BRCA1 c.3270A>G, p.(Gln1090=)

Reasoning

The ENIGMA BRCA1 specification applies BP1_Strong to silent substitutions outside a potentially clinically important functional domain when no splicing is predicted, defined as SpliceAI <=0.1. The variant is synonymous at residue Q1090, outside the specified RING aa 2-101, coiled-coil aa 1391-1424, and BRCT repeats aa 1650-1857, and its SpliceAI maximum delta score is 0.002; all governing conditions are met.

Rule

ENIGMA BRCA1 v1.2 BP1_Strong: silent substitution outside a potentially clinically important functional domain AND no predicted splicing (SpliceAI <=0.1).

Evidence considered

• ENIGMA BP1_Strong rule: apply to silent substitutions outside a potentially clinically important functional domain with SpliceAI <=0.1.
• Q1090 is outside the ENIGMA BRCA1 domains RING aa 2-101, coiled-coil aa 1391-1424, and BRCT repeats aa 1650-1857.
• The case SpliceAI result is max delta 0.002, satisfying the governing <=0.1 threshold.
• The exact variant is reported in Judkins et al. as Q1090Q and labeled P (benign polymorphism), in a 55,630-patient BRCA1 sequencing dataset; this is concordant context but is not required for the ENIGMA BP1 rule.

Sources

Reasoning

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

Rule

Apply BP6 only for an exact-variant ClinVar expert-panel classification of Benign or Likely benign; assign Supporting strength.

Evidence considered

• ClinVar variation 187419 exactly matches NM_007294.4:c.3270A>G (p.Gln1090=) and is classified Likely benign with review status reviewed by expert panel.
• The exact protein synonym p.Q1090= is confirmed by the normalized variant record, establishing identity with p.Gln1090=.
• ClinVar expert panel classification

Sources

Reasoning

The ENIGMA BRCA1 VCEP defines PM2 Supporting as absence from controls in gnomAD v2.1 non-cancer exomes and gnomAD v3.1 non-cancer genomes, with adequate local read depth. This variant is present in both specified non-cancer datasets, with 2 alleles in gnomAD v2.1 non-cancer exomes and 2 alleles in gnomAD v3.1 non-cancer genomes. Because it is not absent from the governing control datasets, PM2 is not met.

Rule

Absent from controls in an outbred population, from gnomAD v2.1 non-cancer exome-only subset and gnomAD v3.1 non-cancer genomes; average regional read depth must be >=25.

Evidence considered

• ENIGMA BRCA1 VCEP specification v1.2 requires absence from gnomAD v2.1 non-cancer exomes and gnomAD v3.1 non-cancer genomes for PM2 Supporting.
• The case evidence reports gnomAD v2.1 non-cancer exomes AC 2 of 236062 and gnomAD v3.1 non-cancer genomes AC 2 of 147892, with zero homozygotes; presence in either governing dataset prevents PM2.

Still missing

• No exact c.3270A>G, p.Gln1090=, or p.Q1090= entry was found in SupplementaryTables_V1.2_2024-11-18.xlsx.txt, Specifications_V1.2_2024-11-18.docx.txt, Appendices_V1.2_2024-11-18.docx.txt, or HUMU-40-1557-s001.xlsx.txt; the governing rule was therefore used.

Sources

Reasoning

The variant is synonymous (NM_007294.4:c.3270A>G; p.Gln1090=), so PP3 is considered only through the ENIGMA splice-prediction path. The governing ENIGMA BRCA1 specification applies PP3 for predicted splicing at SpliceAI max delta >=0.2. SpliceAI is available and reports DS_AG 0.002, DS_AL 0.0, DS_DG 0.0, and DS_DL 0.0, with maximum delta 0.002; therefore the threshold is not reached and PP3 is not met. No exact variant-level entry was found when searching SupplementaryTables_V1.2_2024-11-18.xlsx.txt, Specifications_V1.2_2024-11-18.docx.txt, Appendices_V1.2_2024-11-18.docx.txt, or PMID_22505045_Houdayer_2012_HumMutat.pdf.txt for c.3270A>G, p.Gln1090=, or p.Q1090=.

Rule

ENIGMA BRCA1/2 Specifications v1.2: PP3 for predicted splicing in silent variants requires SpliceAI >=0.2.

Evidence considered

• ENIGMA BRCA1/2 Specifications v1.2 state that PP3 applies to predicted splicing for silent variants when SpliceAI is >=0.2.
• SpliceAI reports DS_AG 0.002, DS_AL 0.0, DS_DG 0.0, and DS_DL 0.0 for NM_007294.4:c.3270A>G; the maximum delta is 0.002.
• The variant is synonymous, annotated as NP_009225.1:p.(Gln1090=) / p.(Q1090=).
• The four declared VCEP full-text files were searched for c.3270A>G, p.Gln1090=, and p.Q1090=; no exact entry was found in any of them.

Still missing

• No exact c.3270A>G, p.Gln1090=, or p.Q1090= entry was found in SupplementaryTables_V1.2_2024-11-18.xlsx.txt.
• No exact c.3270A>G, p.Gln1090=, or p.Q1090= entry was found in Specifications_V1.2_2024-11-18.docx.txt.
• No exact c.3270A>G, p.Gln1090=, or p.Q1090= entry was found in Appendices_V1.2_2024-11-18.docx.txt.
• No exact c.3270A>G, p.Gln1090=, or p.Q1090= entry was found in PMID_22505045_Houdayer_2012_HumMutat.pdf.txt.

Sources

Reasoning

The exact ClinVar record for NM_007294.4(BRCA1):c.3270A>G (p.Gln1090=) is ClinVar variation 187419 and has an expert-panel classification of Likely benign. Under the instructed PP5 rule, only an exact-variant expert-panel Pathogenic or Likely pathogenic classification supports PP5; this expert-panel classification is benign-direction evidence and therefore does not meet PP5.

Rule

Apply PP5 only for an exact-variant ClinVar expert-panel classification of Pathogenic or Likely pathogenic.

Evidence considered

• ClinVar variation 187419 exactly matches NM_007294.4:c.3270A>G (p.Gln1090=) and is classified Likely benign with review status reviewed by expert panel.
• Ordinary laboratory submissions and aggregate labels were not used to trigger PP5.

Sources

Reasoning

The ENIGMA BRCA1 VCEP requires filter allele frequency above 0.001 in gnomAD v2.1 non-cancer exomes and/or gnomAD v3.1 non-cancer non-founder populations for BA1. The variant's maximum reported filter allele frequency was 3.25e-06 in gnomAD v2.1 non-cancer exomes and 4.88e-06 in gnomAD v3.1 non-cancer genomes, both far below 0.001. Therefore BA1 is not met.

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 populations.

Evidence considered

• ENIGMA BRCA1 VCEP specification v1.2 sets BA1 at filter allele frequency >0.001 in gnomAD v2.1 non-cancer exomes and/or gnomAD v3.1 non-cancer populations.
• The case evidence reports gnomAD v2.1 non-cancer exome grpmax FAF 3.25e-06 and gnomAD v3.1 non-cancer genome grpmax FAF 4.88e-06; neither reaches 0.001.

Still missing

• No exact c.3270A>G, p.Gln1090=, or p.Q1090= entry was found in SupplementaryTables_V1.2_2024-11-18.xlsx.txt, Specifications_V1.2_2024-11-18.docx.txt, Appendices_V1.2_2024-11-18.docx.txt, or HUMU-40-1557-s001.xlsx.txt; the governing rule was therefore used.

Sources

Reasoning

The ENIGMA BRCA1 VCEP requires filter allele frequency above 0.0001 for BS1 Strong, or above 0.00002 through 0.0001 for BS1 Supporting, using gnomAD v2.1 non-cancer exomes and/or gnomAD v3.1 non-cancer genomes. The maximum reported filter allele frequency was 4.88e-06, below even the Supporting threshold. Therefore BS1 is not met at any specified strength.

Rule

Filter allele frequency (FAF) is above 0.0001 for BS1 Strong, or above 0.00002 and <=0.0001 for BS1 Supporting, in gnomAD v2.1 non-cancer exomes and/or gnomAD v3.1 non-cancer non-founder populations.

Evidence considered

• ENIGMA BRCA1 VCEP specification v1.2 sets BS1 Strong at FAF >0.0001 and BS1 Supporting at FAF >0.00002 to <=0.0001 in the specified non-cancer gnomAD datasets.
• The case evidence reports maximum filter allele frequencies of 3.25e-06 in gnomAD v2.1 non-cancer exomes and 4.88e-06 in gnomAD v3.1 non-cancer genomes, both below 0.00002.

Still missing

• No exact c.3270A>G, p.Gln1090=, or p.Q1090= entry was found in SupplementaryTables_V1.2_2024-11-18.xlsx.txt, Specifications_V1.2_2024-11-18.docx.txt, Appendices_V1.2_2024-11-18.docx.txt, or HUMU-40-1557-s001.xlsx.txt; the governing rule was therefore used.

Sources

Reasoning

The ENIGMA BRCA1 specification reserves PS3 for well-established functional studies demonstrating a damaging protein effect, or combined mRNA-and-protein evidence. The governing Specifications Table 9 has no entry for NM_007294.4:c.3270A>G, c.3270A>G, p.Gln1090=, or p.Q1090=. The supplementary functional-assay dataset (ST4) and the Parsons multifactorial supplement also have no exact entry for this variant. Therefore, no calibrated variant-specific damaging assay result is available to apply PS3.

Rule

ENIGMA v1.2 PS3: apply only for well-established functional studies supportive of a damaging effect measured via protein alone or mRNA and protein combined; use Table 9 calibrated recommendations when present.

Evidence considered

• ENIGMA BRCA1 v1.2 specifies PS3 for well-established in vitro or in vivo studies supportive of a damaging effect measured through protein alone or mRNA and protein together; mRNA-only damaging results are handled under the alternative RNA code rather than PS3.
• Specifications Table 9 contains no row matching c.3270A>G, p.Gln1090=, or p.Q1090=, so no pre-assigned PS3 strength governs this variant.
• Supplementary Table 4 functional-assay data and HUMU-40-1557-SuppT4 contain no exact entry for this variant; no calibrated assay metric or control comparison is available for PS3.

Still missing

• No entry for c.3270A>G, p.Gln1090=, or p.Q1090= in Specifications_Table9_V1.2_2024-11-18.xlsx.txt.
• No exact variant entry in the functional-assay dataset ST4 of SupplementaryTables_V1.2_2024-11-18.xlsx.txt.
• No exact variant entry in HUMU-40-1557-s001.xlsx.txt.
• No calibrated variant-specific protein or combined mRNA-and-protein assay result was identified; the available variant-specific publication finding is a benign-polymorphism label, not functional assay evidence.

Sources

Reasoning

The ENIGMA BRCA1 specification governs PS4 as strong when a case-control study shows p-value <=0.05 and OR >=4, with the lower confidence interval excluding 2.0. No exact-variant case-control dataset, odds ratio, p-value, or confidence interval was provided for NM_007294.4:c.3270A>G (p.Gln1090=/p.Q1090=). The exact variant is absent from Specifications_V1.2_2024-11-18.docx.txt; the available literature extraction reports only a general clinical observation of Q1090Q in a BRCA1 haplotype table, not case-control enrichment. Therefore PS4 cannot be assessed.

Rule

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).

Evidence considered

• The ENIGMA rule states: "Case-control studies; p-value <=0.05 and OR >=4 (lower confidence interval excludes 2.0)."
• The exact variant was not found in the searched full-text VCEP specification, and the available exact-variant paper finding reports a haplotype observation rather than case-control enrichment.

Still missing

• No exact-variant case-control prevalence dataset, OR, p-value, or confidence interval for NM_007294.4:c.3270A>G.
• No exact c.3270A>G, p.Gln1090=, or p.Q1090= entry found in Specifications_V1.2_2024-11-18.docx.txt.

Sources

Reasoning

The ENIGMA BRCA1 VCEP specification restricts PM3 to patients with a phenotype consistent with BRCA1-related Fanconi anemia and a co-occurrent variant in the same gene, with PM3 strength determined from Table 6 points for a pathogenic or likely pathogenic variant in trans, homozygous state, or unknown phase. The available case evidence provides no affected-proband Fanconi-anemia phenotype, chromosome-breakage result, co-occurring pathogenic or likely pathogenic BRCA1 variant, or phase information for c.3270A>G (p.Gln1090=; p.Q1090=). PMID:16267036 reports Q1090Q as a benign polymorphism in a haplotype table but does not establish an informative trans observation, phase, or Fanconi-anemia phenotype. Therefore PM3 cannot be assigned from the available evidence.

Rule

ENIGMA BRCA1 PM3_VariableWeight: apply only for a patient with phenotype consistent with BRCA1-related Fanconi anemia and co-occurrent variants in the same gene; PM3 = 2 points, PM3_Supporting = 1 point, and PM3_Strong = 4 or more points.

Evidence considered

• ENIGMA BRCA1 VCEP Specifications V1.2, Table 1 and Table 6: PM3 is restricted to a BRCA1-related Fanconi-anemia phenotype with a same-gene co-occurrent variant; 2 points are required for PM3, 1 point for PM3_Supporting, and at least 4 points for PM3_Strong.
• The case evidence contains no affected-proband Fanconi-anemia phenotype, chromosome-breakage result, same-gene pathogenic/likely pathogenic co-occurring variant, or phase assignment for this variant.
• PMID:16267036 lists Q1090Q, corresponding to p.Q1090=, as a benign polymorphism in Table 2, Haplotype 1, but does not provide an informative trans observation, phase determination, or Fanconi-anemia phenotype for this variant.
• A direct search of Specifications_V1.2_2024-11-18.docx.txt for c.3270A>G, p.Gln1090=, and p.Q1090= found no variant-specific entry.

Still missing

• No affected-proband Fanconi-anemia phenotype or chromosome-breakage result is available.
• No co-occurring pathogenic or likely pathogenic BRCA1 variant and no trans, cis, homozygous, or unknown-phase observation is documented.
• No entry for c.3270A>G, p.Gln1090=, or p.Q1090= was found when Specifications_V1.2_2024-11-18.docx.txt was searched.
• The exact variant is not reported in the available phase/co-occurrence evidence beyond PMID:16267036, which lists Q1090Q as a benign polymorphism without informative phase or Fanconi-anemia data.

Sources

Reasoning

The ENIGMA specification requires co-segregation with disease in multiple affected family members and a quantitative Bayes co-segregation score. It assigns PP1 Supporting at LR >=2.08:1, Moderate at LR >=4.3:1, Strong at LR >=18.7:1, and Very Strong at LR >=350:1, with additional caution for a single family or isolated population. No proband-level pedigree, affected-relative genotypes, meioses, or quantitative co-segregation LR is provided for NM_007294.4:c.3270A>G. The searched Specifications_V1.2_2024-11-18.docx and HUMU-40-1557-s001.xlsx contain no entry for this variant under the requested notations relevant to PP1.

Rule

PP1 variable weight requires quantitative co-segregation: Supporting LR >=2.08:1; Moderate LR >=4.3:1; Strong LR >=18.7:1; Very Strong LR >=350:1.

Evidence considered

• The ENIGMA specification defines PP1 as co-segregation with disease in multiple affected family members measured by a quantitative co-segregation method, with thresholds of LR >=2.08:1 for Supporting, >=4.3:1 for Moderate, >=18.7:1 for Strong, and >=350:1 for Very Strong.
• The case evidence provides no family pedigree, affected-relative genotype results, meioses count, or calculated co-segregation LR for this synonymous variant.
• Easton et al. (PMID:17924331) reports Q1090Q as a benign polymorphism in Table 2, but the extracted finding provides no variant-specific segregation LR or affected-family segregation data and therefore does not establish PP1.

Still missing

• No proband-level pedigree, affected-relative genotypes, meioses, or quantitative co-segregation LR was found in the case evidence.
• No entry for c.3270A>G, p.Gln1090=, or p.Q1090= was found in Specifications_V1.2_2024-11-18.docx when searched for this criterion.
• No entry for c.3270A>G, p.Gln1090=, or p.Q1090= was found in HUMU-40-1557-s001.xlsx when searched for this criterion.

Sources

Reasoning

ENIGMA restricts PP4 to a combined multifactorial likelihood ratio toward pathogenicity, with Supporting at LR >=2.08:1, Moderate at LR >=4.3:1, Strong at LR >=18.7:1, and Very Strong at LR >=350:1. The gene-specific clinical-history table contains c.3270A>T but no exact c.3270A>G record, and no exact combined LR for this variant is available. The exact variant is absent from PMID_31853058_BRCA1_clinical_history_LR.xlsx.txt and PMID_17924331_Easton_2007_AJHG.pdf.txt. Therefore PP4 cannot be assessed.

Rule

Use ONLY to capture combined LR towards pathogenicity, based on multifactorial likelihood clinical data; PP4 Supporting requires LR >=2.08:1.

Evidence considered

• The ENIGMA PP4 rules state Supporting LR >=2.08:1, Moderate LR >=4.3:1, Strong LR >=18.7:1, and Very Strong LR >=350:1.
• The gene-specific clinical-history table was searched for c.3270A>G and contains only the different c.3270A>T record; no exact-variant combined LR was identified.

Still missing

• No exact c.3270A>G record in PMID_31853058_BRCA1_clinical_history_LR.xlsx.txt; c.3270A>T is a different variant.
• No exact c.3270A>G, p.Gln1090=, or p.Q1090= entry found in PMID_17924331_Easton_2007_AJHG.pdf.txt.
• No exact-variant combined multifactorial LR supplied by the case evidence.

Sources

Reasoning

The ENIGMA BRCA1 VCEP applies BS2 only from qualifying clinically or research-cohort probands observed as homozygotes or with specified co-occurrence/phase and age or cancer-unaffectedness criteria, in the absence of Fanconi Anemia features. The available population data report zero homozygotes, but the VCEP explicitly excludes gnomAD observations from BS2 and no qualifying phenotyped adult observation with the required clinical and phase information was identified.

Rule

Apply BS2 from qualifying phenotyped individuals without Fanconi Anemia features, using Table 8 point thresholds; do not apply BS2 to gnomAD frequency observations.

Evidence considered

• ENIGMA BRCA1 VCEP Table 8 requires BS2 points from phenotyped individuals meeting specified age or cancer-unaffectedness criteria and applies the code in the absence of Fanconi Anemia features.
• ENIGMA explicitly states that homozygote observations in gnomAD are not to be used for BS2 because frequency-based codes capture those observations.
• The case evidence reports zero homozygotes in gnomAD v2.1 non-cancer exomes and zero homozygotes in gnomAD v3.1 non-cancer genomes, which is not qualifying BS2 evidence.

Still missing

• No qualifying clinically or research-cohort proband with documented age, cancer status, phase/co-occurrence, and absence of Fanconi Anemia features was identified for BS2.
• No exact c.3270A>G, p.Gln1090=, or p.Q1090= entry was found in SupplementaryTables_V1.2_2024-11-18.xlsx.txt, Specifications_V1.2_2024-11-18.docx.txt, Appendices_V1.2_2024-11-18.docx.txt, or HUMU-40-1557-s001.xlsx.txt.

Sources

Reasoning

The ENIGMA BRCA1 specification reserves BS3 for well-established functional studies demonstrating no damaging effect on protein function, with protein-only or combined mRNA-and-protein assay designs; silent variants require functional data that captures both mRNA and protein effects. The governing Specifications Table 9 has no entry for NM_007294.4:c.3270A>G, c.3270A>G, p.Gln1090=, or p.Q1090=. The supplementary functional-assay dataset (ST4) and the Parsons multifactorial supplement also have no exact entry. Therefore, no calibrated variant-specific benign assay result is available to apply BS3.

Rule

ENIGMA v1.2 BS3: apply only for well-established functional studies showing no damaging effect on protein function, measured via protein alone or mRNA and protein combined; for silent variants, use assays capturing mRNA and protein effects.

Evidence considered

• ENIGMA BRCA1 v1.2 specifies BS3 for well-established functional studies showing no damaging effect on protein function, measured through protein alone or mRNA and protein together; mRNA-only benign results use the alternative RNA code.
• For silent variants, Table 9 evaluates functional data only from assays that measure mRNA and protein; no Table 9 row matches c.3270A>G, p.Gln1090=, or p.Q1090=.
• Supplementary Table 4 functional-assay data and HUMU-40-1557-SuppT4 contain no exact entry for this variant; no calibrated assay metric, benign-control comparison, or non-damaging result is available for BS3.

Still missing

• No entry for c.3270A>G, p.Gln1090=, or p.Q1090= in Specifications_Table9_V1.2_2024-11-18.xlsx.txt.
• No exact variant entry in the functional-assay dataset ST4 of SupplementaryTables_V1.2_2024-11-18.xlsx.txt.
• No exact variant entry in HUMU-40-1557-s001.xlsx.txt.
• No calibrated variant-specific protein or combined mRNA-and-protein assay result was identified; the available variant-specific publication finding is a benign-polymorphism label, not functional assay evidence.

Sources

Reasoning

The ENIGMA specification requires lack of segregation in affected family members measured by a quantitative co-segregation method. It assigns BS4 Supporting for LR <=0.48 and >0.23, Moderate for LR <=0.23, Strong for LR <=0.05, and Very Strong for LR <=0.00285, with a stipulation to assess bilinearity before applying benign Very Strong evidence. No non-segregating affected relatives, pedigree, meioses, or quantitative LR is provided for NM_007294.4:c.3270A>G. The searched Specifications_V1.2_2024-11-18.docx and HUMU-40-1557-s001.xlsx contain no entry for this variant under the requested notations relevant to BS4.

Rule

BS4 variable weight requires quantitative lack-of-segregation evidence: Supporting LR <=0.48 and >0.23; Moderate LR <=0.23; Strong LR <=0.05; Very Strong LR <=0.00285.

Evidence considered

• The ENIGMA specification defines BS4 as lack of segregation in affected family members measured by a quantitative co-segregation method, with Supporting LR <=0.48 and >0.23, Moderate LR <=0.23, Strong LR <=0.05, and Very Strong LR <=0.00285.
• The case evidence provides no affected-relative non-segregation data, pedigree, meioses count, or calculated LR for this variant.
• Easton et al. (PMID:17924331) reports Q1090Q as a benign polymorphism in Table 2, but the extracted finding provides no variant-specific non-segregation LR or affected-family segregation data and therefore does not establish BS4.

Still missing

• No affected-relative non-segregation observations, pedigree, meioses, or quantitative co-segregation LR was found in the case evidence.
• No entry for c.3270A>G, p.Gln1090=, or p.Q1090= was found in Specifications_V1.2_2024-11-18.docx when searched for this criterion.
• No entry for c.3270A>G, p.Gln1090=, or p.Q1090= was found in HUMU-40-1557-s001.xlsx when searched for this criterion.

Sources

Reasoning

ENIGMA restricts BP5 to a combined multifactorial likelihood ratio against pathogenicity, with Supporting at LR <=0.48:1, Moderate at LR <=0.23:1, Strong at LR <=0.05:1, and Very Strong at LR <=0.00285:1. No exact c.3270A>G clinical-history or combined multifactorial LR is available; the gene-specific table contains the different c.3270A>T record only. Consequently, no value can be substituted into the required inequality and BP5 cannot be assessed.

Rule

Use ONLY to capture combined LR against pathogenicity, based on multifactorial likelihood clinical data; BP5 Supporting requires LR <=0.48:1.

Evidence considered

• The ENIGMA BP5 rule literally uses the downward comparison operator: Supporting LR <=0.48:1; Moderate LR <=0.23:1; Strong LR <=0.05:1; Very Strong LR <=0.00285:1.
• No exact-variant LR value is available, so an explicit substituted inequality cannot be completed.

Still missing

• No exact c.3270A>G record in PMID_31853058_BRCA1_clinical_history_LR.xlsx.txt; c.3270A>T is a different variant.
• No exact c.3270A>G, p.Gln1090=, or p.Q1090= entry found in PMID_17924331_Easton_2007_AJHG.pdf.txt.
• No exact-variant combined multifactorial LR supplied by the case evidence.

Sources