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TP53
Final classification
Likely Benign
TP53 c.684C>G · p.Asp228Glu
TP53

NM_000546.5:c.684C>G (p.Asp228Glu) is a missense variant in exon 7 of TP53.

Gene
TP53
Transcript
NM_000546.5
HGVS · transcript:coding
NM_000546.5:c.684C>G
Consequence
N/A
GRCh38
chr17:7674279 G>C
GRCh37
chr17:7577597 G>C
Basis Total points: PM2_Supporting (+1) + BS3 (-4) + BP4_Moderate (-2) = -5. Per the TP53 VCEP v2.4.0 Tavtigian Bayesian point-based framework, a score of -5 falls in the Likely Benign range (Rule4: -6 to -2).
Total points: PM2_Supporting (+1) + BS3 (-4) + BP4_Moderate (-2) = -5. Per the TP53 VCEP v2.4.0 Tavtigian Bayesian point-based framework, a score of -5 falls in the Likely Benign range (Rule4: -6 to -2).
Classification rationale
PM2 BS3BP4 Likely Benign
TP53 c.684C>G

NM_000546.5:c.684C>G (p.Asp228Glu) is a missense variant in exon 7 of TP53. The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada (PM2_Supporting; +1 point).1 Functional evidence from the TP53 VCEP Functional-worksheet demonstrates the variant retains wild-type-like function: Kato et al. assay shows Functional activity, and all eligible assays (Giacomelli, Kotler, Kawaguchi) report no loss of function (BS3; -4 points).2 In silico evidence supports a benign interpretation: BayesDel score is -0.133538 (Class C0), and SpliceAI predicts no splicing impact (max delta 0.00). The VCEP PP3-BP4-codes spreadsheet assigns BP4_moderate (-2 points).3 Codon 228 is not among the VCEP-defined hotspot codons (175, 245, 248, 249, 273, 282), and the variant is not listed in cancerhotspots.org; PM1 is not met. PP3 is not met per VCEP in silico flowchart: BayesDel score does not meet the ≥0.16 threshold and aGVGD class is C0.4 PS3 is not met: the functional evidence favors a benign interpretation; the VCEP pre-assigned code is BS3, not PS3.5 Total points: PM2_Supporting (+1) + BS3 (-4) + BP4_Moderate (-2) = -5. Per the Tavtigian Bayesian point-based framework (TP53 VCEP v2.4.0), a score of -5 falls in the Likely Benign range (-6 to -2).6 This variant has been reported in ClinVar as Uncertain significance by 5 clinical laboratories and as Likely benign by 1 clinical laboratory (ClinVar ID: 926556).7 COSMIC reports 6 somatic occurrences (COSV52662428). OncoKB classifies the variant as Likely Oncogenic with likely loss-of-function effect, which is inconsistent with the VCEP functional data showing retained function; the VCEP functional worksheet takes precedence for germline classification.8 No de novo, segregation, proband, or case-control data are available; PS2, PS4, PP1, PP4, BS2, and BS4 remain unassessed.

PM2 + BS3 + BP4 Likely Benign
3 vcep_pp3_bp4_codesbayesdelspliceai ↗
4 vcep_pp3_bp4_codes
5 vcep_functional_worksheet
6 final_classification_framework
Gene diagram · NM_000546.5 · variants mapped to exon structure
TP53 NM_000546.5
Fetching transcript structure from UCSC…
Applied criteria · 3 applied · 13 assessed
Applied · 3
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
The variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, meeting the TP53 VCEP PM2_Supporting threshold of allele frequency <0.00003 (0.003%).
Absent from gnomAD v2.1 (exomes). Absent from gnomAD v4.1 (exomes). Absent from gnomAD-Canada v1.0 (genomes).
BS3 strong Benign
The TP53 VCEP Functional-worksheet pre-assigns BS3 (strong benign functional evidence) for p.Asp228Glu. The variant is Functional in the Kato et al. (PMID:12826609) systematic assay and shows no loss of function (noLOF) across all eligible assays: Giacomelli et al. (PMID:30224644), Kotler et al. (PMID:29979965), and Kawaguchi et al. This meets the VCEP BS3 rule: 'Functional on Kato et al. data AND no loss of function (LOF) by the majority of available eligible assays.'
VCEP Functional-worksheet: D228E → BS3. Kato: Functional. Giacomelli: noLOF. Kotler: noLOF. Kawaguchi: noLOF.
BP4 moderate Benign
The variant has a BayesDel score of -0.133538, which is ≤ -0.008, and SpliceAI predicts no splicing impact (max delta = 0.00, which is <0.2). The aGVGD class is C0 (not C65). Per the TP53 VCEP PP3-BP4 missense flowchart: BayesDel ≤ -0.008 + no predicted splicing differences + not C65 = BP4_Moderate. The VCEP PP3-BP4-codes spreadsheet confirms this with a pre-assigned code of BP4_moderate.
VCEP PP3-BP4-codes: c.684C>G assigned BP4_moderate. BayesDel: -0.133538 (≤ -0.008). SpliceAI max delta: 0.00 (<0.2). aGVGD Class C0.
Assessed · not applied
Pathogenic
PS1 PS1 requires a different nucleotide change resulting in the same amino acid substitution (p.Asp228Glu) that has been classified as Pathogenic or Likely Pathogenic per TP53 VCEP specifications.
PS2 PS2 requires tallying de novo proband points using the TP53 VCEP LFS cancer scoring table.
PS3 PS3 requires evidence of a damaging functional effect.
PS4 PS4 requires tallying proband points based on LFS-associated cancer diagnoses per the TP53 VCEP PS4-Points-Table.
PM1 PM1 requires the variant to be located in a VCEP-defined hotspot codon (175, 245, 248, 249, 273, 282) or listed in cancerhotspots.org with ≥2 somatic occurrences.
PM5 PM5 requires a different pathogenic or likely pathogenic missense variant at the same amino acid residue (Asp228) classified per TP53 VCEP specifications.
PP1 PP1 requires cosegregation data (≥3 meioses for supporting, 5-6 for moderate, ≥7 for strong).
PP3 PP3 for missense variants requires aGVGD Class C65 with BayesDel ≥0.16 (moderate) or Class C25-C55 with BayesDel ≥0.16 (supporting).
PP4 PP4 requires observation of the variant at low variant allele fraction (VAF 5-35%) suggesting somatic mosaicism or constitutional mosaicism.
Benign
BA1 BA1 requires a filtering allele frequency ≥0.001 (0.1%) in any gnomAD continental subpopulation.
BS1 BS1 requires a filtering allele frequency ≥0.0003 (0.03%) but <0.001 in a gnomAD continental subpopulation.
BS2 BS2 requires observations in unrelated cancer-free females who have reached at least 60 years of age.
BS4 BS4 requires lack of segregation in affected family members with LFS-associated cancers.
N/A · 12 PVS1 · PM3 · PM4 · PM6 · PP2 · PP5 · BP1 · BP2 · BP3 · BP5 · BP6 · BP7
Research & evidence
Population frequency · supports benign
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
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 (5 clinical laboratories) and as Likely benign (1 clinical laboratory). (ClinVarID = 926556)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.37. BayesDel score = -0.133538.
Functional / OncoKB screenshot
Functional Likely Oncogenic
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV52662428, n = 6 times).
Hotspots
This variant does not lie in a statistically significant hotspot.
Literature · how each cited paper was used
3papers cited
Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 6 further PMIDs triaged but not cited — see Sources & References.
Rule & framework references · cited for criterion definitions, not variant evidence
12826609 ↗ Understanding the function-structure and function-mutation relationships of p53 tumor suppressor protein by high-resolution missense mutation analysis.
29979965 ↗ A Systematic p53 Mutation Library Links Differential Functional Impact to Cancer Mutation Pattern and Evolutionary Conservation.
30224644 ↗ Mutational processes shape the landscape of TP53 mutations in human cancer.
Sources & reference links
9Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 6 PMIDs not cited in assessment
11900253 ↗ Rescuing the function of mutant p53. ONCOKB
8023157 ↗ Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations. ONCOKB
25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR
17392385 ↗ American Cancer Society guidelines for breast screening with MRI as an adjunct to mammography. CLINVAR
26324357 ↗ American Society of Clinical Oncology Policy Statement Update: Genetic and Genomic Testing for Cancer Susceptibility. CLINVAR
26140447 ↗ Points to Consider: Ethical, Legal, and Psychosocial Implications of Genetic Testing in Children and Adolescents. CLINVAR