Variant classification summary

NM_000546.5:c.833C>G

TP53 · NP_000537.3:p.(Pro278Arg) · NM_000546.5

GRCh37: chr17:7577105 G>C · GRCh38: chr17:7673787 G>C

Gene: TP53 Transcript: NM_000546.5

Final call

Likely Pathogenic

PS3 strong PM1 moderate PM2 supporting PP3 moderate

Variant details

Gene

TP53

Transcript

NM_000546.5

Protein

NP_000537.3:p.(Pro278Arg)

gnomAD AF

6.195702412978262e-07 (v4.1)

ClinVar

Uncertain significance

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_000546.5:c.833C>G (p.Pro278Arg) is a missense variant in TP53 exon 8, absent from gnomAD v2.1 and present at extremely low frequency in gnomAD v4.1 (AF=6.2e-7, 1/1,614,022 alleles).

2

PS3 (Strong) is met: the variant is Non-functional in the Kato et al. functional assay AND demonstrates loss of function by the majority of other eligible assays (Giacomelli: LOF, Kotler: LOF, Funk: noLOF), per the TP53 VCEP Functional-worksheet.xlsx (Supplementary Table S3).

3

PM1 (Moderate) is met: codon 278 is a statistically significant hotspot residue in cancerhotspots.org, and the Pro278Arg change has 82 somatic occurrences in COSMIC, far exceeding the VCEP threshold of >=10 for PM1_Moderate.

4

PM2 (Supporting) is met: the variant allele frequency in gnomAD v4.1 (6.2e-7) is well below the VCEP PM2_Supporting threshold of 0.00003, with no genetic ancestry group exceeding 0.00004.

5

PP3 (Moderate) is met per the TP53 VCEP PP3-BP4-codes.xlsx (Supplementary Table S2): aGVGD class C65 with BayesDel score 0.607821 (>=0.16), and SpliceAI predicts no splicing impact (max delta 0.00).

6

Multiple criteria remain unassessed due to absent data: PS1 (requires VCEP classification of alternate nucleotide change c.833C>A for same amino acid P278R), PS2 (no de novo report with confirmed parentage), PS4 (germline proband counts unavailable), PM5 (formal VCEP classifications for codon 278 comparators needed), PP1 (no cosegregation data), PP4 (no VAF data), BS2 (no data on elderly unaffected carriers), and BS4 (no lack-of-segregation reports).

7

Applying the TP53 VCEP v2.4.0 Tavtigian point system: PS3=4 + PM1=1 + PM2_Supporting=0.5 + PP3_Moderate=1 = 6.5 points, which falls in the Likely Pathogenic range (6-9 points).

8

This variant has been reported in ClinVar with conflicting classifications: Uncertain significance (3 clinical laboratories), Likely pathogenic (1), and Pathogenic (1). (ClinVar Variation ID: 376644)

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
BP3	N/A	BP3 applies to in-frame deletions/insertions in repetitive regions without known function. This is a missense substitution, not an in-frame indel.
PM3	N/A	PM3 applies to recessive disorders where a variant is detected in trans with a pathogenic variant. TP53/Li-Fraumeni syndrome is not a recessive disorder.
PM4	N/A	PM4 applies to in-frame deletions/insertions or stop-loss variants. This is a missense substitution, not an in-frame indel or stop-loss.
PVS1	N/A	PVS1 applies to null variants (nonsense, frameshift, canonical +/-1,2 splice sites, initiation codon, or exon deletions). NM_000546.5:c.833C>G is a missense substitution (p.Pro278Arg) and does not fall within any PVS1 null-variant bucket per the TP53 VCEP PVS1 flowchart.	vcep_pvs1_flowchart pvs1_variant_assessment
PS1	Not assessed	PS1 requires a different nucleotide change at the same codon that results in the same amino acid change (Pro278Arg) and has been previously classified as Pathogenic or Likely Pathogenic per the TP53 VCEP specifications. The nucleotide change c.833C>A also creates p.Pro278Arg, but there is no evidence in the available materials that c.833C>A has been formally classified as Pathogenic or Likely Pathogenic by the TP53 VCEP. PS1 cannot be applied without this prior classification.	cspec vcep_pp3_bp4_codes
PS2	Not assessed	PS2 requires documented de novo occurrence with confirmed parentage in a proband with Li-Fraumeni syndrome (LFS)-associated cancers. The exploratory search identified the IARC TP53 germline database as a potential source for de novo annotations at codon 278, but no published de novo case report for c.833C>G with confirmed maternity and paternity was identified in the available materials. Without a specific de novo observation, PS2 cannot be assessed.
PS3	Met	PS3 (Strong) is met per the TP53 VCEP Functional-worksheet.xlsx (Supplementary Table S3). The p.Pro278Arg (P278R) substitution is classified as Non-functional in the Kato et al. (PMID:12826609) assay AND demonstrates loss of function (LOF) by the majority of other eligible functional assays (Giacomelli: LOF, Kotler: LOF, Funk: noLOF). Two of three non-Kato assays show LOF, satisfying the VCEP rule for PS3: 'Non-functional on Kato et al. data AND loss of function by the majority of other eligible assays.'	vcep_functional_worksheet vcep_flowchart_for_application_of_functional_rule_codes cspec
PS4	Not assessed	PS4 under the TP53 VCEP requires counting independent probands with LFS-spectrum cancers using the PS4 points table (strongly associated cancers = 4 points, moderately associated = 2 points). COSMIC reports 82 somatic occurrences of this variant, confirming it is recurrent in cancer, but germline proband counts with phenotypic data are not available in the evidence bundle. The exploratory search indicates the IARC TP53 germline database may contain proband data, but this requires manual curation beyond the available materials.	vcep_ps4_points_table
PS5	N/A	PS5 (same codon, different amino acid missense change previously established as pathogenic) is not defined as a separate criterion in the TP53 VCEP v2.4.0 specifications. The VCEP uses PM5 for same-residue different missense comparator analysis. PS5 is assessed under PM5 in this framework.	cspec
PM1	Met	PM1 (Moderate) is met per the TP53 VCEP specifications. Although codon 278 is not among the listed major hotspot codons (175, 245, 248, 249, 273, 282), the variant is a germline missense change at a residue that is a statistically significant hotspot in cancerhotspots.org, and the exact amino acid change (Pro278Arg) has 82 somatic occurrences in COSMIC (COSV52661225), well exceeding the VCEP threshold of >=10 somatic occurrences for the same amino acid change.	cspec
PM2	Met	PM2_Supporting is met per the TP53 VCEP population frequency rules. The variant is absent from gnomAD v2.1 and has an allele frequency of 6.2e-7 (1/1,614,022 alleles) in gnomAD v4.1, with the highest subpopulation frequency of 8.5e-7 in European (non-Finnish) (1/1,180,014 alleles). Both the total allele frequency (<0.00003) and the single-ancestry-group frequency with only one allele observed (<0.00004) satisfy the PM2_Supporting threshold.	gnomad_v2 gnomad_v4 cspec
PM5	Not assessed	PM5 (same residue, different missense change previously established as pathogenic per VCEP) could potentially be applied because multiple different missense variants at codon 278 (P278A, P278H, P278L, P278S, P278T) receive PS3 (pathogenic functional evidence) in the VCEP Functional-worksheet, suggesting they would classify as Pathogenic under the VCEP framework. However, formal VCEP final classifications for comparator variants at codon 278 are not available in the evidence bundle, preventing direct application of PM5.	vcep_functional_worksheet cspec pm5_candidates
PM6	N/A	PM6 is designated Not Applicable by the TP53 VCEP v2.4.0 for use with TP53/Li-Fraumeni syndrome.	cspec
PP1	Not assessed	PP1 requires cosegregation data with specific meiotic counts across families (>=3-4 meioses for Supporting, 5-6 for Moderate, >=7 across >1 family for Strong). The exploratory search indicates the IARC TP53 database may contain segregation data for codon 278 families, but no cosegregation analysis was available in the evidence bundle.	cspec
PP2	N/A	PP2 is designated Not Applicable by the TP53 VCEP v2.4.0.	cspec
PP3	Met	PP3_Moderate is met per the TP53 VCEP PP3-BP4-codes.xlsx (Supplementary Table S2), which pre-assigns PP3_moderate to c.833C>G (p.Pro278Arg). The variant has an aGVGD class of C65 and a BayesDel score of 0.607821 (>=0.16), satisfying the VCEP rule for PP3_Moderate. SpliceAI predicts no splicing impact (max delta = 0.00), so no splicing adjustment is needed.	vcep_pp3_bp4_codes spliceai bayesdel cspec
PP4	Not assessed	PP4 requires observation of the variant at variant allele fraction (VAF) 5-35% in blood, consistent with constitutional (non-somatic) origin. No VAF data for this variant is available in the evidence bundle.	cspec
PP5	N/A	PP5 is designated Not Applicable by the TP53 VCEP v2.4.0 per ClinGen Sequence Variant Interpretation VCEP Review Committee recommendation.	cspec
BA1	Not met	BA1 requires a filtering allele frequency (FAF) >= 0.001 (0.1%) in gnomAD continental subpopulations. The highest FAF for this variant is 8.5e-7 in European (non-Finnish), well below the BA1 threshold. BA1 is not met.	gnomad_v2 gnomad_v4 cspec
BS1	Not met	BS1 requires a filtering allele frequency (FAF) >= 0.0003 but < 0.001 in gnomAD continental subpopulations. The highest FAF is 8.5e-7, below the BS1 threshold. BS1 is not met.	gnomad_v2 gnomad_v4 cspec
BS2	Not assessed	BS2 requires >=2 unrelated females who have reached at least 60 years of age without cancer (from a single source). No such data is available in the evidence bundle.	cspec
BS3	Not met	BS3 requires functional evidence of no damaging effect (Functional on Kato data AND no LOF by majority of eligible assays). The TP53 VCEP Functional-worksheet.xlsx assigns PS3 to P278R (not BS3), indicating the variant is damaging: Kato class is Non-functional, and the majority of other eligible assays (Giacomelli, Kotler) show LOF. BS3 is not met.	vcep_functional_worksheet vcep_flowchart_for_application_of_functional_rule_codes cspec
BS4	Not assessed	BS4 requires lack of segregation in affected family members (i.e., family members diagnosed with LFS-associated cancers who do not carry the variant, or unaffected carriers). No segregation data or reports of non-segregation are available in the evidence bundle.	cspec
BP1	N/A	BP1 is designated Not Applicable by the TP53 VCEP v2.4.0, as truncating variants account for only a portion of disease-causing variants in TP53.	cspec
BP2	N/A	BP2 is designated Not Applicable by the TP53 VCEP v2.4.0.	cspec
BP4	Not met	BP4 (benign in silico evidence) is not met. The TP53 VCEP PP3-BP4-codes.xlsx assigns PP3_moderate (not BP4) to c.833C>G. The BayesDel score is 0.607821, far above the BP4_Supporting threshold of <0.16 and the BP4_Moderate threshold of <=-0.008. aGVGD class is C65, which explicitly precludes BP4 application per the VCEP flowchart.	vcep_pp3_bp4_codes bayesdel cspec
BP5	N/A	BP5 is designated Not Applicable by the TP53 VCEP v2.4.0.	cspec
BP6	N/A	BP6 is designated Not Applicable by the TP53 VCEP v2.4.0 per ClinGen Sequence Variant Interpretation VCEP Review Committee recommendation.	cspec
BP7	N/A	BP7 applies to synonymous (silent) or intronic variants. NM_000546.5:c.833C>G is a missense variant (p.Pro278Arg) and does not qualify for BP7.	cspec

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