TP53 c.672+6G>A, p.?

Reasoning

PS1 requires the variant under evaluation to produce the same amino acid change as a previously established pathogenic missense variant (different nucleotide, same codon change). TP53 VCEP v2.4 additionally restricts PS1 to variants asserted Pathogenic (Strong) or Likely Pathogenic (Moderate) under the VCEP's specifications and requires splicing effects to be excluded. NM_000546.5:c.672+6G>A is an intronic substitution at the +6 position of the exon 6 donor splice site with no amino acid change (NP_000537.3:p.?; VariantValidator maps the position to intron 6, '6i'), so there is no protein-level change to compare with any established pathogenic missense. The +6 position falls within the 9-nt 5' splice-site consensus (PMID:17576681), confirming this acts at the RNA/splicing level, not as an amino acid substitution. No same-amino-acid established pathogenic variant was identified in the case evidence. PS1 is therefore structurally inapplicable.

Rule

TP53 VCEP v2.4 PS1 (applicable): Strong if the variant is asserted Pathogenic, Moderate if Likely Pathogenic, per TP53 VCEP specifications; same amino acid change as an established pathogenic variant regardless of nucleotide change; splicing must be excluded (RNA data or SpliceAI < 0.2).

Evidence considered

• Governing framework is the ClinGen TP53 Expert Panel Specifications v2.4 (cspec), framework_mode 'vcep'.
• Variant normalized as NM_000546.5:c.672+6G>A; predicted protein consequence NP_000537.3:p.?; VariantValidator reports variant_exonic_positions start/end '6i' (intron 6), confirming an intronic, non-missense variant.
• CSPEC PS1 rule text: 'Can be applied to variants asserted as Pathogenic following the TP53 VCEP's specifications' (Strong) and 'asserted as Likely Pathogenic' (Moderate); instructions restrict comparison to variants classified under TP53 VCEP specifications and require no splicing difference (RNA or SpliceAI < 0.2).
• paper_extracts for PMID:17576681 state the human 5'ss consensus MAG|GURAGU spans position -3 to +6 relative to the exon-intron junction, so c.672+6G>A falls within the intronic 5' splice-site consensus and is an RNA-level change rather than an amino acid substitution; the paper does not mention this variant or any TP53 residue comparator.
• No evidence in the case bundle of any established pathogenic variant producing the same amino acid change as this variant (which produces none).

Sources

Reasoning

Governing framework is the ClinGen TP53 VCEP ACMG/AMP Specifications v2.4 (cspec doc 135637581; framework_mode=vcep). Under this specification PS3 is defined exclusively through protein-function assays — Kato et al. 2003 (PMID 12826609) transactivation as the primary assay, with Giacomelli 2018 (PMID 30224644), Kawaguchi 2005 (PMID 16007150), Kotler 2018 (PMID 29979965), and Funk 2025 (PMID 39774325) as eligible supporting assays — and the 'Flowchart for application of functional rule codes' together with Functional-worksheet.xlsx (Supplementary Table S3) scope these codes to missense variants and small in-frame deletions. NM_000546.5:c.672+6G>A is an intronic variant at the +6 position of the exon 6 donor splice site (variant_exonic_positions 6i; predicted protein p.?): it is neither a missense variant nor an in-frame deletion, so no amino-acid substitution exists to look up in the functional worksheet and none of the eligible protein-level assays can have a result for it. The VCEP v2.4 functional-rule caveat additionally states that protein-level functional codes must not be applied when splicing is the effect under assessment: laboratory/RNA evidence of a splicing aberration would be handled under PVS1_Variable Weight (RNA), and PS3 must not be applied at any weight from protein-level assays if PP3 is applied on the basis of SpliceAI. No RNA-based or other functional assay for this exact variant is present anywhere in the case record (literature_pass.json contains no variant-level functional paper; every extracted full text reports variant_mentioned=false), so PS3 cannot be met on any evidence. Generic ACMG is not invoked because an applicable VCEP specification exists. PS3 is therefore not applicable at the variant-type scope gate of the governing framework, and no alternative RNA-based functional evidence is available to assess.

Rule

TP53 VCEP v2.4 PS3 (protein-function assay rules for missense variants and small in-frame deletions only; splicing/RNA evidence routed to PVS1_Variable Weight (RNA))

Evidence considered

• ClinGen TP53 VCEP specifications v2.4 (cspec doc 135637581) PS3 rule: PS3_Strong = Non-functional on Kato et al. data AND LOF by majority of other eligible assays; PS3_Moderate = Partially functional on Kato AND LOF by majority of other available assays; PS3_Supporting = Non-functional on Kato AND abnormal on Kawaguchi regardless of other assays (or small deletions with LOF on the majority of available assays). All strengths hinge on Kato transactivation class (non-functional <=20%, partially functional >20-<=75%, functional >75% activity).
• VCEP 'Flowchart for application of functional rule codes' (and index guidance) states PS3/BS3 are applied via protein function for missense variants (left branch) and small deletions (right branch); eligible studies are Kato (PMID 12826609), Funk (PMID 39774325), Giacomelli (PMID 30224644), Kotler (PMID 29979965), Kawaguchi (PMID 16007150), plus other assays after expert interpretation as previously reported (PMID 33300245).
• VCEP v2.4 release note and PS3/BS3 instructionsToUse caveat: 'Do not apply PS3 at any weight for missense variants using assays done at the protein level (such as Kato et al. or Giacomelli et al.) if PP3 is applied based on SpliceAI. If there is any laboratory evidence, including RNA-seq data, of splicing aberration for the genetic variant being assessed, for which PVS1_Variable Weight (RNA) might be considered instead. Functional missense codes should not be applied if PVS1 is applied for splicing.'
• Variant NM_000546.5:c.672+6G>A is intronic at the +6 position of the exon 6 donor (VariantValidator variant_exonic_positions 6i; hgvs_predicted_protein_consequence NP_000537.3:p.?), not a missense or in-frame deletion, so no protein-level assay result (Kato/Giacomelli/Kawaguchi/Kotler/Funk) exists or can exist for it.
• Case literature review found no functional study of this variant: literature_pass.json high-priority papers are ClinVar-attached splicing-statistics/guideline papers with no candidate functional criteria; paper_extracts.json reports variant_mentioned=false for every fetched full text (PMID 17392385, 25394175, 17576681, 25741868, 9536098); no c.672+6G>A row appears in the parsed VCEP PVS1-Splicing worksheet rows or PP3-BP4 codes rows (those list c.672G>C, c.672G>T, c.672+1G>C — different variants).
• PMID 25741868 (ACMG/AMP 2015 standards) was consulted to calibrate what counts as functional evidence for a splice-region variant: 'Although splice site variants are predicted to lead to a null effect, confirmation of impact requires functional analysis by either RNA or protein analysis' — i.e., in silico prediction alone is not functional evidence for PS3.
• PMID 17576681 (Buratti et al. 2007) was consulted for mechanism context only: the human 5' splice-site consensus (MAG|GURAGU) spans -3 to +6, so the +6 intronic position of c.672+6G>A falls within the consensus, but the paper provides no TP53 variant-level functional data (variant_mentioned=false) and cannot support PS3.
• SpliceAI lookup for this variant (max delta score 0.135, DS_DL 0.135 donor-loss signal) is an in silico prediction below the VCEP 0.2 splice-effect threshold; it was not treated as functional assay evidence for PS3.

Still missing

• No RNA-based functional assay of c.672+6G>A (patient-derived RNA RT-PCR, minigene, or splice reporter) exists in the case record — the only functional modality that could bear on an intronic variant; under the TP53 VCEP, RNA evidence of a splicing aberration would be applied as PVS1_Variable Weight (RNA) rather than PS3.
• No variant-specific entry exists or could exist in the VCEP Functional-worksheet (protein-level assay rows cover amino-acid substitutions and small in-frame deletions only); the worksheet contents were not parsed into the bundle, but an intronic +6 variant has no amino-acid-change key regardless.

Sources

Reasoning

The TP53 VCEP v2.4 PM1 rule applies only to missense variants located within hotspot codons 175, 245, 248, 249, 273, 282 (transcript NM_000546.4) at Moderate, or to germline missense variants with 2-9 (Supporting) or >=10 (Moderate) somatic occurrences for the same amino acid change in cancerhotspots.org. NM_000546.5:c.672+6G>A is an intronic variant (intron 6, +6 of the exon 6 donor) with no amino acid change (p.?), so it is not a missense variant, does not alter any listed hotspot codon, and the somatic-occurrence prong (which is limited to missense changes) cannot apply. vcep_materials.json domain_tables contains no entries for TP53 ({}), so no authoritative VCEP domain table places this position in an approved critical functional domain; the CSPEC hotspot-codon list is the operative PM1 scope. COSMIC has no record of this variant. PM1 is not applicable.

Rule

TP53 VCEP v2.4 PM1 (applicable): Moderate for missense variants within codons 175, 245, 248, 249, 273, 282 (NM_000546.4) or germline missense with >=10 cancerhotspots.org somatic occurrences for the same amino acid change; Supporting for germline missense with 2-9 somatic occurrences.

Evidence considered

• CSPEC PM1 rule text: Moderate for 'Missense variants within the following codons using transcript NM_00546.4: 175, 245, 248, 249, 273, 282' or germline missense variants with >=10 cancerhotspots.org somatic occurrences for the same amino acid change; Supporting for germline missense with 2-9 somatic occurrences.
• vcep_materials.json domain_tables is empty ({}) for TP53; no gene-specific domain-table entry was available to map the residue, so PM1 scope was taken from the CSPEC rule text itself.
• Variant is intronic (c.672+6G>A, intron 6 per VariantValidator) with protein consequence p.?, i.e., not a missense variant and no codon is substituted; residue-level hotspot/codon criteria are therefore inapplicable.
• COSMIC search returned no record for TP53 c.672+6G>A (no somatic recurrence evidence); the cancerhotspots.org prong of PM1 additionally requires a missense change, which this variant does not produce.

Sources

Reasoning

The governing framework is the ClinGen TP53 Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for TP53 Version 2.4 (framework_mode=vcep; cspec found, v2.4), which explicitly declares PM3 applicability as 'Not Applicable'. TP53-related Li-Fraumeni syndrome is an autosomal dominant cancer predisposition disorder, and PM3 is a recessive-mechanism code (pathogenic variant observed in trans with a pathogenic variant in a recessive disorder), so it cannot be applied to this dominant-disorder context. Consistent with the specification, the case bundle contains no second TP53 variant, no biallelic or compound-heterozygous observation, and no phase information: ClinVar VCV000854158 holds germline heterozygous 'Uncertain significance' submissions only (2 laboratories, no co-occurring TP53 variant asserted) and gnomAD v2.1 reports 1/250,952 alleles with 0 homozygotes. PM3 therefore contributes no evidence to this case.

Evidence considered

• Governing specification: ClinGen TP53 Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for TP53 Version 2.4 (source_registry key 'cspec'; cspec.genome.network rule set), retrieved for this case and serialized in case_summary.json. The specification's criterion rule list declares PM3 'Not Applicable'.
• Direct rule text as serialized in case_summary.json cspec section: {"label": "PM3", "applicability": "Not Applicable"}.
• TP53-associated Li-Fraumeni syndrome is an autosomal dominant disorder (ClinVar VCV000854158 conditions: Hereditary cancer-predisposing syndrome, Li-Fraumeni syndrome); PM3 in generic ACMG/AMP (PMID 25741868) applies to recessive disorders where the variant is detected in trans with a pathogenic variant, a mechanism that does not apply here.
• Case bundle scan for allelic evidence: no second TP53 variant, no phase determination, no trans/cis observation, and no biallelic observation appear anywhere in case_summary.json, prefetch.json, evidence.json, literature_pass.json, or paper_extracts.json (searched terms: second variant, in trans, biallelic, compound heterozyg, homozygous, phase, co-occurrence - all absent).
• ClinVar VCV000854158 (source_registry key 'clinvar'): 2 germline 'Uncertain significance' submissions (Labcorp SCV001223750, Color SCV007438756); neither submission asserts a co-occurring second TP53 variant or provides phase information.
• gnomAD v2.1 (source_registry key 'gnomad_v2'): variant 17-7578171-C-T present at 1/250,952 alleles (AF 3.98e-06), 0 homozygotes - single heterozygous population observation only, no biallelic carrier.

Sources

Reasoning

PM5 applies to a novel missense change at an amino acid residue where a different missense change has previously been determined Pathogenic/Likely Pathogenic under the TP53 VCEP's specifications (Strong: >=2 different pathogenic missense variants at the residue; Moderate: 1 pathogenic; Supporting: 1 likely pathogenic with clinical data demonstrating pathogenicity). NM_000546.5:c.672+6G>A is intronic with no amino acid change (p.?), so it is not a missense variant and there is no residue substitution to compare against any pathogenic comparator. The pm5_candidates artifact confirms the consequence class is not missense (recommendation level 'not_applicable', 0 same-residue candidates seen). PM5 is therefore structurally inapplicable; no same-residue missense comparator evidence exists in the case bundle.

Rule

TP53 VCEP v2.4 PM5 (applicable): Strong for a missense variant at a residue with >=2 different missense variants previously determined pathogenic per TP53 VCEP specs; Moderate for 1 such pathogenic variant; Supporting for 1 likely pathogenic variant with clinical data demonstrating pathogenicity.

Evidence considered

• CSPEC PM5 rule text: Missense variant at a residue where >=2 different missense variants previously determined pathogenic per TP53 VCEP specs (Strong), 1 pathogenic (Moderate), or 1 likely pathogenic with clinical data demonstrating pathogenicity (Supporting); instructions require splicing to be ruled out with RNA data or SpliceAI < 0.2 and Grantham comparison of the missense changes.
• pm5_candidates summary: pm5_mode 'classic_same_residue_missense', eligible_for_classic_pm5_search false because the variant consequence class (unknown) is not missense; total same-residue candidates seen = 0.
• Variant is intronic (c.672+6G>A, intron 6) with protein consequence p.?, so it cannot be a 'novel missense change at an amino acid residue' as PM5 requires.

Sources

Reasoning

PM6 is not applicable under the governing gene-specific framework: the ClinGen TP53 VCEP v2.4 specification marks PM6 as 'Not applicable' and, in the PS2 instructions, states the VCEP has 'opted to drop PM6 and use PS2 exclusively for de novo evidence' (all de novo evidence, including assumed de novo, is handled through the PS2 points system). Because an applicable VCEP specification exists for TP53, the generic ACMG/AMP PM6 rule is not used for this variant. Independently of framework applicability, no observation of this variant as an assumed de novo event (e.g., parental testing not performed) is documented in ClinVar VCV000854158, the retrieved literature, or any other source in the case bundle.

VCEP rule

TP53 VCEP v2.4 (cspec doc 135637581), PM6: applicability = Not applicable; instructionsToUse = 'See above for PS2_PM6 combined rule'; the PS2 rule text states the VCEP 'opted to drop PM6 and use PS2 exclusively for de novo evidence.'

Evidence considered

• ClinGen TP53 VCEP ACMG/AMP Specifications v2.4 (cspec doc 135637581): PM6 entry has applicability 'Not applicable' with instructionsToUse 'See above for PS2_PM6 combined rule', and the PS2 entry states 'To avoid redundancy and increase consistency, the TP53 VCEP has opted to drop PM6 and use PS2 exclusively for de novo evidence.'
• Because the TP53 VCEP (an applicable gene-specific ACMG/AMP specification) explicitly removes PM6, generic ACMG/AMP PM6 (assumed de novo without confirmation of maternity/paternity) is not applied to this variant.
• Even under a generic fallback reading, no de novo observation of c.672+6G>A - confirmed or assumed - appears in the ClinVar record or any other source in the evidence bundle, so PM6 would not be met regardless.

Sources

Reasoning

The TP53 VCEP v2.4 specifications declare PP2 'Not applicable' for TP53 (applicability listing and instructionsToUse both state not applicable), so the gene-level missense-mechanism calibration that PP2 encodes is not part of the governing framework. Independently, PP2 by definition applies to missense variants, and c.672+6G>A is an intronic variant with no amino acid change (p.?). PP2 is not applicable on both grounds.

VCEP rule

TP53 VCEP v2.4 PP2: Not applicable (VCEP does not use PP2 for TP53).

Evidence considered

• CSPEC PP2 entry: applicability 'Not applicable'; instructionsToUse 'Not applicable'. The TP53 VCEP does not apply PP2.
• Variant is intronic (c.672+6G>A) with protein consequence p.?, i.e., not a missense variant, so the criterion's premise (a missense variant in a gene with low benign missense rate where missense is a common mechanism) cannot be evaluated for this variant.

Sources

Reasoning

The governing ClinGen TP53 VCEP specification v2.4 (cspec) declares PP5 'Not Applicable' ('This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee'), so PP5 is formally removed from TP53 application under this framework. Independently of the specification, the only permitted trigger for PP5 under this pipeline's policy - an exact-variant ClinVar expert-panel (3-star) classification of Pathogenic/Likely Pathogenic - does not exist for this variant: ClinVar VCV000854158 shows expert_panels empty (no expert-panel submissions), an aggregate 'Uncertain significance' label (2 stars, two single-submitter laboratory submissions), and no pathogenic assertion from any reputable expert source. Ordinary laboratory VUS submissions and the aggregate ClinVar label must not trigger PP5. PP5 therefore contributes no evidence toward pathogenicity.

VCEP rule

Not Applicable for this VCEP - PP5 not for use as recommended by the ClinGen SVI VCEP Review Committee (ClinGen TP53 VCEP v2.4).

Evidence considered

• Governing specification (source_registry key 'cspec'): ClinGen TP53 VCEP v2.4 declares PP5 applicability 'Not Applicable for this VCEP' with instruction 'This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee' (serialized in case_summary.json/prefetch.json).
• ClinVar VCV000854158 (source_registry key 'clinvar'): expert_panels = {} (no ClinGen or other expert-panel submission exists for this variant); aggregate classification 'Uncertain significance' from 2 single-submitter clinical laboratories (Labcorp/Invitae SCV001223750; Color SCV007438756); no Pathogenic/Likely Pathogenic expert-panel classification of the exact variant is present, so the expert-panel-only PP5 policy trigger is not met.

Sources

Reasoning

Under the governing ClinGen TP53 VCEP v2.4 specification, BS3 is defined through protein-function assay results (Kato et al. 2003 primary transactivation data plus Giacomelli/Kawaguchi/Kotler/Funk as eligible assays) and is scoped by the functional-rule flowchart and Functional-worksheet.xlsx to missense variants and small in-frame deletions: BS3_Strong = functional on Kato AND no LOF by the majority of available eligible assays; BS3_Supporting = partially functional on Kato AND no evidence of LOF by all available assays. NM_000546.5:c.672+6G>A is an intronic +6 donor variant (p.?) with no amino-acid substitution, so none of these protein-level assays applies and no worksheet row can exist for it. The only splicing-relevant datum in the case, SpliceAI (max delta 0.135), is an in silico prediction and does not constitute a 'well-established functional study showing no damaging effect' (the original ACMG BS3 definition); under the VCEP, absence of a predicted splice effect is addressed by BP4/BP7 rules (BP7_Strong would require RNA splicing assay data demonstrating no splicing aberration per the BP7 rule's Walker et al. 2023 recommendation), not by BS3. No RNA-based functional assay demonstrating normal splicing of this variant is present in the case record. BS3 therefore cannot be met and is not applicable at the variant-type scope gate of the governing framework; generic ACMG is not invoked because an applicable VCEP specification exists.

Rule

TP53 VCEP v2.4 BS3 (protein-function assay rules for missense variants and small in-frame deletions only; no-splice-effect RNA evidence handled under BP7_Strong)

Evidence considered

• ClinGen TP53 VCEP specifications v2.4 (cspec doc 135637581) BS3 rule: BS3_Strong = Functional on Kato et al. data AND no loss of function (LOF) by the majority of available eligible assays; BS3_Supporting = Partially functional on Kato et al. data AND no evidence of LOF by all available assays. Kato functional class thresholds: non-functional <=20%, partially functional >20-<=75%, functional >75% activity; BS3 applies only where a Kato (protein-level) result exists for the amino-acid change.
• VCEP 'Flowchart for application of functional rule codes' scopes BS3 to missense variants and small in-frame deletions via protein function; c.672+6G>A is intronic (exon 6 donor +6; p.?) and is outside this scope, so no BS3 worksheet lookup applies.
• VCEP v2.4 caveat (functional codes and splicing): protein-level functional codes should not be applied where splicing is the assessed effect; laboratory/RNA evidence of a splicing aberration is handled under PVS1_Variable Weight (RNA), and the BP7_Strong rule requires RNA splicing assay data demonstrating no splicing aberration (per Walker et al., 2023 recommendation cited in the BP7 rule) — BS3 is not the VCEP vehicle for intronic splicing evidence in either direction.
• SpliceAI lookup for c.672+6G>A (max delta score 0.135; DS_DL 0.135) is an in silico prediction below the VCEP 0.2 splice-effect threshold and was not treated as a validated functional assay; it cannot satisfy BS3's requirement for well-established functional evidence of no damaging effect (original ACMG BS3 definition in PMID 25741868).
• No functional assay of the exact variant exists in the case record: paper_extracts.json reports variant_mentioned=false for all fetched full texts, and none of the eligible TP53 functional assay publications (Kato PMID 12826609, Giacomelli PMID 30224644, Kawaguchi PMID 16007150, Kotler PMID 29979965, Funk PMID 39774325) was retrieved for this case; moreover those assays test amino-acid substitutions and cannot interrogate an intronic +6 change.
• PMID 25741868 (ACMG/AMP 2015 standards) was consulted: BS3's original definition is 'well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing'; the paper also states that for splice-site variants, 'confirmation of impact requires functional analysis by either RNA or protein analysis', reinforcing that absence of a confirmed splice effect (in silico only) does not constitute BS3 evidence.
• PMID 17576681 (Buratti et al. 2007) was consulted for mechanism context only: +6 lies within the 9-nt human 5' splice-site consensus but single-nucleotide substitutions at +6 are uncommon activators of cryptic sites; the paper contains no TP53 variant-level functional data (variant_mentioned=false) and does not demonstrate normal splicing of this variant.

Still missing

• No RNA assay data demonstrating normal splicing of c.672+6G_A exists in the case record; such data would be evaluated under the TP53 VCEP BP7_Strong rule (RNA splicing assay demonstrates no splicing aberration), not BS3, and SpliceAI alone is insufficient.
• No variant-specific entry exists or could exist in the VCEP Functional-worksheet for this intronic variant (protein-level assay rows cover amino-acid substitutions and small in-frame deletions only).

Sources

Reasoning

The TP53 VCEP v2.4 specifications declare BP1 'Not applicable': 'This rule code does not apply to these genes, as truncating variants account for only a portion of disease causing variants' (TP53 is a missense-dominated mechanism gene). Independently, BP1 by definition applies to missense variants, and c.672+6G>A is an intronic variant with no amino acid change (p.?). BP1 is not applicable on both grounds.

VCEP rule

TP53 VCEP v2.4 BP1: Not applicable (truncating variants account for only a portion of TP53 disease-causing variants).

Evidence considered

• CSPEC BP1 entry: applicability 'Not applicable'; instructionsToUse 'This rule code does not apply to these genes, as truncating variants account for only a portion of disease causing variants.'
• Variant is intronic (c.672+6G>A) with protein consequence p.?, i.e., not a missense variant, so the criterion's premise (missense variant in a gene where primarily truncating variants cause disease) cannot apply.

Sources

Reasoning

The governing ClinGen TP53 VCEP specification v2.4 explicitly declares BP2 applicability as 'Not Applicable', so the generic ACMG BP2 rule (variant observed in trans with a pathogenic variant in a fully dominant disorder, or in cis with a pathogenic variant in any inheritance pattern) is not applied under this framework. Independently of the specification, no allelic-configuration evidence exists in the case bundle: no co-occurring second TP53 variant, no phase determination, and no trans/cis observation are documented (ClinVar VCV000854158 contains only heterozygous germline VUS submissions; gnomAD reports a single heterozygous allele with 0 homozygotes). BP2 therefore contributes no evidence to this case under any framework.

Evidence considered

• Governing specification: ClinGen TP53 Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for TP53 Version 2.4 (source_registry key 'cspec'), retrieved for this case and serialized in case_summary.json. The specification's criterion rule list declares BP2 'Not Applicable'.
• Direct rule text as serialized in case_summary.json cspec section: {"label": "BP2", "applicability": "Not Applicable"}.
• Generic ACMG/AMP BP2 (PMID 25741868) would require the variant to be observed in trans with a pathogenic variant for a fully dominant disorder (or in cis with a pathogenic variant in any inheritance pattern); the TP53 VCEP supersedes generic ACMG and removes this code from TP53 application.
• Case bundle scan for allelic evidence: no second TP53 variant, no phase determination, no trans/cis observation, and no co-occurrence data appear anywhere in case_summary.json, prefetch.json, evidence.json, literature_pass.json, or paper_extracts.json (searched terms: second variant, in trans, biallelic, compound heterozyg, phase, co-occurrence - all absent).
• ClinVar VCV000854158 (source_registry key 'clinvar'): 2 germline 'Uncertain significance' submissions (Labcorp SCV001223750, Color SCV007438756); neither asserts a second TP53 variant, phase, or trans/cis configuration.
• gnomAD v2.1 (source_registry key 'gnomad_v2'): 1/250,952 alleles (AF 3.98e-06), 0 homozygotes - no biallelic carrier observation that could inform any allelic-configuration argument.

Sources

Reasoning

The governing ClinGen TP53 Expert Panel specification v2.4 (cspec) declares BP5 applicability 'Not Applicable', removing the generic ACMG/AMP BP5 rule (variant found in a case with an alternate molecular basis for disease) from TP53 application under this framework. The specification provides no TP53-specific alternative for this code, so no alternate-molecular-basis evidence can be weighed for NM_000546.5:c.672+6G>A. BP5 therefore contributes no benign evidence to this case.

VCEP rule

Not Applicable for this VCEP - BP5 declared Not Applicable by the ClinGen TP53 VCEP v2.4 specification.

Evidence considered

• Governing specification (source_registry key 'cspec'): ClinGen TP53 VCEP v2.4 criterion rule list declares BP5 applicability 'Not Applicable' (serialized in case_summary.json cspec section).
• Generic ACMG/AMP BP5 (PMID 25741868) would require documentation of an alternate molecular basis for disease in a case carrying the variant; the TP53 VCEP supersedes generic ACMG for this gene and formally excludes BP5 from TP53 application.

Sources

Reasoning

The governing ClinGen TP53 VCEP specification v2.4 (cspec) declares BP6 'Not Applicable' ('This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee'), so BP6 is formally removed from TP53 application under this framework. Independently of the specification, the only permitted trigger for BP6 under this pipeline's policy - an exact-variant ClinVar expert-panel (3-star) classification of Benign/Likely Benign - does not exist for this variant: ClinVar VCV000854158 shows expert_panels empty (no expert-panel submissions) and an aggregate 'Uncertain significance' label from two single-submitter laboratory submissions; no benign assertion from any reputable expert source is present. Ordinary laboratory VUS submissions and the aggregate ClinVar label must not trigger BP6. BP6 therefore contributes no benign evidence to this case.

VCEP rule

Not Applicable for this VCEP - BP6 not for use as recommended by the ClinGen SVI VCEP Review Committee (ClinGen TP53 VCEP v2.4).

Evidence considered

• Governing specification (source_registry key 'cspec'): ClinGen TP53 VCEP v2.4 declares BP6 applicability 'Not Applicable for this VCEP' with instruction 'This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee' (serialized in case_summary.json/prefetch.json).
• ClinVar VCV000854158 (source_registry key 'clinvar'): expert_panels = {} (no expert-panel submission exists for this variant); aggregate classification 'Uncertain significance' from 2 single-submitter clinical laboratories (Labcorp/Invitae SCV001223750; Color SCV007438756); no Benign/Likely Benign expert-panel classification of the exact variant is present, so the expert-panel-only BP6 policy trigger is not met.

Sources