Starting
Initialising…
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TP53
Final classification
VUS
TP53 c.587G>T · p.Arg196Leu
TP53

The TP53 c.587G>T (p.Arg196Leu; p.R196L) variant has been observed in somatic cancers in COSMIC (COSV52667931, n=3) and has been reported in ClinVar as a variant of uncertain significance.

Gene
TP53
Transcript
NM_000546.6
HGVS · transcript:coding
NM_000546.6:c.587G>T
Consequence
N/A
GRCh38
chr17:7674944 C>A
GRCh37
chr17:7578262 C>A
Basis Tavtigian et.al., 2020 - Bayesian adaptation of Richards et.al., 2015 v2.4.0 point-based framework: PM2 supporting (+1) + PP3 moderate (+2) + BS3 supporting (-1) = 2 points, which maps to VUS.
Tavtigian et.al., 2020 - Bayesian adaptation of Richards et.al., 2015 v2.4.0 point-based framework: PM2 supporting (+1) + PP3 moderate (+2) + BS3 supporting (-1) = 2 points, which maps to VUS.
Classification rationale
PM2PP3 BS3 VUS
TP53 c.587G>T

The TP53 c.587G>T (p.Arg196Leu; p.R196L) variant has been observed in somatic cancers in COSMIC (COSV52667931, n=3) and has been reported in ClinVar as a variant of uncertain significance.1 This variant is absent from gnomAD v2.1 and gnomAD v4.1, which is below the TP53 VCEP PM2_Supporting population threshold of 0.00003.2 In TP53 VCEP-curated functional datasets, Kato transactivation data were partially functional and other eligible assays showed no loss of function, supporting BS3_Supporting rather than PS3.3 TP53 VCEP in silico criteria assign PP3_Moderate for c.587G>T based on aGVGD Class C65 with BayesDel 0.583489; SpliceAI shows no significant splice effect (max delta 0.14), and REVEL is high at 0.933.4

PM2 + PP3 + BS3 VUS
3 vcep_functional_worksheetvcep_flowchart_for_application_of_functional_rule_codesPMID:12826609 ↗PMID:29979965 ↗PMID:30224644 ↗
4 vcep_pp3_bp4_codesvcep_flowchart_for_application_of_pp3_2c_bp4_2c_and_bp7bayesdelspliceai ↗revel
Gene diagram · NM_000546.6 · variants mapped to exon structure
TP53 NM_000546.6
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
      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 Uncertain significance (5 clinical laboratories). (ClinVarID = 100814)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.14). REVEL score = 0.933. BayesDel score = 0.583489.
      Functional / OncoKB screenshot
      Functional Inconclusive
      OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Inconclusive; curated oncogenicity label: Inconclusive.
      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; COSV52667931, n = 3 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
      BS3 supports · met
      PMID PMID:29979965
      Found
      Structured finding pending for this record — see source link.
      Applied to
      BS3 supports · met
      PMID PMID:30224644
      Found
      Structured finding pending for this record — see source link.
      Applied to
      BS3 supports · met
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots