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TP53
Final classification
VUS
TP53 c.845G>T · p.Arg282Leu
TP53

NM_000546.5:c.845G>T (p.Arg282Leu) is a missense variant in exon 8 of TP53, assessed under the ClinGen TP53 Variant Curation Expert Panel specifications version 2.4.0 (Tavtigian point-based framework).

Gene
TP53
Transcript
NM_000546.5
HGVS · transcript:coding
NM_000546.5:c.845G>T
Consequence
N/A
GRCh38
chr17:7673775 C>A
GRCh37
chr17:7577093 C>A
Basis Tavtigian et.al., 2020 - Bayesian adaptation of Richards et.al., 2015 v2.4.0 point-based framework: PM1 moderate (+2) + PM2 supporting (+1) + PP3 moderate (+2) + BS3 strong (-4) = 1 points, which maps to VUS.
Tavtigian et.al., 2020 - Bayesian adaptation of Richards et.al., 2015 v2.4.0 point-based framework: PM1 moderate (+2) + PM2 supporting (+1) + PP3 moderate (+2) + BS3 strong (-4) = 1 points, which maps to VUS.
Classification rationale
PM1PM2PP3 BS3 VUS
TP53 c.845G>T

NM_000546.5:c.845G>T (p.Arg282Leu) is a missense variant in exon 8 of TP53, assessed under the ClinGen TP53 Variant Curation Expert Panel specifications version 2.4.0 (Tavtigian point-based framework).1 This variant affects codon 282, a well-established mutational hotspot within the DNA-binding domain explicitly listed in the TP53 VCEP PM1 rule. The residue is a statistically significant cancer hotspot with 10 somatic occurrences in COSMIC, satisfying PM1 at moderate strength (+2 points).2 The variant is extremely rare in population databases: gnomAD v4.1 reports an allele frequency of 3.10×10⁻⁶ (5/1,613,954 alleles; grpmax FAF=7.9×10⁻⁷), and it is absent from gnomAD v2.1. All subpopulation frequencies are well below the TP53 VCEP PM2_Supporting cutoff of <0.003%, satisfying PM2 at supporting level (+1 point).3 In silico predictors support a deleterious effect: aGVGD Class C65 with BayesDel score 0.360452 and REVEL score 0.898. Per the TP53 VCEP PP3-BP4-codes worksheet, this variant is assigned PP3_moderate (+2 points). SpliceAI predicts no splicing impact (max delta=0.00).4 Functional data from the TP53 VCEP Functional-worksheet demonstrates that p.Arg282Leu is functional in the Kato assay and shows no loss of function in Giacomelli, Kotler, and Kawaguchi assays. This satisfies BS3 at strong benign strength (−4 points): functional on Kato AND no LOF by the majority of eligible assays.5 The variant has been reported in ClinVar as Uncertain Significance by 6 clinical laboratories and as Uncertain Significance by the ClinGen TP53 Variant Curation Expert Panel (ClinVar ID: 182938). No proband data meeting Li-Fraumeni syndrome criteria was available for PS4 assessment.6 No de novo observations, cosegregation data, VAF data, or BS2/BS4 evidence was identified for this variant. PVS1 is not applicable to this missense variant. PS1 has no alternative nucleotide change comparator. PM5 requires curator review of VCEP classifications for comparator codon 282 variants. Final Tavtigian point total: PM1_Moderate (+2) + PM2_Supporting (+1) + PP3_Moderate (+2) + BS3_Strong (−4) = +1 point. This falls within the Uncertain Significance range (−1 to +5) per the TP53 VCEP v2.4.0 Tavtigian point-based rules. The classification is consistent with the ClinGen TP53 VCEP expert panel determination of Uncertain Significance for this variant.7

PM1 + PM2 + PP3 + BS3 VUS
4 vcep_pp3_bp4_codesbayesdelrevelspliceai ↗
5 vcep_functional_worksheetcspec ↗
Gene diagram · NM_000546.5 · variants mapped to exon structure
TP53 NM_000546.5
Fetching transcript structure from UCSC…
Applied criteria · 4 applied · 11 assessed
Applied · 4
Strength Supporting Moderate Strong Very strong
PM1 moderate Pathogenic
This missense variant affects codon 282 (p.Arg282), which is explicitly listed in the TP53 VCEP PM1 rule as a moderate-strength hotspot codon (alongside codons 175, 245, 248, 249, 273). Additionally, the residue is a statistically significant cancer hotspot (cancerhotspots.org), and COSMIC records 10 somatic occurrences at this amino acid change, independently satisfying the PM1_Moderate threshold (≥10 somatic occurrences for the same amino acid change).
TP53 VCEP PM1 rule: codon 282 is explicitly listed for PM1_ModerateCancer Hotspots: residue 282 is a statistically significant hotspotCOSMIC: 10 somatic occurrences (COSV53068318) — satisfies ≥10 threshold for PM1_Moderate per VCEP
PM2 supporting Pathogenic
This variant is extremely rare in population databases. In gnomAD v4.1, the total allele frequency is 3.10×10⁻⁶ (5/1,613,954 alleles), with a grpmax filtering allele frequency of 7.9×10⁻⁷. The highest subpopulation frequency is in East Asian (2.23×10⁻⁵; 1/44,858 alleles). Both the total AF and subpopulation AF are well below the TP53 VCEP PM2_Supporting cutoff of <0.00003 (0.003%) total and <0.00004 (0.004%) per genetic ancestry group. The variant is absent from gnomAD v2.1. No founder-effect populations are implicated.
gnomAD v4.1: AF=3.10×10⁻⁶ (5/1613954 alleles
PP3 moderate Pathogenic
Per the TP53 VCEP PP3-BP4-codes worksheet (Supplementary Table S2), this variant is assigned aGVGD Class C65 with BayesDel score 0.360452 and the pre-computed code PP3_moderate. The VCEP PP3 rule specifies that aGVGD Class C65 with BayesDel ≥0.16 qualifies for PP3 at moderate strength. SpliceAI predicts no splicing impact (max delta = 0.00), so the in silico assessment proceeds via the missense pathway without splicing considerations. REVEL score (0.898) independently supports a deleterious prediction.
VCEP PP3-BP4-codes.xlsx: c.845G>T → aGVGD Class C65BayesDel=0.360452code=PP3_moderate
BS3 strong Benign
Per the TP53 VCEP Functional-worksheet (Supplementary Table S3), the p.Arg282Leu variant is functional in the Kato et al. assay and demonstrates no loss of function in the Giacomelli, Kotler, and Kawaguchi assays (all noLOF). This satisfies the TP53 VCEP BS3_Strong rule: 'Functional on Kato et al. data AND no loss of function (LOF) by the majority of available eligible assays.' The variant retains wild-type-like protein function across multiple orthogonal functional assays, providing strong evidence for a benign functional effect.
VCEP Functional-worksheet: R282L → Kato=FunctionalGiacomelli=noLOFKotler=noLOF
Assessed · not applied
Pathogenic
PS2 No confirmed de novo observation with confirmed maternity/paternity has been identified for this variant.
PS3 Per the TP53 VCEP Functional-worksheet (Supplementary Table S3), the p.Arg282Leu substitution is functional in the Kato assay and demonstrates no loss of function across Giacomelli, Kotler, and Kawaguchi assays.
PS4 No verified proband data meeting Li-Fraumeni syndrome criteria is available to assign PS4 points.
PM5 Multiple different missense variants exist at codon 282 (R282G, R282P, R282W — all assigned PS3 in the VCEP functional worksheet).
PP1 No verified cosegregation data is available for this variant.
PP4 PP4 per TP53 VCEP requires observation of the variant at low variant allele fraction (VAF 5-35%) in blood, indicative of somatic mosaicism or clonal hematopoiesis.
Benign
BA1 The variant is extremely rare, not common.
BS1 The variant's population frequency is too low to meet BS1.
BS2 BS2 per TP53 VCEP requires observations of the variant in unrelated females aged ≥60 years without cancer, from a single source.
BS4 BS4 per TP53 VCEP requires lack of segregation in affected family members (family members diagnosed with LFS-associated cancers who do not carry the variant).
BP4 The variant's BayesDel score (0.360452) is above the BP4 threshold (<0.16).
N/A · 13 PVS1 · PS1 · PM3 · PM4 · PM6 · PP2 · PP5 · BP1 · BP2 · BP3 · BP5 · BP6 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 3.09798e-06; MAF= 0.00031%, 5/1613954 alleles, homozygotes = 0) and has highest observed frequency in the East Asian population (AF= 2.22926e-05; MAF= 0.00223%, 1/44858 alleles, homozygotes = 0); grpmax FAF= 7.9e-07.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
This variant is absent from gnomAD-Canada.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.00031% · 5 / 1,613,954
0 hom · FAF 7.9e-05%
East Asian
1 / 44,858
0.0022%
European (non-Finnish)
4 / 1,180,030
0.00034%
+ 8 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant has been reported in ClinVar as Uncertain significance (6 clinical laboratories) and as Uncertain Significance by ClinGen TP53 Variant Curation Expert Panel, ClinGen (expert panel). (ClinVarID = 182938)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.898. BayesDel score = 0.360452.
Functional / OncoKB screenshot
Functional Likely Neutral
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Neutral; curated oncogenicity label: Likely Neutral.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Hotspot
COSMIC
This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV53068318, n = 10 times).
Hotspots
This variant lies in a statistically significant hotspot.
Sources & reference links
8Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 7 PMIDs not cited in assessment
12826609 ↗ Understanding the function-structure and function-mutation relationships of p53 tumor suppressor protein by high-resolution missense mutation analysis. ONCOKB
29979965 ↗ A Systematic p53 Mutation Library Links Differential Functional Impact to Cancer Mutation Pattern and Evolutionary Conservation. ONCOKB
30224644 ↗ Mutational processes shape the landscape of TP53 mutations in human cancer. ONCOKB
12365217 ↗ p53 mutations as tumor markers in fine needle aspirates of palpable breast masses. ONCOKB
26619011 ↗ Identifying recurrent mutations in cancer reveals widespread lineage diversity and mutational specificity. ONCOKB
27328919 ↗ TP53 Variations in Human Cancers: New Lessons from the IARC TP53 Database and Genomics Data. ONCOKB
28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR