BRCA1 c.3260G>C, p.(Gly1087Ala)

Reasoning

The variant is a missense substitution at residue 1087, outside all ENIGMA-defined clinically important BRCA1 functional domains (RING aa 2-101, coiled-coil aa 1391-1424, BRCT repeats aa 1650-1857). SpliceAI predicts no significant splice impact (maximum delta score 0.015, below the ENIGMA threshold of 0.1). The ENIGMA v1.2 rule therefore supports BP1_Strong.

Rule

ENIGMA v1.2 BP1_Strong: apply for a silent, missense, or in-frame insertion/deletion/delins variant outside a potentially clinically important functional domain and with no predicted splicing effect (SpliceAI <=0.1).

Evidence considered

• The case variant is NM_007294.4:c.3260G>C, p.(Gly1087Ala), a missense substitution at residue 1087.
• The governing ENIGMA domain definitions are BRCA1 RING aa 2-101, coiled-coil aa 1391-1424, and BRCT repeats aa 1650-1857; residue 1087 is outside every listed domain.
• SpliceAI reports DS_AG 0.0, DS_AL 0.015, DS_DG 0.001, and DS_DL 0.001, with maximum delta 0.015; this is below the ENIGMA BP1 threshold of 0.1.

Sources

Reasoning

NM_007294.4:c.3260G>C is a missense substitution, p.(Gly1087Ala), with an unchanged predicted protein endpoint (residue 1087). It does not create a premature termination codon, frameshift, canonical splice-site alteration, initiation-codon alteration, or exon deletion; therefore it is not a null variant and does not meet the ENIGMA BRCA1/2 PVS1 rule. NMD and exon-level PVS1 weighting are consequently not applicable to this consequence.

Rule

ENIGMA BRCA1/2 v1.2 PVS1: null variant in a gene where loss of function is a known disease mechanism; apply only at the flowchart-determined strength.

Evidence considered

• Normalization in the case bundle identifies NM_007294.4:c.3260G>C as NP_009225.1:p.(Gly1087Ala); the reference and predicted proteins both terminate at residue 1864, so this single amino-acid substitution does not alter protein length.
• The ENIGMA BRCA1/2 specification limits PVS1 to null variants (nonsense, frameshift, canonical +/-1 or 2 splice variants, initiation-codon variants, and single- or multi-exon deletions), with weight determined by its PVS1 flowchart and exon context.

Sources

Reasoning

PM2 is not met because the variant is observed in population controls. ENIGMA requires absence from controls in an outbred population in gnomAD v2.1 non-cancer exomes and gnomAD v3.1 non-cancer, with regional average read depth >=25. This variant is present in gnomAD v2.1 (1/250,540 alleles) and gnomAD v4.1 (29/1,613,632 alleles), with zero homozygotes in both datasets. The presence of the allele is sufficient to fail the absence requirement; read-depth information is not needed to reverse that result.

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.

Evidence considered

• ENIGMA BRCA1/2 v1.2 PM2 rule: variant must be absent from controls in an outbred population in gnomAD v2.1 non-cancer exomes and gnomAD v3.1 non-cancer, with average read depth around the variant >=25; use Supporting strength.
• gnomAD v2.1 observes 1 alternate allele among 250,540 alleles (AF 3.991e-06) and zero homozygotes.
• gnomAD v4.1 observes 29 alternate alleles among 1,613,632 alleles (AF 1.797e-05) and zero homozygotes.

Still missing

• Regional average read depth is not reported in the case bundle, but this does not change the result because the variant is not absent from controls.

Sources

Reasoning

ENIGMA BRCA1/2 v1.2 PP3 applies to missense variants in a clinically important domain with BayesDel no-AF >=0.28, or to predicted splice impact with SpliceAI >=0.2. p.(Gly1087Ala) lies outside the defined BRCA1 RING (aa 2-101), coiled-coil (aa 1391-1424), and BRCT (aa 1650-1857) domains. Its maximum SpliceAI delta is 0.015, below 0.2; therefore neither PP3 path is met.

Rule

ENIGMA BRCA1/2 v1.2: PP3 for missense/in-frame variants inside RING aa 2-101, coiled-coil aa 1391-1424, or BRCT aa 1650-1857 with BayesDel no-AF >=0.28; or for predicted splicing in silent, missense/in-frame, or eligible intronic variants with SpliceAI >=0.2.

Evidence considered

• The normalized consequence is BRCA1 p.(Gly1087Ala), a missense substitution at residue 1087, outside the ENIGMA-defined RING, coiled-coil, and BRCT clinically important domains.
• SpliceAI maximum delta score is 0.015 (DS_AL 0.015), below the ENIGMA PP3 splice threshold of 0.2.
• BayesDel no-AF score is -0.184442; the ENIGMA domain-based BayesDel PP3 path is not applicable because residue 1087 is outside a clinically important domain.

Sources

Reasoning

The exact-variant ENIGMA clinical-history likelihood-ratio record reports combined LR 0.3100887017422507, which is below every PP4 threshold; therefore PP4 is not met.

Rule

ENIGMA BRCA1/2 v1.2 PP4 uses only combined multifactorial clinical LR: >=2.08 supporting, >=4.3 moderate, >=18.7 strong, >=350 very strong.

Evidence considered

• The ENIGMA BRCA1/2 specification restricts PP4 to combined likelihood ratios toward pathogenicity from multifactorial clinical data, with thresholds of >=2.08 supporting, >=4.3 moderate, >=18.7 strong, and >=350 very strong.
• The exact BRCA1 c.3260G>C row reports combined LR 0.3100887017422507 from four probands.
• CHECKLIST step pp4_1: is combined_multifactorial_lr >= 350? — FALSE — combined_multifactorial_lr = 0.3100887017422507.
• CHECKLIST step pp4_2: is combined_multifactorial_lr >= 18.7? — FALSE — combined_multifactorial_lr = 0.3100887017422507.
• CHECKLIST step pp4_3: is combined_multifactorial_lr >= 4.3? — FALSE — combined_multifactorial_lr = 0.3100887017422507.
• CHECKLIST step pp4_4: is combined_multifactorial_lr >= 2.08? — FALSE — combined_multifactorial_lr = 0.3100887017422507; terminal result is status=not_met, strength=None.

Sources

Reasoning

BA1 is not met. The ENIGMA BRCA1/2 specification requires FAF >0.001 in gnomAD v2.1 non-cancer exomes and/or gnomAD v3.1 non-cancer non-founder populations. The observed frequency is far below this threshold: gnomAD v2.1 total AF is 3.991e-06, and gnomAD v4.1 grpmax FAF is 1.567e-05.

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).

Evidence considered

• ENIGMA BRCA1/2 v1.2 BA1 rule: apply only when filter allele frequency (FAF) is above 0.1% (FAF >0.001) in gnomAD v2.1 non-cancer exome and/or gnomAD v3.1 non-cancer non-founder populations.
• gnomAD v2.1 reports 1 alternate allele among 250,540 alleles (AF 3.991e-06), with zero homozygotes; the highest listed population AF is 6.153e-05 in African/African American individuals.
• gnomAD v4.1 reports 29 alternate alleles among 1,613,632 alleles (AF 1.797e-05), zero homozygotes, and grpmax FAF 1.567e-05.

Sources

Reasoning

BS1 is not met under the strict ENIGMA frequency rule because the available current FAF is below the supporting threshold. The gnomAD v4.1 grpmax FAF is 1.567e-05, whereas ENIGMA BS1 Supporting requires FAF >0.00002 and <=0.0001. An older ENIGMA supplementary-table record reports a single historical observation with maximum MAF 6.711e-05 in an African population, but it is explicitly categorized as a one-count, not-informative observation and is not a current FAF measurement. The discrepancy is a frequency/threshold artifact that warrants review rather than assignment of BS1.

Rule

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).

Evidence considered

• ENIGMA BRCA1/2 v1.2 BS1 Supporting rule: FAF must be above 0.002% (FAF >0.00002) and no greater than 0.01% (FAF <=0.0001) in gnomAD v2.1 non-cancer exomes and/or gnomAD v3.1 non-cancer non-founder populations.
• gnomAD v4.1 reports grpmax FAF 1.567e-05, below 2.0e-05; its highest population AF is 2.288e-05 in European non-Finnish individuals, but that AF is not the FAF required by the rule.
• gnomAD v2.1 reports one allele among 250,540 total alleles and a highest listed population AF of 6.153e-05 in African/African American individuals, but no FAF is provided.
• The ENIGMA HUMU-40-1557 supplementary exact-match row reports maximum gnomAD MAF 6.711409395973154e-05 in an African population and labels the frequency evidence as one count, not informative.
• ENIGMA Supplementary Table 8 assigns the >0.00002 to <=0.0001 maximum-MAF category a conservative Supporting Benign option, but that category-level calibration does not replace the case-specific v1.2 FAF rule.

Still missing

• No directly comparable gnomAD v2.1/v3.1 FAF value is available for the historical one-count observation; the v2.1 record exposes population AF but no FAF.
• The ENIGMA rule names gnomAD v2.1/v3.1, while the newer gnomAD v4.1 value is below the BS1 threshold. Human review is needed if the historical maximum MAF is considered for this criterion.

Sources

Reasoning

ENIGMA BRCA1/2 v1.2 BP4 for a missense variant requires that it be inside a clinically important functional domain and have both BayesDel no-AF <=0.15 and SpliceAI <=0.1. Although the BayesDel no-AF score is -0.184442 and the maximum SpliceAI delta is 0.015, p.(Gly1087Ala) is outside the defined BRCA1 domains, so the missense BP4 rule is not satisfied.

Rule

ENIGMA BRCA1/2 v1.2: BP4 for missense/in-frame variants requires location inside RING aa 2-101, coiled-coil aa 1391-1424, or BRCT aa 1650-1857, BayesDel no-AF <=0.15, and SpliceAI <=0.1.

Evidence considered

• The normalized consequence is BRCA1 p.(Gly1087Ala), a missense substitution at residue 1087, outside the ENIGMA-defined RING, coiled-coil, and BRCT clinically important domains.
• BayesDel no-AF score is -0.184442, which is at or below the ENIGMA BP4 cutoff of 0.15.
• SpliceAI maximum delta score is 0.015, which is at or below the ENIGMA BP4 cutoff of 0.1.
• The favorable predictor values do not override the ENIGMA location requirement for missense BP4.

Sources

Reasoning

The exact-variant ENIGMA record reports combined multifactorial LR 0.3100887017422507, which exceeds the BP5 supporting cutoff of 0.48, so BP5 is not met. Whether the separate co-observation exclusion applies is not documented.

Rule

ENIGMA BRCA1/2 v1.2 BP5 uses only combined multifactorial clinical LR against pathogenicity: <=0.48 supporting, <=0.23 moderate, <=0.05 strong, <=0.00285 very strong; exclude specified multi-gene co-observation.

Evidence considered

• ENIGMA BRCA1/2 v1.2 restricts BP5 to combined multifactorial clinical LR against pathogenicity, with thresholds <=0.48 supporting, <=0.23 moderate, <=0.05 strong, and <=0.00285 very strong; BP5 is not applicable to the specified multi-gene co-observation scenario.
• The exact BRCA1 c.3260G>C row reports combined LR 0.3100887017422507; this is above the BP5 supporting cutoff of 0.48 and therefore does not support BP5.
• CHECKLIST step bp5_0: is co_observation_with_pathogenic_variants_in_different_known_breast_ovarian_cancer_risk_genes == True? — NA — The bundle does not explicitly provide this boolean or sufficient case-level co-observation detail.
• CHECKLIST step bp5_1: is combined_multifactorial_lr <= 0.00285? — FALSE — combined_multifactorial_lr = 0.3100887017422507.
• CHECKLIST step bp5_2: is combined_multifactorial_lr <= 0.05? — FALSE — combined_multifactorial_lr = 0.3100887017422507.
• CHECKLIST step bp5_3: is combined_multifactorial_lr <= 0.23? — FALSE — combined_multifactorial_lr = 0.3100887017422507.
• CHECKLIST step bp5_4: is combined_multifactorial_lr <= 0.48? — FALSE — combined_multifactorial_lr = 0.3100887017422507; terminal result is status=not_met, strength=None.

Still missing

• The case bundle does not explicitly establish whether this variant was co-observed with pathogenic variants in two or more different known breast-ovarian cancer risk genes.

Sources

Reasoning

The variant is a missense substitution, NM_007294.4:c.3260G>C (NP_009225.1:p.(Gly1087Ala)), and SpliceAI predicts no significant splice impact (maximum delta score 0.015), so the protein-change branch of the ENIGMA PS1 rule is applicable. However, the consolidated evidence bundle does not provide a verified previously classified pathogenic or likely pathogenic BRCA1 variant producing the same amino-acid change or an adequately documented same-codon comparator. PS1 cannot be assigned without that comparator evidence.

Rule

ENIGMA v1.2 PS1: apply for a predicted missense substitution with a previously classified pathogenic variant acting through protein change and no confirmed or predicted splice effect; PS1_Moderate may apply for a previously classified likely pathogenic comparator. See Table 5 and Appendices E, J, and K.

Evidence considered

• The case variant is NM_007294.4:c.3260G>C, predicted to encode p.(Gly1087Ala).
• ENIGMA BRCA1/2 v1.2 specifies PS1 for a predicted missense substitution when a previously classified pathogenic variant is considered to act through protein change and there is no confirmed or predicted splice effect; the bundle reports SpliceAI maximum delta 0.015.
• The bundle contains no verified same-amino-acid pathogenic comparator or adequate same-codon pathogenic comparator for this variant.

Still missing

• A verified previously classified pathogenic or likely pathogenic variant with the same amino-acid change, or a documented same-codon comparator meeting ENIGMA Table 5 requirements, is not available in the bundle.

Sources

Reasoning

The applicable ENIGMA BRCA1/2 VCEP v1.2 framework requires well-established functional studies showing a damaging effect, with calibrated assay recommendations in Table 9. The exact missense variant NM_007294.4:c.3260G>C (p.(Gly1087Ala)) is not present in the extracted Table 9 or ST4 functional-assay records, and the available paper extracts do not report this variant. Therefore, no validated protein-function or combined mRNA/protein assay evidence is available to assess PS3.

Rule

ENIGMA BRCA1/2 VCEP v1.2 PS3: apply for well-established in vitro or in vivo functional studies supportive of a damaging effect when the assay measures protein function alone or mRNA and protein together; use calibrated published assay recommendations in Table 9. Damaging mRNA-only findings are assigned to PVS1 (RNA) at the appropriate strength instead.

Evidence considered

• ENIGMA BRCA1/2 VCEP specification v1.2 states that PS3 is for well-established in vitro or in vivo functional studies supportive of a damaging effect, applying to assays measuring protein function alone or mRNA and protein together; mRNA-only damaging results are handled under RNA-specific PVS1 guidance rather than PS3.
• ENIGMA Table 9 is the curated list of calibrated functional assay results for PS3/BS3, but no row for NM_007294.4:c.3260G>C or p.(Gly1087Ala) was found.
• ENIGMA Supplementary Table 4 (ST4), the functional assay results dataset, contains no exact match for BRCA1 c.3260G>C or p.(Gly1087Ala).
• The available precomputed literature extracts for PMID:15385441, PMID:25741868, PMID:26467025, PMID:28492532, PMID:31911673, PMID:10923033, and PMID:23918944 state that the exact variant is not mentioned or provide no variant-specific functional result.

Still missing

• A variant-specific, biologically relevant functional assay with appropriate benign and pathogenic controls is needed.
• If an assay is identified, its calibration, reproducibility, assay endpoint, and whether it measures protein function rather than mRNA alone must be reviewed under ENIGMA Figure 1C/Table 9 guidance.

Sources

Reasoning

The ENIGMA BRCA1/2 specification requires case-control evidence with p-value <=0.05 and OR >=4 with a lower confidence bound excluding 2.0; no case-control counts, OR/LR estimate, confidence interval, or p-value for this exact variant are available.

Rule

ENIGMA BRCA1/2 v1.2 PS4 Strong: case-control p-value <=0.05, OR >=4, and lower confidence interval excludes 2.0; use matched case/control datasets and do not use Proband Counting.

Evidence considered

• ENIGMA BRCA1/2 v1.2 specifies PS4 Strong only for case-control evidence with p-value <=0.05, OR >=4, and a lower confidence interval excluding 2.0; it also requires ethnicity- and country-matched cases and controls and says not to use Proband Counting.
• The exact-variant ENIGMA supplementary row has no Case-Control LR value, so no qualifying case-control enrichment estimate can be assessed.
• CHECKLIST item ps4_review: Review and apply this criterion's VCEP guidance directly: Case dataset should be ethnicity and country-matched to control dataset. If case-control LR estimates are available for a given dataset, these should be used in preference to case-control OR data, under code PP4 (or BP5, if appropriate). Do not use Proband Counting as originally described. The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls. Note 1: Relative risk (RR) or odds ratio (OR), as obtained from case-control studies, is >5.0 and the confidence interval around the estimate of RR or OR does not include 1.0. See The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls. Case-control studies; p-value <=0.05 and OR >=4 (lower confidence interval excludes 2.0). See Appendix F for details. — NA — Required case-control dataset matching, enrichment estimate, confidence interval, and significance value are unavailable.

Still missing

• Exact-variant case and ethnicity/country-matched control counts or a validated case-control OR/LR with confidence interval and p-value are missing.

Sources

Reasoning

The applicable ClinGen ENIGMA BRCA1/2 specification restricts PM3 to a patient with a phenotype consistent with BRCA1- or BRCA2-related Fanconi anemia and co-occurring variants in the same gene, with strength assigned from the PM3 point total. The case bundle contains no affected-proband phenotype, chromosome-breakage result, second BRCA1 variant, or phase information establishing pathogenic variants in trans or cis. Therefore PM3 cannot be applied from the available case evidence.

Rule

ENIGMA BRCA1/2 v1.2 PM3: apply only for a patient with phenotype consistent with BRCA1- or BRCA2-related Fanconi anemia and co-occurring variants in the same gene; assign strength by the Table 6 PM3 point total (Supporting = 1 point, Moderate = 2 points, Strong = at least 4 points).

Evidence considered

• The ENIGMA BRCA1/2 specification states that PM3 requires a patient with a phenotype consistent with BRCA1/2-related Fanconi anemia and co-occurring variants in the same gene; PM3 Supporting corresponds to 1 point, PM3 to 2 points, and PM3 Strong to at least 4 points.
• The ENIGMA supplementary-table match for BRCA1 c.3260G>C (p.(Gly1087Ala)) reports four probands and a co-occurrence likelihood ratio of 1.0330920372, but it does not provide the affected-proband Fanconi-anemia phenotype, the identity/pathogenicity of a second BRCA1 variant, or cis/trans phase needed to assign PM3 under the specification.
• The available case summary and evidence bundle do not document affected-proband observations, a second allele, or phase; absence of those data is treated as insufficient evidence rather than evidence against PM3.

Still missing

• Affected-proband Fanconi anemia phenotype and chromosome-breakage result are not provided.
• No co-occurring BRCA1 variant is documented for an affected proband.
• Phase information (in trans or in cis) is not provided.
• The ENIGMA PM3 point total cannot be calculated.

Sources

Reasoning

PP1 is applicable under the ENIGMA BRCA1/BRCA2 specification only when co-segregation with disease is supported by a quantitative co-segregation analysis. The exact-variant BRCA1 multifactorial dataset row contains no segregation LR, and the case bundle provides no affected-relative genotypes, number of informative meioses, family structure, or quantitative co-segregation result. The available combined LR is not a segregation result and cannot be used to assign PP1. Thus PP1 cannot be assessed.

Rule

ENIGMA BRCA1/BRCA2 v1.2 PP1: quantitative co-segregation with disease; Supporting LR >=2.08, Moderate LR >=4.3, Strong LR >=18.7, Very Strong LR >=350.

Evidence considered

• ENIGMA BRCA1/BRCA2 v1.2 requires quantitative co-segregation analysis for PP1 and assigns Supporting at LR >=2.08, Moderate at LR >=4.3, and Strong at LR >=18.7; it states that LR >0.48 and <2.08 provides no supporting evidence in either direction.
• The exact-match row for BRCA1 c.3260G>C (p.(Gly1087Ala)) in SuppT1 has a blank Segregation LR field; no family-level segregation observations or quantitative co-segregation calculation are provided in the bundle.
• The exact-match row reports a combined LR of 0.6744313608969007, but that combined multifactorial value is not a segregation LR and is not used for PP1.

Still missing

• Affected and unaffected relative phenotypes and genotypes
• Informative meioses and family structure
• Quantitative co-segregation analysis or segregation likelihood ratio for c.3260G>C

Sources

Reasoning

BS2 cannot be assessed from the case bundle. ENIGMA specifies BS2 for absence of features of recessive disease, namely a BRCA1-related Fanconi Anemia phenotype, with strength determined from qualifying proband points. The bundle contains no patient-level phenotype, age, chromosome-breakage result, biallelic genotype, or qualifying proband count for this assessment.

Rule

Applied in absence of features of recessive disease, namely Fanconi Anemia phenotype. See Specification Table 8 for additional stipulations and point-based BS2 assignment.

Evidence considered

• ENIGMA BRCA1/2 v1.2 BS2 rule: apply in the absence of features of recessive disease, namely Fanconi Anemia phenotype; assign strength from the BS2-related proband point total in Specification Table 8.
• The consolidated case bundle provides variant and population observations but no clinical phenotype or proband-point data relevant to BS2.

Still missing

• Patient-level Fanconi Anemia phenotype and chromosome-breakage information are unavailable.
• No qualifying BS2 proband-point data or count is available.

Sources

Reasoning

The applicable ENIGMA BRCA1/2 VCEP v1.2 framework requires well-established functional studies showing no damaging effect, with calibrated assay recommendations in Table 9. The exact missense variant NM_007294.4:c.3260G>C (p.(Gly1087Ala)) is not present in the extracted Table 9 or ST4 functional-assay records, and the available paper extracts do not report this variant. Therefore, no validated protein-function or combined mRNA/protein assay evidence is available to assess BS3.

Rule

ENIGMA BRCA1/2 VCEP v1.2 BS3: apply for well-established in vitro or in vivo functional studies showing no damaging effect when the assay measures protein function alone or mRNA and protein together; use calibrated published assay recommendations in Table 9. Normal mRNA-only findings are assigned to BP7 (RNA) at the appropriate strength instead.

Evidence considered

• ENIGMA BRCA1/2 VCEP specification v1.2 states that BS3 is for well-established in vitro or in vivo functional studies showing no damaging effect when the assay measures protein function alone or mRNA and protein together; mRNA-only normal transcript findings are handled as BP7 (RNA) rather than BS3.
• ENIGMA Table 9 is the curated list of calibrated functional assay results for PS3/BS3, but no row for NM_007294.4:c.3260G>C or p.(Gly1087Ala) was found.
• ENIGMA Supplementary Table 4 (ST4), the functional assay results dataset, contains no exact match for BRCA1 c.3260G>C or p.(Gly1087Ala).
• The available precomputed literature extracts for PMID:15385441, PMID:25741868, PMID:26467025, PMID:28492532, PMID:31911673, PMID:10923033, and PMID:23918944 state that the exact variant is not mentioned or provide no variant-specific functional result.

Still missing

• A variant-specific, biologically relevant functional assay demonstrating normal function against appropriate controls is needed.
• If an assay is identified, its calibration, reproducibility, assay endpoint, and whether it measures protein function rather than mRNA alone must be reviewed under ENIGMA Figure 1C/Table 9 guidance.

Sources

Reasoning

BS4 is applicable under the ENIGMA BRCA1/BRCA2 specification only when lack of segregation in affected family members is supported by a quantitative co-segregation analysis. The exact-variant BRCA1 multifactorial dataset row contains no segregation LR, and the case bundle provides no non-segregating affected relatives, relative genotypes, informative meioses, family structure, or quantitative BS4 likelihood ratio. The available combined LR is not a BS4 result. Therefore BS4 cannot be assessed.

Rule

ENIGMA BRCA1/BRCA2 v1.2 BS4: 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/BRCA2 v1.2 requires quantitative co-segregation analysis for BS4 and assigns Supporting at LR <=0.48, Moderate at LR <=0.23, Strong at LR <=0.05, and Very Strong at LR <=0.00285; it cautions that LR >0.48 and <2.08 provides no supporting evidence in either direction.
• The exact-match row for BRCA1 c.3260G>C (p.(Gly1087Ala)) in SuppT1 has a blank Segregation LR field; no non-segregating affected relatives or quantitative analysis are provided in the bundle.
• The exact-match row reports a combined LR of 0.6744313608969007, but that combined multifactorial value is not a BS4 segregation LR and is not used for BS4.

Still missing

• Affected relatives who do not carry the variant
• Confirmation that the reported relatives have disease relevant to BRCA1 cancer predisposition
• Informative meioses and family structure
• Quantitative non-segregation analysis or segregation likelihood ratio for c.3260G>C

Sources

Reasoning

This is a missense, not synonymous, variant. Under ENIGMA BRCA1/2 v1.2, BP7_Strong (RNA) can be used for a missense variant outside a clinically important domain only when a well-established mRNA-only study demonstrates no damaging transcript-profile effect. No variant-specific RNA assay result is present in the case evidence. BP7 Supporting is limited to silent variants in a clinically important domain or qualifying intronic variants when BP4 is met, neither of which applies.

Rule

ENIGMA BRCA1/2 v1.2: BP7_Strong (RNA) requires a well-established mRNA-only study showing no damaging transcript-profile effect and may apply to missense/in-frame variants outside the defined domains; BP7 Supporting is restricted to specified silent or intronic contexts when BP4 is met.

Evidence considered

• The normalized consequence is BRCA1 p.(Gly1087Ala), a missense substitution outside the ENIGMA-defined clinically important domains.
• SpliceAI maximum delta score is 0.015, but this prediction alone does not meet the ENIGMA requirement for BP7_Strong (RNA) in an eligible missense variant.
• No variant-specific RNA transcript-profile study is supplied in the case bundle or its pre-computed paper extractions.

Still missing

• No variant-specific, well-established mRNA-only transcript-profile assay demonstrating no damaging effect was provided.

Sources