Variant classification summary

NM_000546.6:c.524G>A

TP53 · NP_000537.3:p.(Arg175His) · NM_000546.6

GRCh37: chr17:7578406 C>T · GRCh38: chr17:7675088 C>T

Gene: TP53 Transcript: NM_000546.6

Final call

Likely Pathogenic

PS3 strong PM1 moderate PM2 supporting PP3 supporting PP5 supporting

Variant details

Gene

TP53

Transcript

NM_000546.6

Protein

NP_000537.3:p.(Arg175His)

gnomAD AF

4.336884208908951e-06 (v4.1)

ClinVar

Pathogenic

OncoKB

Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

1

PS3 (Strong): R175H is non-functional in the Kato et al. systematic functional assay and demonstrates loss of function in all three other eligible VCEP assays (Giacomelli, Kotler, Kawaguchi). This meets the TP53 VCEP v2.4.0 PS3 rule: non-functional on Kato data AND LOF by the majority of other eligible assays.

2

PM1 (Moderate): The variant is located at codon 175, which is explicitly listed in the TP53 VCEP PM1 criteria as a codon where PM1 (Moderate) applies. COSMIC reports 2,560 somatic occurrences at this residue.

3

PM2 (Supporting): The variant is extremely rare in population databases. gnomAD v4.1 reports an allele frequency of 4.34e-06 (7/1,614,062 alleles), well below the VCEP PM2_Supporting threshold of <0.003%. The highest subpopulation frequency (European non-Finnish) is 5.93e-06, below the <0.004% subpopulation threshold.

4

PP3 (Supporting): The VCEP PP3-BP4-codes.xlsx assigns PP3 to c.524G>A. The variant has aGVGD Class C25 and BayesDel score 0.54619 (≥0.16), meeting the VCEP PP3_Supporting rule. SpliceAI predicts no splicing impact (max delta = 0.01).

5

PS4, PM5, PP1, and PS2 were not assessed due to absent or incomplete proband-level data in the evidence package; the VCEP expert panel's Pathogenic classification on ClinVar suggests these criteria may contribute additional points in the full VCEP curation. The expert panel classification in ClinVar as Pathogenic (ClinVar ID 12374) is noted but the VCEP does not permit PP5 for independent criterion application.

6

Based on assessable evidence, four criteria are met: PS3 (Strong, +4 points), PM1 (Moderate, +2 points), PM2 (Supporting, +1 point), PP3 (Supporting, +1 point). Total = 8 points. Under the Tavtigian point-based framework adopted by the TP53 VCEP v2.4.0, 8 points falls in the 6-9 range → Likely Pathogenic. The ClinGen TP53 VCEP expert panel has independently classified this variant as Pathogenic on ClinVar, which likely incorporates additional evidence (PS4, PM5, PP1) beyond what is available in the current evidence package.

Final determination: Tavtigian et.al., 2020 - Bayesian adaptation of Richards et.al., 2015 v2.4.0 point-based framework yields a total score of 9, which maps to Likely Pathogenic under the specified Tavtigian-style ranges.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	PVS1 is not applicable to missense variants. This variant (c.524G>A, p.Arg175His) is a missense substitution and does not fall into the null-variant categories of nonsense, frameshift, canonical splice site (+/-1,2), initiation codon, or exon-level deletion covered by the TP53 VCEP PVS1 flowchart.	pvs1_gene_context pvs1_variant_assessment vcep_pvs1_flowchart
PS1	N/A	PS1 requires a different nucleotide change producing the same amino acid change as a previously established pathogenic variant. The only nucleotide change that produces p.Arg175His (R175H) is c.524G>A; no alternative nucleotide substitution at this codon yields the same histidine substitution. There is no comparator variant for PS1.	cspec
PS2	Not assessed	No de novo data are available in the evidence package. The TP53 VCEP PS2 rule requires proband-level LFS cancer type point scoring using the Table of LFS Cancers and Points for PS2 and PP1 Code Application; no proband data with cancer phenotypes were provided for this variant.	vcep_table_of_lfs_cancers_and_points_for_ps2_and_pp1_code_application
PS3	Met	R175H is assigned PS3 (Strong) in the TP53 VCEP Functional-worksheet.xlsx (Supplementary Table S3). The variant is non-functional in the Kato et al. (PMID:12826609) comprehensive functional assay and demonstrates loss of function in all three other eligible assays: Giacomelli et al. (PMID:30224644), Kotler et al. (PMID:29979965), and Kawaguchi et al. (PMID:16007150). Per TP53 VCEP v2.4.0 PS3 rule: non-functional on Kato data AND LOF by the majority of other eligible assays meets PS3 (Strong).	vcep_functional_worksheet vcep_flowchart_for_application_of_functional_rule_codes PMID:12826609 PMID:15781620 cspec
PS4	Not assessed	The TP53 VCEP PS4 rule requires proband-level point scoring based on strongly associated (4 pts) and moderately associated (2 pts) LFS cancers using the PS4-Points-Table. While ClinVar reports 31 clinical laboratories classifying this variant as Pathogenic and the VCEP expert panel classifies it as Pathogenic, the evidence package does not contain the individual proband cancer phenotype data required to compute PS4 points.	clinvar vcep_ps4_points_table cspec
PS5	Not assessed	PS5 requires a different missense variant at the same nucleotide position (c.524) that has been established as pathogenic by the TP53 VCEP. The PP3-BP4-codes.xlsx identifies c.524G>T (p.Arg175Leu) and c.524G>C (p.Arg175Pro) at this position with PP3_moderate assignments, but full VCEP pathogenic classifications for these comparator variants are not available in the evidence package. Without confirmed VCEP pathogenic classification of a comparator, PS5 cannot be applied.	vcep_pp3_bp4_codes pm5_candidates
PM1	Met	The variant is located at codon 175, which is explicitly listed in the TP53 VCEP v2.4.0 PM1 rule as a codons where PM1 (Moderate) applies: 'Missense variants within the following codons: 175, 245, 248, 249, 273, 282.' Additionally, COSMIC reports n=2560 somatic occurrences at this residue, exceeding the ≥10 somatic occurrences threshold for PM1_Moderate via cancerhotspots.org.	cspec vcep_flowchart_for_application_of_functional_rule_codes
PM2	Met	The variant is present at extremely low frequency in gnomAD. In v4.1, overall AF = 4.34e-06 (7/1,614,062 alleles, 0.000434%), which is below the VCEP PM2_Supporting threshold of <0.003% (0.00003). The highest subpopulation frequency is European (non-Finnish) at AF = 5.93e-06 (7/1,180,032, 0.000593%), also below the <0.004% (0.00004) subpopulation threshold. In v2.1, only 1 allele was observed (1/251,276, AF = 3.98e-06). The variant is absent from gnomAD-Canada v1.0. Per VCEP PM2_Supporting rules, these frequencies meet the PM2_Supporting criterion.	gnomad_v2 gnomad_v4 cspec
PM5	Not assessed	The TP53 VCEP PM5 rule requires ≥1 (moderate) or ≥2 (strong) different missense variants at the same residue previously determined to be pathogenic according to the VCEP's specifications. Multiple missense variants exist at codon 175 (R175G, R175C, R175L, R175P, etc.), and R175G has a PS3 assignment in the Functional-worksheet (non-functional on Kato, LOF on all assays). However, full VCEP pathogenic classifications for comparator variants at codon 175 are not available in the evidence package, so PM5 cannot be independently applied. In addition, the pm5_candidates.json pipeline artifact incorrectly flagged the variant class as non-missense; the variant is a canonical missense substitution (c.524G>A, p.Arg175His).	pm5_candidates vcep_functional_worksheet cspec
PM6	N/A	PM6 is marked as 'Not Applicable' by the TP53 VCEP v2.4.0. This criterion is not for use under this gene-specific framework.	cspec
PP1	Not assessed	No cosegregation data are available in the evidence package. The TP53 VCEP PP1 rule requires cosegregation observed in ≥3 meioses (supporting), 5-6 meioses (moderate), or ≥7 meioses (strong) across one or more families. No family segregation data were provided.	cspec vcep_table_of_lfs_cancers_and_points_for_ps2_and_pp1_code_application
PP2	N/A	PP2 is marked as 'Not Applicable' by the TP53 VCEP v2.4.0. This criterion (missense variant in a gene with low rate of benign missense variation) is not used under this gene-specific framework.	cspec
PP3	Met	The TP53 VCEP PP3-BP4-codes.xlsx (Supplementary Table S2) assigns PP3 to c.524G>A. The variant has aGVGD Class C25 and BayesDel score 0.54619 (≥0.16), meeting the VCEP PP3_Supporting rule: 'aGVGD class C25-C55 and BayesDel score ≥0.16.' SpliceAI max delta = 0.01, indicating no predicted splicing effect. REVEL score = 0.922 (deleterious).	vcep_pp3_bp4_codes vcep_flowchart_for_application_of_pp3_2c_bp4_2c_and_bp7 revel bayesdel spliceai cspec
PP4	Not assessed	The TP53 VCEP PP4 rule requires observation of the variant with variant allele fraction (VAF) 5-35%. No patient-specific VAF data are available in the evidence package. While the variant is well-established as a germline pathogenic variant in Li-Fraumeni syndrome, individual proband phenotype and VAF data were not provided for PP4 scoring.	cspec clinvar
PP5	Met	Expert panel ClinGen TP53 Variant Curation Expert Panel, ClinGen classified as Pathogenic.	cspec clinvar
BA1	Not met	The TP53 VCEP BA1 rule requires filtering allele frequency (FAF) ≥0.001 (0.1%) in a single gnomAD continental subpopulation (excluding founder populations) with ≥2,000 alleles and ≥2 alleles present. The gnomAD v4.1 grpmax FAF = 2.47e-06, which is several orders of magnitude below the BA1 threshold. BA1 is not met.	gnomad_v2 gnomad_v4 cspec
BS1	Not met	The TP53 VCEP BS1 rule requires filtering allele frequency (FAF) ≥0.0003 (0.03%) but <0.001 in a single gnomAD continental subpopulation (excluding founder populations) with ≥2,000 alleles and ≥2 alleles present. The gnomAD v4.1 grpmax FAF = 2.47e-06 is below the 0.0003 threshold. BS1 is not met.	gnomad_v2 gnomad_v4 cspec
BS2	Not assessed	The TP53 VCEP BS2 rule requires ≥2 (supporting), 4-7 (moderate), or ≥8 (strong) unrelated females who have reached at least 60 years of age without cancer, all from a single source. No data on healthy elderly female carriers are available in the evidence package.	cspec
BS3	Not met	The TP53 VCEP Functional-worksheet.xlsx assigns PS3 (not BS3) to R175H. The variant is non-functional in the Kato assay and shows loss of function in all eligible assays (Giacomelli, Kotler, Kawaguchi). BS3 requires functional (BS3_Strong) or partially functional (BS3_Supporting) outcomes on Kato data with no LOF on other assays. R175H is the opposite of BS3: it demonstrates complete loss of function across all assay platforms.	vcep_functional_worksheet vcep_flowchart_for_application_of_functional_rule_codes cspec
BS4	Not assessed	No segregation data are available in the evidence package. The TP53 VCEP BS4 rule requires lack of segregation in affected family members diagnosed with LFS-associated cancers. No family segregation studies were provided.	cspec vcep_table_of_lfs_cancers_and_points_for_ps2_and_pp1_code_application
BP1	N/A	BP1 is marked as 'Not Applicable' by the TP53 VCEP v2.4.0. This criterion (missense variant in a gene where primarily truncating variants cause disease) is not used under this gene-specific framework.	cspec
BP2	N/A	BP2 is marked as 'Not Applicable' by the TP53 VCEP v2.4.0. This criterion (observed in trans with a pathogenic variant in a recessive disorder) is not used under this gene-specific framework.	cspec
BP4	Not met	The TP53 VCEP PP3-BP4-codes.xlsx assigns PP3 (not BP4) to c.524G>A. BP4_Moderate requires BayesDel ≤ -0.008, and BP4_Supporting requires BayesDel <0.16 and >-0.008. The variant's BayesDel score is 0.54619, which is far above both BP4 thresholds and falls within the PP3 range. SpliceAI max delta = 0.01, confirming no predicted splicing effect, but this alone is insufficient for BP4 when in silico scores are strongly pathogenic. BP4 is not met.	vcep_pp3_bp4_codes vcep_flowchart_for_application_of_pp3_2c_bp4_2c_and_bp7 bayesdel spliceai revel cspec
BP5	N/A	BP5 is marked as 'Not Applicable' by the TP53 VCEP v2.4.0. This criterion (variant found in a case with an alternate molecular basis for disease) is not used under this gene-specific framework.	cspec
BP6	N/A	BP6 is marked as 'Not Applicable' by the TP53 VCEP v2.4.0. This criterion (reputable source reports variant as benign) is not used under this gene-specific framework.	cspec
BP7	N/A	BP7 applies to synonymous (silent) or intronic variants with no predicted splicing impact. This variant (c.524G>A) is a missense substitution (p.Arg175His), not a synonymous or intronic variant. BP7 is not applicable.	cspec vcep_flowchart_for_application_of_pp3_2c_bp4_2c_and_bp7

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