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TP53
Final classification
VUS
TP53 c.469G>T · p.Val157Phe
TP53

The TP53 NM_000546.6:c.469G>T (p.Val157Phe, p.V157F) variant has been reported in ClinVar with Likely pathogenic and Pathogenic clinical submissions.

Gene
TP53
Transcript
NM_000546.6
HGVS · transcript:coding
NM_000546.6:c.469G>T
Consequence
N/A
GRCh38
chr17:7675143 C>A
GRCh37
chr17:7578461 C>A
Basis Tavtigian et.al., 2020 - Bayesian adaptation of Richards et.al., 2015 v2.4.0 point-based framework: PS3 strong (+4) + PM2 supporting (+1) = 5 points, which maps to VUS.
Tavtigian et.al., 2020 - Bayesian adaptation of Richards et.al., 2015 v2.4.0 point-based framework: PS3 strong (+4) + PM2 supporting (+1) = 5 points, which maps to VUS.
Classification rationale
PS3PM2 VUS
TP53 c.469G>T

The TP53 NM_000546.6:c.469G>T (p.Val157Phe, p.V157F) variant has been reported in ClinVar with Likely pathogenic and Pathogenic clinical submissions.1 This variant is absent from gnomAD v2.1 and gnomAD v4.1, including 0 of 1,614,132 alleles in gnomAD v4.1, which supports PM2_Supporting under the TP53 VCEP threshold of less than 0.00003.2 In the TP53 VCEP functional framework, p.Val157Phe is assigned PS3 because Kato-based transactivation results are non-functional and the majority of other eligible assays show loss of function; additional published studies describe abnormal mutant behavior and structural destabilization consistent with impaired normal p53 activity.3 SpliceAI predicts no significant splice impact with a maximum delta score of 0.00, and although REVEL is 0.708 and BayesDel is 0.314073, the TP53 VCEP precomputed in silico table assigns c.469G>T as 'No evidence', so neither PP3 nor BP4 was applied.4

PS3 + PM2 VUS
3 vcep_functional_worksheetvcep_flowchart_for_application_of_functional_rule_codesPMID:16778209 ↗PMID:21561095 ↗
4 spliceai ↗revelbayesdelvcep_pp3_bp4_codesvcep_flowchart_for_application_of_pp3_2c_bp4_2c_and_bp7
Gene diagram · NM_000546.6 · variants mapped to exon structure
TP53 NM_000546.6
Fetching transcript structure from UCSC…
Applied criteria · 2 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
      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= 0; MAF= 0.00000%, 0/1614132 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0; MAF= 0.00000%, 0/75036 alleles, homozygotes = 0).
      v2.1
      Absent from gnomAD v2.1.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      Absent · 0 / 1,614,132
      0 hom
      Not observed in any ancestry group.
      + 10 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American, European (non-Finnish))
      gnomAD v2.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Likely pathogenic (4 clinical laboratories) and as Pathogenic (2 clinical laboratories). (ClinVarID = 12353)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.708. BayesDel score = 0.314073.
      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 lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV52667015, n = 375 times).
      Hotspots
      This variant lies in a statistically significant hotspot.
      Literature · how each cited paper was used
      2papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 7 further PMIDs triaged but not cited — see Sources & References.
      PMID PMID:16778209
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PS3 supports · met
      PMID PMID:21561095
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PS3 supports · met
      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
      15037740 ↗ A global suppressor motif for p53 cancer mutants. ONCOKB
      16778209 ↗ Mutant p53 induces the GEF-H1 oncogene, a guanine nucleotide exchange factor-H1 for RhoA, resulting in accelerated cell proliferation in tumor cells. ONCOKB
      21561095 ↗ Structural effects of the L145Q, V157F, and R282W cancer-associated mutations in the p53 DNA-binding core domain. ONCOKB
      10713666 ↗ Quantitative analysis of residual folding and DNA binding in mutant p53 core domain: definition of mutant states for rescue in cancer therapy. CLINVAR
      10754498 ↗ Clinical significance of p53 functional loss in squamous cell carcinoma of the oropharynx. CLINVAR
      27993330 ↗ Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR