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TP53
Final classification
VUS
TP53 c.1010G>T · p.Arg337Leu
TP53

The TP53 c.1010G>T (p.Arg337Leu; p.R337L) variant has been observed in somatic cancers in COSMIC (COSV52665150, n=69) and has been reported in ClinVar, including a ClinGen TP53 expert panel classification of Likely Pathogenic.

Gene
TP53
Transcript
NM_000546.6
HGVS · transcript:coding
NM_000546.6:c.1010G>T
Consequence
N/A
GRCh38
chr17:7670699 C>A
GRCh37
chr17:7574017 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) + PP5 supporting (+1) + BP4 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) + PP5 supporting (+1) + BP4 supporting (-1) = 5 points, which maps to VUS.
Classification rationale
PS3PM2PP5 BP4 VUS
TP53 c.1010G>T

The TP53 c.1010G>T (p.Arg337Leu; p.R337L) variant has been observed in somatic cancers in COSMIC (COSV52665150, n=69) and has been reported in ClinVar, including a ClinGen TP53 expert panel classification of Likely Pathogenic.1 This variant is absent from gnomAD v2.1 and gnomAD v4.1, supporting rarity and meeting the TP53 PM2_Supporting threshold of less than 0.00003.2 In TP53 functional data summarized by the TP53 VCEP, p.Arg337Leu was non-functional with loss-of-function findings and monomerization, supporting a damaging effect on protein function and meeting PS3.3 In the TP53-specific computational framework, SpliceAI predicts no splice effect (max delta score 0.00) and the TP53 VCEP bioinformatic worksheet assigns BP4 with a BayesDel score of 0.0670081; REVEL was 0.765, but the TP53 precomputed PP3/BP4 assignment supports BP4 rather than PP3 for this variant.4

PS3 + PM2 + PP5 + BP4 VUS
3 vcep_functional_worksheetvcep_flowchart_for_application_of_functional_rule_codesPMID:12826609 ↗PMID:16007150 ↗PMID:30224644 ↗
4 spliceai ↗bayesdelrevelvcep_pp3_bp4_codesvcep_flowchart_for_application_of_pp3_2c_bp4_2c_and_bp7cspec ↗
Gene diagram · NM_000546.6 · variants mapped to exon structure
TP53 NM_000546.6
Fetching transcript structure from UCSC…
Applied criteria · 4 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
      Absent from gnomAD v4.1.
      v2.1
      Absent from gnomAD v2.1.
      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.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Likely pathogenic (4 clinical laboratories) and as Pathogenic (1 clinical laboratory) and as Likely Pathogenic by ClinGen TP53 Variant Curation Expert Panel, ClinGen (expert panel). (ClinVarID = 142828)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.765. BayesDel score = 0.0670081.
      Functional No data
      No calibrated functional assay or RNA evidence was identified for this variant.
      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; COSV52665150, n = 69 times).
      Hotspots
      This variant lies 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.
      PMID PMID:12826609
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PS3 supports · met
      PMID PMID:16007150
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PS3 supports · met
      PMID PMID:30224644
      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