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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 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      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.
      Understanding the function-structure and function-mutation relationships of p53 tumor suppressor protein by high-resolution missense mutation analysis.
      Searched
      c.684C>GD228EAsp228Glucodon 228p.D228
      Found
      Kato et al. performed systematic functional analysis of 2,314 p53 missense mutations using a yeast-based transactivation assay. The variant p.Asp228Glu was not identified by name in the main text; however, the VCEP Functional-worksheet (Supplementary Table S3) includes pre-assigned functional codes derived from this study's data, reporting D228E as Functional in the Kato assay.
      Variant
      ◇ Residue / gene-level — variant not named
      Applied to
      BS3 supports · met
      Why
      Variant not identified in main text; functional data from this study used by VCEP to pre-assign BS3 for D228E via the Functional-worksheet.
      Location VCEP pre-assigned code in Supplementary Table S3 (Functional-worksheet.xlsx), not in main text  ·  full text
      A Systematic p53 Mutation Library Links Differential Functional Impact to Cancer Mutation Pattern and Evolutionary Conservation.
      Searched
      c.684C>GD228EAsp228Glucodon 228p.D228
      Found
      Kotler et al. created a synthetic p53 mutation library covering ~10,000 DNA-binding domain variants and measured functional impact. The variant p.Asp228Glu was not identified by name in the full text. The VCEP Functional-worksheet reports noLOF for D228E in the Kotler assay.
      Variant
      ◇ Residue / gene-level — variant not named
      Applied to
      BS3 supports · met
      Why
      Variant not identified in main text; functional data from this study used by VCEP to confirm noLOF for D228E, supporting BS3 assignment.
      Location VCEP pre-assigned code in Supplementary Table S3 (Functional-worksheet.xlsx), not in main text  ·  full text
      Mutational processes shape the landscape of TP53 mutations in human cancer.
      Searched
      c.684C>GD228EAsp228Glucodon 228p.D228
      Found
      Giacomelli et al. interrogated TP53 loss-of-function screens in human cancer cell lines to characterize the mutational landscape. The variant p.Asp228Glu was not identified by name in the full text. The VCEP Functional-worksheet reports noLOF for D228E in the Giacomelli assay.
      Variant
      ◇ Residue / gene-level — variant not named
      Applied to
      BS3 supports · met
      Why
      Variant not identified in main text; functional data from this study used by VCEP to confirm noLOF for D228E, supporting BS3 assignment.
      Location VCEP pre-assigned code in Supplementary Table S3 (Functional-worksheet.xlsx), not in main text  ·  full text
      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