BRCA2 c.6546_6574del, p.(Lys2182AsnfsTer5)

Rule

ENIGMA BRCA1/BRCA2 VCEP Specification v1.2, PVS1 (default strength Pathogenic Very Strong for null variants in a gene with established LOF mechanism, per PVS1 flowchart and Specifications Table 4/Appendix D).

Evidence considered

• case_summary.json compact_evidence.normalization: NM_000059.4:c.6546_6574del predicts NP_000050.3:p.(Lys2182AsnfsTer5), a frameshift.
• prefetch.json mutalyzer protein prediction: position_first=2181, position_last_original=3419, position_last_predicted=2186, i.e. truncation well before the native C-terminus.
• prefetch.json selector_short coding-exon coordinate map places c.6546_6574 within the c.1910_6841 exon span, corresponding to BRCA2 exon 11.
• pvs1_gene_context.json: lof_mechanism_supported=true, pvs1_gene_gate='eligible', BRCA2 germline LOF is an established disease mechanism per official ENIGMA CSPEC/VCEP.
• pvs1_variant_assessment.json: consequence_class='frameshift', variant_bucket='frameshift', suggested_default_strength='PVS1', apply_generic_pvs1_framework=true.
• ENIGMA BRCA1/BRCA2 CSPEC v1.2 (case_summary.json cspec.criteria PVS1 entry): null variants (nonsense, frameshift, splice site, initiation codon, single/multi-exon deletion) in BRCA2 apply PVS1 at appropriate strength per the PVS1 flowchart considering clinically important functional domains; default strength is Pathogenic Very Strong.
• ENIGMA Table 4 BRCA2 exon-level PVS1 decision table: exon 11 rows show PVS1 code applicability for splice/PTC variants in this exon; exon 11 is not among the PM5_N/A-excluded exons (E12, E27, E6), and no PVS1_N/A flag is present for exon 11.
• PMID:10570174 (full text) reports that BRCA2 truncations removing the C-terminal 156 aa (containing NLS1/NLS3) fail to localize to the nucleus and are non-functional, supporting the general BRCA2 LOF-via-truncation mechanism, though this exact variant is not mentioned.
• PMID:11239455 (full text) reports BRCA2 C-terminal truncating mutations severely impair homology-directed repair, supporting the LOF mechanism generally; this exact variant is not mentioned.
• PMID:20878484, PMID:22193408, PMID:24312913 (full text) provide general BRCA2 truncation/LOF mechanistic context but do not mention this exact variant; used only as background, not as variant-specific evidence.

Still missing

• No variant-specific RNA/NMD assay was available to directly confirm transcript decay for this exact deletion; classification relies on positional/bioinformatic PVS1 prediction per the ENIGMA flowchart and generic ClinGen SVI PVS1 recommendations.
• Exact BRCA2 exon number (11) was inferred from Mutalyzer coding-region coordinates cross-referenced against the ENIGMA Table 4 exon map rather than a directly stated exon annotation in the prefetch output.

Sources

Rule

PP5 Supporting only for an exact-variant ClinVar expert-panel Pathogenic/Likely pathogenic assertion.

Evidence considered

• ClinVar was queried using the exact transcript HGVS and genomic HGVS representations; the bundle reports no exact match, no variation ID, and no ClinVar result.
• Only an exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic assertion would support PP5; ordinary laboratory submissions, aggregate labels, and non-expert assertions are not used.

Sources

Rule

Filter allele frequency (FAF) is above 0.1% (FAF > 0.001) in gnomAD v2.1 (non-cancer, exome only subset) and/or gnomAD v3.1 (non-cancer), non-founder population(s). See Appendix G for details.

Evidence considered

• The governing ClinGen ENIGMA BRCA2 specification v1.2 defines BA1 as filter allele frequency (FAF) >0.001 in gnomAD v2.1 non-cancer exome and/or gnomAD v3.1 non-cancer, non-founder populations.
• The case bundle reports the variant as absent from gnomAD v2.1 and absent from gnomAD v4.1; no elevated population frequency or threshold artifact is reported.

Sources

Rule

Filter allele frequency (FAF) is above 0.01% (FAF > 0.0001) in gnomAD v2.1 (non-cancer, exome only subset) and/or gnomAD v3.1 (non-cancer), non-founder population(s) for BS1 Strong; FAF is above 0.002% (FAF > 0.00002) and less than or equal to 0.01% (FAF <= 0.0001) for BS1 Supporting. See Appendix G for details.

Evidence considered

• The governing ClinGen ENIGMA BRCA2 specification v1.2 defines BS1 Strong as FAF >0.0001 and BS1 Supporting as FAF >0.00002 and <=0.0001 in specified non-cancer, non-founder gnomAD populations.
• The case bundle reports absence of the variant from gnomAD v2.1 and gnomAD v4.1, with no reported allele count, FAF, ancestry-specific enrichment, or frequency above a BS1 threshold.

Sources

Rule

BP6 Supporting only for an exact-variant ClinVar expert-panel Benign/Likely benign assertion.

Evidence considered

• ClinVar was queried using the exact transcript HGVS and genomic HGVS representations; the bundle reports no exact match, no variation ID, and no ClinVar result.
• Only an exact-variant ClinVar expert-panel Benign or Likely benign assertion would support BP6; ordinary laboratory submissions, aggregate labels, and non-expert assertions are not used.

Sources

Evidence considered

• ENIGMA BRCA1/2 v1.2 Specifications Table 9 use-note restricts PS3/BS3 functional-assay code lookups to missense and synonymous variant types; c.6546_6574del is a frameshift deletion and is out of scope.
• cspec PS3 rule text: 'Well-established in vitro or in vivo functional studies supportive of a damaging effect. Apply PS3 for assays measuring effect via protein only OR mRNA and protein combined... See Specifications Table 9...' or 'as measured by effect on mRNA transcript profile (mRNA assay only). Apply as PVS1 (RNA)' — neither pathway has variant-specific assay data for this deletion.
• SpliceAI evidence_sentence in prefetch: 'SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01)' — no basis for an mRNA-assay-driven PVS1(RNA)/PS3 pathway.
• No row for c.6546_6574del or p.(Lys2182AsnfsTer5) found in the extracted Specifications_Table9 functional assay data (Findlay/Dace interim report rows) present in the bundle.

Still missing

• No calibrated functional assay (protein-level or mRNA-level) covering NM_000059.4:c.6546_6574del was found in the ENIGMA Table 9 curated dataset or in any fetched publication for this case.
• This variant type (frameshift deletion) falls outside the missense/synonymous scope of the ENIGMA PS3/BS3 functional-assay track; PVS1 (not PS3) is the applicable pathway for null-variant classification and is handled by a separate criterion group.

Rule

ENIGMA BRCA2 PS4: case-control prevalence significantly increased in affected individuals; p<=0.05 and OR>=4 with lower confidence interval excluding 2.0.

Evidence considered

• The ENIGMA BRCA2 specification requires a case-control study with p<=0.05, OR>=4, and a lower confidence limit excluding 2.0 for PS4.
• The supplied evidence bundle contains no case count, control count, OR, confidence interval, p-value, or case-control likelihood ratio for this exact variant.

Still missing

• A variant-specific, matched case-control analysis meeting the ENIGMA PS4 threshold is needed.

Sources

Rule

Absent from controls in an outbred population, from gnomAD v2.1 (non-cancer, exome only subset) and gnomAD v3.1 (non-cancer). Region around the variant must have an average read depth >=25. See Appendix G for details.

Evidence considered

• The governing ClinGen ENIGMA BRCA2 specification v1.2 defines PM2 Supporting as absent from controls in an outbred population in gnomAD v2.1 non-cancer exome and gnomAD v3.1 non-cancer, with average read depth >=25 around the variant.
• The case bundle reports absence from gnomAD v2.1 and gnomAD v4.1, but does not report gnomAD v3.1 or average read depth. Absence from gnomAD v4.1 cannot substitute for the explicitly specified v3.1 and depth requirements without an applicable framework instruction.

Still missing

• A gnomAD v3.1 non-cancer result is not provided.
• The required average read depth >=25 around the variant is not provided.
• Ancestry-specific coverage and callable-region quality metrics are not provided.

Sources

Rule

ENIGMA BRCA2 v1.2 PM3: apply only with a co-occurrent P/LP variant in the same gene and a phenotype consistent with BRCA1/2-related Fanconi anemia; assign strength from the Table 6 PM3 point total.

Evidence considered

• The ENIGMA BRCA2 v1.2 rule states that PM3 requires a co-occurrent pathogenic or likely pathogenic variant in the same gene in a patient with a phenotype consistent with BRCA1- or BRCA2-related Fanconi anemia; phenotype and chromosome-breakage requirements, plus Table 6 point-based strength assignment, are specified.
• The case bundle contains no affected-proband Fanconi anemia findings, chromosome-breakage result, second BRCA2 variant, parental testing, or phase determination.
• The assessed variant is reported absent from gnomAD v2.1 and gnomAD v4.1, so the VCEP rarity gate is not the limiting issue.

Still missing

• Affected-proband Fanconi anemia phenotype and chromosome-breakage testing are not documented.
• No co-occurrent pathogenic or likely pathogenic BRCA2 variant is documented.
• No parental testing or other phase information establishes variants in trans or cis.
• No Table 6 PM3 point total can be calculated.

Sources

Rule

ENIGMA BRCA1/BRCA2 CSPEC v1.2 PM5_PTC: PTC variant in an exon with a different proven pathogenic PTC previously observed; strength set per exon in Specifications Table 4.

Evidence considered

• ENIGMA CSPEC v1.2 PM5 rule: 'Protein termination codon (PTC) variant in an exon where a different proven pathogenic PTC variant has been seen before. Use to justify additional weight for PTC variants annotated as PVS1. See Specifications Table 4 for PM5_PTC code strengths applicable per exon.'
• Case bundle Table 4 excerpt: 'PM5_N/A exons for BRCA2: E12, E27, E6. PM5_PTC applicable exons for BRCA2 include E11' -- confirming exon 11 (containing c.6546_6574del) is eligible in principle for PM5_PTC, but the excerpted exon-11 rows only list PVS1 splice/deletion/duplication entries, not a resolvable PM5_PTC strength code.
• pm5_candidates.json for this case: pm5_mode='ptc_gene_specific', eligible_for_classic_pm5_search=false, recommendation level='not_applicable' pending review of same-exon comparator pathogenic PTC variants against the governing PM5_PTC rule -- the automated candidate search did not resolve a usable comparator or strength.

Still missing

• Exact PM5_PTC strength code (Strong/Moderate/Supporting) for BRCA2 exon 11 not resolved from the Table 4 excerpt available in this bundle.
• No specific previously-classified pathogenic PTC variant within exon 11 was identified/cited in the bundle to anchor the PM5_PTC comparison.
• Full Specifications_Table4_V1.2_2024-11-18.xlsx should be consulted directly (beyond the excerpted rows) to confirm the exon-11 PM5_PTC strength assignment.

Sources

Rule

Apply PP1 only for cosegregation with disease in multiple affected family members, measured by a quantitative cosegregation analysis method: PP1 Supporting LR >= 2.08:1, PP1 Moderate LR >= 4.3:1, PP1 Strong LR >= 18.7:1, and PP1 Very Strong LR >= 350:1.

Evidence considered

• The ENIGMA BRCA2 Version 1.2 rule requires cosegregation with disease in multiple affected family members measured by a quantitative cosegregation method; the bundle provides no such case-level data.
• The framework states that LR greater than 0.48 and less than 2.08 provides no supporting evidence in either direction, but no segregation LR is available for this case.

Still missing

• Obtain family pedigree and phenotype data.
• Obtain variant testing results for affected and unaffected relatives, including parental testing where relevant.
• Obtain the number of informative meioses and a quantitative cosegregation likelihood ratio from COOL, CAL-Leiden, or an equivalent validated method.

Sources

Rule

ENIGMA BRCA2 PP4: use only a combined multifactorial clinical LR toward pathogenicity; do not use phenotype/family history alone.

Evidence considered

• The ENIGMA BRCA2 specification permits PP4 only for a combined multifactorial clinical LR toward pathogenicity, with Supporting at LR>=2.08, Moderate at >=4.3, and Strong at >=18.7.
• The supplied BRCA2 clinical-history LR workbook was checked for the normalized exact HGVS c.6546_6574del and contains no matching entry; it therefore provides no variant-specific clinical-history LR.
• No other combined clinical LR or separately documented clinical components for this exact variant are present in the bundle.

Still missing

• A variant-specific combined clinical LR, or its independently sourced components, is needed; PP4 Supporting requires LR>=2.08.

Sources

Rule

Applied in absence of features of recessive disease, namely Fanconi Anemia phenotype. See Specifications Table 8 for additional stipulations, and approach to assign points per proband, and final BS2 code assignment based on the sum of BS2-related points.

Evidence considered

• The governing ClinGen ENIGMA BRCA2 specification v1.2 states that BS2 is applied in the absence of features of recessive disease, namely Fanconi Anemia phenotype, using additional stipulations and point assignment in Specification Table 8.
• The case bundle provides no clinical phenotype or homozygote/biallelic observation that can be evaluated under that rule.

Still missing

• Fanconi Anemia phenotype assessment is not provided.
• No case-level homozygote or biallelic observation is provided.
• No ENIGMA Specification Table 8 BS2 point calculation is available.

Sources

Evidence considered

• ENIGMA BRCA1/2 v1.2 Specifications Table 9 use-note restricts PS3/BS3 functional-assay code lookups to missense and synonymous variant types; c.6546_6574del is a frameshift deletion and is out of scope.
• cspec BS3 rule text: 'Well-established in vitro or in vivo functional studies shows no damaging effect on protein function. Assay measures effect via protein only OR mRNA and protein combined. See Specifications Table 9...' — no variant-specific assay data located.
• No row for c.6546_6574del or p.(Lys2182AsnfsTer5) found in the extracted Specifications_Table9 functional assay data present in the bundle.

Still missing

• No calibrated functional assay (protein-level or mRNA-level) covering NM_000059.4:c.6546_6574del was found in the ENIGMA Table 9 curated dataset or in any fetched publication for this case.
• This variant type (frameshift deletion) falls outside the missense/synonymous scope of the ENIGMA PS3/BS3 functional-assay track.

Rule

Apply BS4 only for lack of segregation in affected family members, measured by a quantitative cosegregation analysis method: BS4 Supporting LR <= 0.48:1, BS4 Moderate LR <= 0.23:1, BS4 Strong LR <= 0.05:1, and BS4 Very Strong LR <= 0.00285:1.

Evidence considered

• The ENIGMA BRCA2 Version 1.2 rule requires lack of segregation in affected family members measured by a quantitative cosegregation method; the bundle provides no such case-level data.
• The framework cautions that phenocopies and multiple pathogenic variants can confound apparent lack of segregation, and states that LR greater than 0.48 and less than 2.08 provides no supporting evidence in either direction; no LR is available for this case.

Still missing

• Obtain family pedigree and phenotype data.
• Obtain variant testing results for affected relatives and other informative relatives.
• Obtain a quantitative cosegregation likelihood ratio and assess possible phenocopies or an alternative pathogenic variant in the family.

Sources

Rule

ENIGMA BRCA2 BP5: use only a combined multifactorial clinical LR against pathogenicity; co-observation in different breast-ovarian cancer risk genes is not applicable.

Evidence considered

• The ENIGMA BRCA2 specification permits BP5 only for a combined multifactorial clinical LR against pathogenicity; Supporting requires LR<=0.48, Moderate <=0.23, and Strong <=0.05.
• The supplied BRCA2 clinical-history LR workbook was checked for the normalized exact HGVS c.6546_6574del and contains no matching entry; it provides no variant-specific clinical-history LR.
• No combined LR against pathogenicity is reported for this exact variant.

Still missing

• A variant-specific combined clinical LR at or below 0.48, with the underlying data available for review, is needed.

Sources