifications V1.2 Table 1 states that PM3 applies only to a patient with phenotype consistent with BRCA1- or BRCA2-related Fanconi anemia and co-occurring variants in the same gene.
ENIGMA BRCA2 VCEP Specifications V1.2 Table 6 assigns PM3-related points using pathogenic/likely pathogenic variants in trans or homozygote versus unknown phase, with PM3_Supporting = 1 point, PM3 = 2 points, and PM3_Strong = 4 or more points.
The case evidence contains no documented Fanconi anemia phenotype, same-gene pathogenic co-occurrence, phase, or affected-proband observation sufficient to calculate PM3 points.
The governing Specifications_V1.2_2024-11-18.docx was searched under c.9738C>T, p.Ala3246=, and p.A3246=; no variant-specific PM3 entry was found.
Still missing
No documented Fanconi anemia phenotype meeting the ENIGMA criteria (chromosome-breakage result and required clinical features).
No documented pathogenic or likely pathogenic BRCA2 co-occurring variant in the same patient and no phase information.
No variant-specific PM3 entry for c.9738C>T, p.Ala3246=, or p.A3246= was found in Specifications_V1.2_2024-11-18.docx.
Sources
vcep_specifications_v1_2_2024_11_18
PP1Not assessed: no pedigree or quantitative co-segregation likelihood ratio is available to compare with the ENIGMA PP1 thresholds of 2.08, 4.3, 18.7, or 350.
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Reasoning
The ENIGMA VCEP requires quantitative co-segregation evidence from multiple affected family members and assigns PP1 strength by likelihood ratio: supporting at LR ≥2.08, moderate at LR ≥4.3, strong at LR ≥18.7, and very strong at LR ≥350. The case bundle and directly reviewed case papers provide no pedigree, tested relatives, parental phase, meioses, phenotype-by-relative data, or quantitative co-segregation LR for NM_000059.4:c.9738C>T. The reports of synonymous BRCA2 substitutions in Mexican breast-cancer cohorts do not provide segregation analysis and cannot establish PP1.
Rule
ENIGMA BRCA1/2 VCEP V1.2: PP1_VariableWeight — quantitative co-segregation with disease in multiple affected family members; supporting LR ≥2.08, moderate LR ≥4.3, strong LR ≥18.7, very strong LR ≥350.
Evidence considered
ENIGMA BRCA1/2 VCEP Specifications V1.2, Table 1: PP1 is variable-weight co-segregation evidence requiring a quantitative Bayes score; PP1 supporting requires LR ≥2.08, PP1 moderate LR ≥4.3, PP1 strong LR ≥18.7, and PP1 very strong LR ≥350.
The consolidated case-evidence bundle contains no pedigree, parental-testing, meiosis, relative-genotype, phenotype-consistency, or quantitative segregation result for this variant.
PMID:12442275 reports BRCA2 9966C>T in two Mexican breast-cancer patients and notes a family containing a male breast-cancer case, but explicitly provides no RNA result and no segregation analysis for the synonymous substitution.
PMID:15889636 reports a BRCA2 synonymous substitution written as C9966T/Ala3246Ala in one patient from a 22-woman Mexican early-onset breast-cancer cohort; the extracted finding provides no segregation analysis.
The available converted HUMU-40-1557-s001.xlsx text was searched under c.9738C>T, p.Ala3246=, and p.A3246= without finding a variant entry; this is a search result, not evidence that segregation evidence is biologically absent.
SupplementaryTables_V1.2.xlsx is declared by the VCEP index for BS4 and PS4, but its full text conversion is unavailable, so its ST7 posterior/LR table could not be checked.
Still missing
No quantitative co-segregation likelihood ratio or COOL/CAL-Leiden result is available.
No pedigree-level list of affected and unaffected relatives, genotypes, phenotypes, or informative meioses is available.
No parental testing or phase information is available.
HUMU-40-1557-s001.xlsx was searched under c.9738C>T, p.Ala3246=, and p.A3246=; no entry was found in the available converted full text.
SupplementaryTables_V1.2.xlsx declares BS4 and PS4, but its full text is unavailable and therefore no ST7 variant-level LR or posterior lookup could be verified.
PP4Not assessed: no exact-variant combined clinical likelihood ratio was available for comparison with the PP4 threshold of LR >=2.08.
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Reasoning
ENIGMA restricts PP4 to a combined multifactorial likelihood ratio for clinical data, with Supporting at LR >=2.08, Moderate at LR >=4.3, Strong at LR >=18.7, and Very Strong at LR >=350. The exact-variant row was not found in PMID_31853058_BRCA2_clinical_history_LR.xlsx, and no exact-variant combined clinical LR was found in HUMU-40-1557-s001.xlsx or the cited case reports. The two legacy-notation case observations are not a calibrated combined LR and cannot be converted into PP4 strength.
Rule
ENIGMA PP4: use only combined multifactorial clinical LR; Supporting LR >=2.08, Moderate LR >=4.3, Strong LR >=18.7, Very Strong LR >=350.
Evidence considered
ENIGMA PP4 thresholds are Supporting LR >=2.08, Moderate LR >=4.3, Strong LR >=18.7, and Very Strong LR >=350.
PMID:31853058 is a clinical-history LR methodology source; its gene-specific variant-level table is the required lookup source.
The exact comparison cannot be written with a substituted value because no exact-variant LR was available: LR >=2.08? not evaluable.
Still missing
No exact c.9738C>T, p.Ala3246=, p.A3246=, or legacy equivalent row was found in PMID_31853058_BRCA2_clinical_history_LR.xlsx.
No exact-variant combined clinical LR was found in HUMU-40-1557-s001.xlsx.
BS2Not assessed: one gnomAD homozygote is frequency evidence, not the VCEP's required phenotyped healthy-adult observation for BS2.
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Reasoning
The BRCA2 VCEP restricts BS2 to phenotyped individuals from clinical or research cohorts who lack features of Fanconi Anemia and assigns points according to age at cancer onset or age at last follow-up, with final strength based on the accumulated points. The single homozygote reported in gnomAD is frequency evidence from an unspecified adult population and is explicitly not eligible for BS2 under the VCEP; it cannot establish the required phenotyped healthy-adult observation. No qualifying clinical or research-cohort BS2 point data for this variant are present in the reviewed case evidence.
Rule
BRCA2 VCEP BS2: apply only to phenotyped clinical or research-cohort individuals meeting the specified age or cancer-unaffected follow-up criteria and lacking Fanconi Anemia features; do not use gnomAD frequency observations for BS2.
Evidence considered
The BRCA2 VCEP defines BS2 as a variable-weight code for phenotyped individuals with a recessive, dominant, or X-linked disorder who lack the relevant disease phenotype; for BRCA2, this requires assessment of Fanconi Anemia features and age or follow-up criteria.
The VCEP explicitly states that homozygotes observed in gnomAD are not to be used for frequency-based BS2 assignment because gnomAD adults are of unspecified age and such observations are captured by BA1 or BS1 instead.
The case evidence reports one homozygote in gnomAD v2.1 non-cancer exomes and one homozygote in gnomAD v4.1 all-comers data, but provides no qualifying phenotyped clinical or research-cohort BS2 observation.
Still missing
No qualifying phenotyped clinical or research-cohort observation with documented absence of Fanconi Anemia features and age or follow-up information was provided for BS2.
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found when searched in Specifications_V1.2_2024-11-18.docx.txt.
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found when searched in Appendices_V1.2_2024-11-18.docx.txt.
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found when searched in HUMU-40-1557-s001.xlsx.txt.
BS3Not assessed: no calibrated benign protein-function or combined mRNA-and-protein assay entry was found for c.9738C>T (p.Ala3246=).
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Reasoning
The ENIGMA BRCA1/2 VCEP specification reserves BS3 for well-established protein-function assays or combined mRNA-and-protein assays showing no damaging effect and directs curators to calibrated Table 9 results. Searches of Specifications_Table9_V1.2_2024-11-18.xlsx, Specifications_V1.2_2024-11-18.docx, Appendices_V1.2_2024-11-18.docx, and HUMU-40-1557-s001.xlsx found no entry for c.9738C>T, p.Ala3246=, or p.A3246=. The case evidence contains no variant-specific benign protein or combined mRNA-and-protein assay result from which BS3 strength can be assigned; synonymous status and SpliceAI max delta 0.013 do not establish BS3.
Rule
Apply BS3 only for well-established in vitro or in vivo assays showing no damaging effect on protein function, using ENIGMA Table 9 calibrated code recommendations; mRNA-only evidence is handled under the alternative RNA code rather than BS3.
Evidence considered
ENIGMA VCEP Specifications v1.2 states that BS3 functional-assay evidence applies to assays measuring protein function alone or mRNA and protein together, with calibrated recommendations in Table 9.
ENIGMA VCEP Appendices v1.2 states that calibrated mammalian assay results were selected for reliable BRCA1/2 protein-function interpretation and that no-impact results can provide strong evidence against pathogenicity when applicable.
The exact notations c.9738C>T, p.Ala3246=, and p.A3246= were searched in the declared VCEP functional files; no matching functional-assay row was found.
The case evidence reports a synonymous consequence and SpliceAI maximum delta 0.013, but neither establishes a benign protein-function result for BS3.
Still missing
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in Specifications_Table9_V1.2_2024-11-18.xlsx.txt.
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in Specifications_V1.2_2024-11-18.docx.txt.
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in Appendices_V1.2_2024-11-18.docx.txt.
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in HUMU-40-1557-s001.xlsx.txt.
No variant-specific benign protein or combined mRNA-and-protein functional assay result was available in the case evidence bundle.
BS4Not assessed: no affected-relative non-segregation result or quantitative likelihood ratio is available to compare with the ENIGMA BS4 thresholds of 0.48, 0.23, 0.05, or 0.00285.
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Reasoning
The ENIGMA VCEP requires quantitative evidence of lack of segregation in affected family members and assigns BS4 strength by likelihood ratio: supporting at LR ≤0.48, moderate at LR ≤0.23, strong at LR ≤0.05, and very strong at LR ≤0.00285. No affected-relative non-segregation, tested-relative genotype, pedigree, phase, or quantitative BS4 LR is provided for NM_000059.4:c.9738C>T. The reviewed cohort papers report observations of synonymous BRCA2 substitutions but do not provide variant-level non-segregation analysis, so BS4 cannot be assigned.
Rule
ENIGMA BRCA1/2 VCEP V1.2: BS4_VariableWeight — quantitative lack of segregation in affected family members; supporting LR ≤0.48, moderate LR ≤0.23, strong LR ≤0.05, very strong LR ≤0.00285.
Evidence considered
ENIGMA BRCA1/2 VCEP Specifications V1.2, Table 1: BS4 is variable-weight lack of segregation in affected family members; BS4 supporting requires LR ≤0.48, moderate LR ≤0.23, strong LR ≤0.05, and very strong LR ≤0.00285.
The consolidated case-evidence bundle contains no affected-relative non-segregation, pedigree, tested-relative genotype, phase, or quantitative BS4 result for this variant.
PMID:12442275 reports BRCA2 9966C>T in breast-cancer patients and mentions the only family in that series containing a male breast-cancer case, but does not report whether the variant segregated or failed to segregate with disease.
PMID:15889636 reports a synonymous BRCA2 substitution written as C9966T/Ala3246Ala in a breast-cancer cohort but provides no variant-level affected-relative non-segregation analysis.
The available converted HUMU-40-1557-s001.xlsx text was searched under c.9738C>T, p.Ala3246=, and p.A3246= without finding a variant entry; this is a search result, not evidence that non-segregation evidence is biologically absent.
SupplementaryTables_V1.2.xlsx is declared by the VCEP index for BS4 and PS4, but its full text conversion is unavailable, so its ST7 posterior/LR table could not be checked.
Still missing
No quantitative non-segregation likelihood ratio or COOL/CAL-Leiden result is available.
No pedigree-level list of affected relatives who lack the variant is available.
No tested-relative genotypes, phase information, phenotype details, or informative meioses are available.
HUMU-40-1557-s001.xlsx was searched under c.9738C>T, p.Ala3246=, and p.A3246=; no entry was found in the available converted full text.
SupplementaryTables_V1.2.xlsx declares BS4 and PS4, but its full text is unavailable and therefore no ST7 variant-level LR or posterior lookup could be verified.
BP5Not assessed: no exact-variant combined LR was available for comparison with the BP5 Supporting threshold of LR <=0.48.
Details ▾Hide ▴
Reasoning
ENIGMA BP5 is restricted to a combined multifactorial likelihood ratio against pathogenicity, with Supporting LR <=0.48, Moderate LR <=0.23, Strong LR <=0.05, and Very Strong LR <=0.00285. The exact-variant row was not found in PMID_31853058_BRCA2_clinical_history_LR.xlsx, and no exact-variant combined LR was found in HUMU-40-1557-s001.xlsx or the cited papers. The ClinVar Benign expert-panel classification is handled under the requested BP6 rule and is not converted into BP5.
Rule
ENIGMA BP5: use only combined multifactorial clinical LR; Supporting LR <=0.48, Moderate LR <=0.23, Strong LR <=0.05, Very Strong LR <=0.00285.
Evidence considered
ENIGMA BP5 thresholds are Supporting LR <=0.48, Moderate LR <=0.23, Strong LR <=0.05, and Very Strong LR <=0.00285.
The exact comparison direction is low LR: LR <=0.48? not evaluable because no exact-variant LR was available.
The ClinVar expert-panel benign result is not used as a multifactorial clinical LR.
Still missing
No exact c.9738C>T, p.Ala3246=, p.A3246=, or legacy equivalent row was found in PMID_31853058_BRCA2_clinical_history_LR.xlsx.
No exact-variant combined clinical LR was found in HUMU-40-1557-s001.xlsx.
Not applicable · 10· recorded as not applicableShow reasons ▾Hide reasons ▴PVS1N/ANot applicable: c.9738C>T is synonymous (p.Ala3246=), with SpliceAI max delta 0.013 and no qualifying loss-of-function consequence.
Details ▾Hide ▴
Reasoning
NM_000059.4:c.9738C>T is a synonymous variant, NP_000050.3:p.(Ala3246=), rather than a nonsense, frameshift, canonical +/-1,2 splice-site, initiation-codon, or deletion variant. The ENIGMA BRCA2 specification limits PVS1 to null-variant mechanisms and mRNA-assay evidence evaluated through its PVS1 variable-weight framework; no qualifying loss-of-function consequence is present. The BRCA2 Table 4 exon-level PVS1 decision table contains no applicable row for this synonymous substitution. SpliceAI max delta is 0.013, below the VCEP no-significant-splice-impact threshold of 0.1, and the variant-level literature extraction reports no RNA assay for the corresponding historical 9966C>T notation.
Rule
ENIGMA BRCA1/2 V1.2: PVS1 is restricted to qualifying null variants or appropriately weighted mRNA evidence; this synonymous variant does not qualify.
Evidence considered
The case normalization identifies NM_000059.4:c.9738C>T as NP_000050.3:p.(Ala3246=), with consequence_class synonymous.
ENIGMA BRCA2 V1.2 specifies PVS1 for null variants and mRNA-assay loss-of-function evidence, not ordinary synonymous substitutions; its Table 4 is an exon-level decision table for initiation, nonsense/frameshift, deletion, duplication, and canonical splice-site variants.
The case SpliceAI result is max delta 0.013; the ENIGMA specification uses SpliceAI <=0.1 for no predicted splice impact in its bioinformatic framework.
The extracted PMID:12442275 finding describes the corresponding historical BRCA2 9966C>T silent substitution and states that no RNA was available to test splicing.
Still missing
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found when searched in Specifications_V1.2_2024-11-18.docx.txt.
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found when searched in Appendices_V1.2_2024-11-18.docx.txt.
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found when searched in Specifications_Table4_V1.2_2024-11-18.xlsx.txt.
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found when searched in PMID_22505045_Houdayer_2012_HumMutat.pdf.txt.
PS1N/ANot applicable: the synonymous p.Ala3246= change is neither a missense match nor a demonstrated pathogenic splice-event match, with SpliceAI max delta 0.013.
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Reasoning
The ENIGMA BRCA2 specification limits PS1 for protein-change evidence to a predicted missense substitution matching a previously pathogenic or likely pathogenic amino-acid substitution, or to variants with the same established splice effect as a pathogenic reference. NM_000059.4:c.9738C>T is synonymous, encodes p.(Ala3246=), and has SpliceAI max delta 0.013, so neither PS1 pathway applies. Searches of Specifications_V1.2_2024-11-18.docx.txt, Appendices_V1.2_2024-11-18.docx.txt, and Specifications_Table4_V1.2_2024-11-18.xlsx.txt found no exact row for c.9738C>T, p.Ala3246=, or p.A3246=.
Rule
PS1 applies to a predicted missense substitution matching a previously classified pathogenic or likely pathogenic protein change, or to an exonic/intronic variant with the same predicted splice impact as a pathogenic reference; the missense pathway requires no confirmed or predicted splice effect (SpliceAI <=0.1).
Evidence considered
ENIGMA BRCA2 v1.2 specifies PS1 for a predicted missense substitution matching a known pathogenic or likely pathogenic protein change, with the splice-matching pathway reserved for the same predicted splicing impact.
The case variant is NM_000059.4:c.9738C>T, p.(Ala3246=), a synonymous substitution; SpliceAI max delta is 0.013, below the specification's no-significant-splice-impact threshold of 0.1.
Still missing
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in Specifications_V1.2_2024-11-18.docx.txt.
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in Appendices_V1.2_2024-11-18.docx.txt.
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in Specifications_Table4_V1.2_2024-11-18.xlsx.txt.
PS2VCEPNot applicable: the ENIGMA VCEP explicitly prohibits PS2 because de novo predictive capacity is uncalibrated for BRCA1/2-related cancers.
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Reasoning
The ENIGMA BRCA1/2 VCEP specification explicitly states that PS2 is not to be used for BRCA1/2-related cancers because there is no calibrated information on the predictive capacity of de novo occurrences. This criterion therefore cannot be assigned regardless of whether parental testing is available in this case.
VCEP rule
ENIGMA BRCA1/2 VCEP V1.2: PS2 — Do not use; no calibrated predictive capacity for de novo occurrences in BRCA1/2-related cancers.
Evidence considered
ENIGMA BRCA1/2 VCEP Specifications V1.2, Table 1: PS2 is listed as 'Do not use' because BRCA1/2-related cancers occur relatively commonly and there is no information to calibrate the predictive capacity of de novo occurrences.
The case materials identify the variant as NM_000059.4:c.9738C>T (NP_000050.3:p.(Ala3246=)), but PS2 remains not applicable under the governing VCEP rule.
The on-record SupplementaryTables_V1.2.xlsx full text is unavailable and was not used to infer PS2; its unavailable conversion is a documented file gap.
Sources
vcep_specifications_v1_2_2024_11_18
PM1VCEPNot applicable: Ala3246 lies outside the ENIGMA BRCA2 critical domains, which end at residue 3186, and the variant is synonymous.
Details ▾Hide ▴
Reasoning
The governing ENIGMA BRCA2 specification defines the clinically important domains as the PALB2-binding domain at amino acids 10-40 and the DNA-binding domain at amino acids 2481-3186. Residue Ala3246 lies outside both domains, and the variant is synonymous rather than a missense change. The case vcep_materials.json domain_tables key is empty, so no additional authoritative domain-table entry supersedes the governing specification. Searches of Specifications_V1.2_2024-11-18.docx.txt and Appendices_V1.2_2024-11-18.docx.txt found no exact row for c.9738C>T, p.Ala3246=, or p.A3246=.
VCEP rule
PM1 concerns a mutational hotspot or critical, well-established functional domain without benign variation; ENIGMA BRCA2 clinically important domains are PALB2 binding aa 10-40 and DNA binding aa 2481-3186.
Evidence considered
ENIGMA BRCA2 v1.2 defines the PALB2-binding domain as residues 10-40 and the DNA-binding domain as residues 2481-3186; Ala3246 is outside both boundaries.
The gene-specific vcep_materials.json domain_tables object is empty, so the complete governing domain list is the specification's domain definition.
Still missing
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in Specifications_V1.2_2024-11-18.docx.txt.
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in Appendices_V1.2_2024-11-18.docx.txt.
vcep_materials.json has an empty domain_tables object; no additional gene-specific domain-table row is available for residue 3246.
Sources
vcep_specifications_v1_2_2024_11_18
PM4VCEPNot applicable: p.Ala3246= causes no protein-length change, and ENIGMA explicitly designates PM4 as not applicable.
Details ▾Hide ▴
Reasoning
The ENIGMA BRCA1/2 V1.2 specification explicitly designates PM4 as not applicable and states that protein-length changes from in-frame insertions/deletions or stop-loss variants are handled through bioinformatic analysis. This variant is synonymous, produces no protein-length change, and is not an in-frame insertion, deletion, delins, or stop-loss variant.
VCEP rule
ENIGMA BRCA1/2 V1.2 PM4: not applicable; protein-length changes are considered through bioinformatic analysis.
Evidence considered
The ENIGMA specification's PM4 row states 'Do not use' and identifies the applicable class as protein-length changes due to in-frame insertions/deletions or stop-loss variants.
The normalized protein consequence is p.(Ala3246=), so protein length is unchanged.
Sources
vcep_specifications_v1_2_2024_11_18
PM5N/ANot applicable: ENIGMA PM5 is restricted to PTC/truncating variants, whereas c.9738C>T is synonymous and yields p.Ala3246=.
Details ▾Hide ▴
Reasoning
The governing ENIGMA BRCA2 v1.2 rule repurposes PM5 for a protein-termination-codon variant in an exon where a different proven pathogenic PTC has been observed, with exon-specific PM5(PTC) weights. NM_000059.4:c.9738C>T is synonymous and produces p.(Ala3246=), not a PTC or truncating variant, so PM5 cannot apply. Searches of Specifications_V1.2_2024-11-18.docx.txt, Appendices_V1.2_2024-11-18.docx.txt, and Specifications_Table4_V1.2_2024-11-18.xlsx.txt found no exact row for c.9738C>T, p.Ala3246=, or p.A3246=.
Rule
PM5 is applied to a PTC variant in an exon where a different proven pathogenic PTC has been seen before; ENIGMA specifies exon-specific PM5(PTC) weights.
Evidence considered
ENIGMA BRCA2 v1.2 defines PM5 as additional evidence for PTC variants in an exon with a different proven pathogenic PTC, using Table 4 exon-specific PM5(PTC) weights.
The assessed variant is synonymous, p.(Ala3246=), and is not a protein-termination or truncating variant.
Still missing
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in Specifications_V1.2_2024-11-18.docx.txt.
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in Appendices_V1.2_2024-11-18.docx.txt.
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in Specifications_Table4_V1.2_2024-11-18.xlsx.txt.
PM6VCEPNot applicable: the ENIGMA VCEP explicitly prohibits PM6 because de novo predictive capacity is uncalibrated for BRCA1/2-related cancers.
Details ▾Hide ▴
Reasoning
The ENIGMA BRCA1/2 VCEP specification explicitly states that PM6 is not to be used for BRCA1/2-related cancers for the same lack of calibrated predictive information for de novo occurrences without confirmed parentage. This criterion therefore cannot be assigned regardless of parental testing details.
VCEP rule
ENIGMA BRCA1/2 VCEP V1.2: PM6 — Do not use; no calibrated predictive capacity for de novo occurrences in BRCA1/2-related cancers.
Evidence considered
ENIGMA BRCA1/2 VCEP Specifications V1.2, Table 1: PM6 is listed as 'Do not use' because BRCA1/2-related cancers occur relatively commonly and there is no information to calibrate the predictive capacity of de novo occurrences.
The case materials identify the variant as NM_000059.4:c.9738C>T (NP_000050.3:p.(Ala3246=)), but PM6 remains not applicable under the governing VCEP rule.
The on-record SupplementaryTables_V1.2.xlsx full text is unavailable and was not used to infer PM6; its unavailable conversion is a documented file gap.
Sources
vcep_specifications_v1_2_2024_11_18
PP2VCEPNot applicable: the governing ENIGMA BRCA2 framework marks PP2 not applicable, and this variant is synonymous rather than missense.
Details ▾Hide ▴
Reasoning
The governing ENIGMA BRCA2 framework explicitly marks PP2 as not applicable. Independently, PP2 is a missense-gene mechanism criterion, while NM_000059.4:c.9738C>T is synonymous and encodes p.(Ala3246=). Searches of Specifications_V1.2_2024-11-18.docx.txt and Appendices_V1.2_2024-11-18.docx.txt found no exact row for c.9738C>T, p.Ala3246=, or p.A3246=.
VCEP rule
PP2 is marked Not Applicable in the governing ENIGMA BRCA2 framework.
Evidence considered
The governing ENIGMA BRCA2 rule set explicitly lists PP2 as Not Applicable.
The case consequence is synonymous, p.(Ala3246=), not missense.
Still missing
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in Specifications_V1.2_2024-11-18.docx.txt.
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in Appendices_V1.2_2024-11-18.docx.txt.
Sources
vcep_specifications_v1_2_2024_11_18
BP2VCEPNot applicable: the ENIGMA BRCA2 VCEP explicitly says BP2 is not used and is applied only in the context of BS2.
Details ▾Hide ▴
Reasoning
The ENIGMA BRCA1/2 VCEP specification explicitly states that BP2 is not to be used and is applied only in the context of BS2. Therefore BP2 is not applicable under the governing BRCA2 framework, regardless of whether cis or trans observations might otherwise be available.
VCEP rule
Do not use; applied only in the context of BS2.
Evidence considered
ENIGMA BRCA2 VCEP Specifications V1.2 Table 1 states for BP2: Do not use; applied only in the context of BS2.
The governing Specifications_V1.2_2024-11-18.docx was searched under c.9738C>T, p.Ala3246=, and p.A3246=; no variant-specific BP2 entry was found.
Still missing
No variant-specific BP2 entry for c.9738C>T, p.Ala3246=, or p.A3246= was found in Specifications_V1.2_2024-11-18.docx.
Sources
vcep_specifications_v1_2_2024_11_18
BP3VCEPNot applicable: c.9738C>T is a synonymous single-nucleotide substitution, not an in-frame insertion or deletion in a repeat region.
Details ▾Hide ▴
Reasoning
The ENIGMA BRCA1/2 V1.2 specification explicitly designates BP3 as not applicable and states that in-frame deletions/insertions in repetitive regions without known function are captured by bioinformatic prediction and domain analysis. This variant is a synonymous single-nucleotide substitution, not an in-frame deletion or insertion, and no repeat-region protein-length alteration exists to evaluate.
VCEP rule
ENIGMA BRCA1/2 V1.2 BP3: not applicable; the criterion is not used for this variant class.
Evidence considered
The ENIGMA specification's BP3 row states 'Do not use' for in-frame deletions/insertions in repetitive regions without known function.
The normalized consequence is synonymous, p.(Ala3246=), with no insertion, deletion, delins, or protein-length change.
Sources
vcep_specifications_v1_2_2024_11_18
Identifiers
Gene
BRCA2
Transcript
NM_000059.4
Coding (HGVS c.)
NM_000059.4:c.9738C>T
Protein (HGVS p.)
NP_000050.3:p.(Ala3246=)
GRCh38
chr13:32398251 C>T
GRCh37
chr13:32972388 C>T
Location and type
Exon 27 · synonymous
ClinVar
52896
Gene diagram
Every interpreted variant in BRCA2, mapped onto the exon structure of NM_000059.4. Select a row to find it on the plot.
BRCA2NM_000059.4
Fetching transcript structure from UCSC…
Exons
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Transcript span
—
Strand
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Variants mapped
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Source
UCSC ncbiRefSeqCurated
All variants in BRCA2—Select a row to find it on the plot; use the link to open its page.
AF 5.5e-05 · 89 / 1,613,924 alleles · 1 hom · FAF 0.0012
Admixed American86 / 59,994
0.00141 hom
Middle Eastern1 / 6,084
0.00016
Remaining individuals2 / 62,488
3.2e-05
0 alternate alleles recorded in 7 other groups: European (Finnish), Amish, East Asian, South Asian, Ashkenazi Jewish, African/African American, European (non-Finnish).
gnomAD v2.1
AF 0.00023 · 65 / 282,692 alleles · 1 hom · FAF 0.0014
Admixed American63 / 35,416
0.00181 hom
Remaining individuals2 / 7,218
0.00028
0 alternate alleles recorded in 6 other groups: African/African American, Ashkenazi Jewish, East Asian, European (Finnish), European (non-Finnish), South Asian.
Statements
gnomAD v4.1
This variant is present in gnomAD v4.1 (AF= 5.51451e-05; MAF= 0.00551%, 89/1613924 alleles, homozygotes = 1) and has highest observed frequency in the Admixed American population (AF= 0.00143348; MAF= 0.14335%, 86/59994 alleles, homozygotes = 1); grpmax FAF= 0.00118865.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 0.000229932; MAF= 0.02299%, 65/282692 alleles, homozygotes = 1) and has highest observed frequency in the Admixed American population (AF= 0.00177886; MAF= 0.17789%, 63/35416 alleles, homozygotes = 1); grpmax FAF= 0.00140947.
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
SpliceAI and Pangolin
SpliceAI acceptor lossat -27 bp
0.004
SpliceAI acceptor gainat +335 bp
0.013
SpliceAI donor lossat -461 bp
0.000
SpliceAI donor gainat -74 bp
0.000
Pangolin splice lossmagnitude shown
-0.011
Pangolin splice gain
0.004
Other predictors
REVEL
Not available
BayesDel
Not available
How the predictions were used
BP4SupportingMet, Supporting: SpliceAI maximum delta 0.013 meets the ENIGMA BP4 threshold of <=0.1 for no predicted splice impact.
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Reasoning
The variant is synonymous (NM_000059.4:c.9738C>T; p.Ala3246=), so BP4 is evaluated through the SpliceAI path and not through REVEL. The ENIGMA BRCA2 specification assigns BP4 Supporting to silent variants inside a potentially clinically important functional domain when SpliceAI is <=0.1. The case SpliceAI maximum delta is 0.013, meeting that governing threshold. No exact variant-level entry was found when searching Specifications_V1.2_2024-11-18.docx, Appendices_V1.2_2024-11-18.docx, or PMID_22505045_Houdayer_2012_HumMutat.pdf for c.9738C>T, p.Ala3246=, and p.A3246=.
Rule
ENIGMA BRCA2 v1.2: apply BP4 Supporting to a silent variant inside a potentially clinically important functional domain when SpliceAI <=0.1.
Evidence considered
The case normalization identifies NM_000059.4:c.9738C>T as the synonymous protein change NP_000050.3:p.(Ala3246=), so the splice-impact path is applicable and REVEL is not used.
The ENIGMA BRCA2 specification states that BP4 applies to a silent variant inside a potentially clinically important functional domain when SpliceAI <=0.1.
The case SpliceAI result reports DS_AG 0.013, DS_AL 0.004, DS_DG 0.0, and DS_DL 0.0, with maximum delta 0.013; this meets the governing <=0.1 threshold.
The governing VCEP files were searched for c.9738C>T, p.Ala3246=, and p.A3246=; no exact variant-level entry was found in the Specifications, Appendices, or Houdayer full-text files.
Still missing
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in Specifications_V1.2_2024-11-18.docx.
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in Appendices_V1.2_2024-11-18.docx.
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in PMID_22505045_Houdayer_2012_HumMutat.pdf.
BP7SupportingMet, Supporting: synonymous p.Ala3246= has SpliceAI maximum delta 0.013, satisfying BP4 and the ENIGMA BP7 requirement for silent variants.
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Reasoning
The variant is synonymous (NM_000059.4:c.9738C>T; p.Ala3246=). The ENIGMA BRCA2 specification states that BP7 Supporting applies to a silent variant inside a potentially clinically important functional domain if BP4 is met, and that BP7 is applied in addition to BP4 to capture the low prior probability of pathogenicity of silent variants. BP4 is met because the SpliceAI maximum delta is 0.013, below the <=0.1 no-impact threshold. No exact variant-level entry was found when searching Specifications_V1.2_2024-11-18.docx, Appendices_V1.2_2024-11-18.docx, or PMID_22505045_Houdayer_2012_HumMutat.pdf for c.9738C>T, p.Ala3246=, and p.A3246=.
Rule
ENIGMA BRCA2 v1.2: apply BP7 Supporting to a silent variant inside a potentially clinically important functional domain if BP4 is met; BP7 is applied in addition to BP4.
Evidence considered
The case normalization identifies NM_000059.4:c.9738C>T as the synonymous protein change NP_000050.3:p.(Ala3246=).
The ENIGMA BRCA2 specification states that BP7 Supporting applies to silent variants inside a potentially clinically important functional domain if BP4 is met, and is applied in addition to BP4.
The case SpliceAI maximum delta is 0.013, which meets the ENIGMA BP4 no-impact threshold of <=0.1 and therefore satisfies the BP7 prerequisite.
The governing VCEP files were searched for c.9738C>T, p.Ala3246=, and p.A3246=; no exact variant-level entry was found in the Specifications, Appendices, or Houdayer full-text files.
Still missing
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in Specifications_V1.2_2024-11-18.docx.
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in Appendices_V1.2_2024-11-18.docx.
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in PMID_22505045_Houdayer_2012_HumMutat.pdf.
PP3Not met: SpliceAI maximum delta 0.013 is below the ENIGMA PP3 threshold of >=0.2 for predicted splicing in silent variants.
Details ▾Hide ▴
Reasoning
The variant is synonymous (NM_000059.4:c.9738C>T; p.Ala3246=), so the applicable computational path is SpliceAI rather than REVEL. The ENIGMA BRCA2 specification applies PP3 to predicted splicing for silent variants when SpliceAI is >=0.2. The case SpliceAI maximum delta is 0.013, below the VCEP threshold, so PP3 is not met. No exact variant-level entry was found when searching Specifications_V1.2_2024-11-18.docx, Appendices_V1.2_2024-11-18.docx, or PMID_22505045_Houdayer_2012_HumMutat.pdf for c.9738C>T, p.Ala3246=, and p.A3246=.
Rule
ENIGMA BRCA2 v1.2: apply PP3 for predicted splicing in silent variants when SpliceAI >=0.2; do not apply PP3 when the calibrated splice prediction does not reach that threshold.
Evidence considered
The case normalization identifies NM_000059.4:c.9738C>T as the synonymous protein change NP_000050.3:p.(Ala3246=), so REVEL is not the applicable path.
The ENIGMA BRCA2 specification states that PP3 applies to predicted splicing in silent variants at SpliceAI >=0.2.
The ENIGMA Appendix J calibration states that SpliceAI <=0.1 supports BP4, values >0.1 and <0.2 are not informative, and values >=0.2 support PP3; the observed maximum delta is 0.013.
The governing VCEP files were searched for c.9738C>T, p.Ala3246=, and p.A3246=; no exact variant-level entry was found in the Specifications, Appendices, or Houdayer full-text files.
Still missing
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in Specifications_V1.2_2024-11-18.docx.
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in Appendices_V1.2_2024-11-18.docx.
No exact c.9738C>T, p.Ala3246=, or p.A3246= entry was found in PMID_22505045_Houdayer_2012_HumMutat.pdf.
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.
Customizing local and systemic therapies for women with early breast cancer: the St. Gallen International Consensus Guidelines for treatment of early breast cancer 2021.
BRCA1 and BRCA2 mutation analysis of early-onset and familial breast cancer cases in Mexico.
Ruiz-Flores P et al. · 2002
The paper reports the corresponding BRCA2 silent substitution under historical notation as 9966C>T in exon 27, observed in two Mexican breast-cancer patients; it provides no RNA assay for this variant and only raises the possibility of an mRNA-level splicing effect.
Even though the BRCA2 9966 C>T alteration doesn't produce an amino acid substitution, it may possibly affect splicing. This alteration was identified in the only family in our series containing a case of male breast cancer. Regrettably, there was no available RNA to test the effect of these variants.
Discussion, paragraph beginning "In addition, nine patients appeared to carry..."
Clinical follow up of mexican women with early onset of breast cancer and mutations in the BRCA1 and BRCA2 genes.
Calderón-Garcidueñas AL et al. · 2005
The paper reports a BRCA2 synonymous polymorphism written as C9966T, resulting in Ala3246Ala, in patient 6. It was identified in a prospective hospital-based cohort of 22 Mexican women with early-onset breast cancer; no functional assay, segregation analysis, or variant-specific interpretation was provided. The submitted c.9738C>T notation is not used.
ACMG SF v3.0 list for reporting of secondary findings in clinical exome and genome sequencing: a policy statement of the American College of Medical Genetics and Genomics (ACMG).
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= 5.51451e-05; MAF= 0.00551%, 89/1613924 alleles, homozygotes = 1) and has highest observed frequency in the Admixed American population (AF= 0.00143348; MAF= 0.14335%, 86/59994 alleles, homozygotes = 1); grpmax FAF= 0.00118865.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 0.000229932; MAF= 0.02299%, 65/282692 alleles, homozygotes = 1) and has highest observed frequency in the Admixed American population (AF= 0.00177886; MAF= 0.17789%, 63/35416 alleles, homozygotes = 1); grpmax FAF= 0.00140947.
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
ClinVar
This variant has been reported in ClinVar as Benign (4 clinical laboratories) and as Likely benign (4 clinical laboratories) and as Uncertain significance (1 clinical laboratory) and as Benign by Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) (expert panel). (ClinVarID = 52896)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01).
Functional
OncoKB identified curated literature and non-variant-specific oncogenicity context for review; listed oncogenicity label: Unknown Oncogenic Effect.
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.
This variant was interpreted by pipeline 8.0.0.
The current version is 11.0.07.
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