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TP53
Final classification
Benign
TP53 c.215C>G · p.Pro72Arg
TP53

The TP53 c.215C>G (p.Pro72Arg, p.P72R) variant has not been observed in COSMIC as a recurrent somatic cancer variant and is reported in ClinVar as benign, including a benign ClinGen TP53 Variant Curation Expert Panel classification.

Gene
TP53
Transcript
NM_000546.5
HGVS · transcript:coding
NM_000546.5:c.215C>G
Consequence
N/A
GRCh38
chr17:7676154 G>C
GRCh37
chr17:7579472 G>C
Basis Tavtigian et.al., 2020 - Bayesian adaptation of Richards et.al., 2015 v2.4.0 point-based framework: BA1 stand-alone benign (-8) + BP4 moderate (-2) = -10 points, which maps to Benign.
Tavtigian et.al., 2020 - Bayesian adaptation of Richards et.al., 2015 v2.4.0 point-based framework: BA1 stand-alone benign (-8) + BP4 moderate (-2) = -10 points, which maps to Benign.
Classification rationale
BA1BP4 Benign
TP53 c.215C>G

The TP53 c.215C>G (p.Pro72Arg, p.P72R) variant has not been observed in COSMIC as a recurrent somatic cancer variant and is reported in ClinVar as benign, including a benign ClinGen TP53 Variant Curation Expert Panel classification.1 This variant is very common in population databases, with gnomAD v4.1 total allele frequency 0.707882 and grpmax filtering allele frequency 0.746273, far above the TP53 BA1 benign threshold of 0.001.2 Available studies of the common TP53 codon 72 polymorphism describe biologic differences between alleles, but no TP53 VCEP-eligible functional code assignment for p.Pro72Arg was identified in the TP53 functional worksheet.3 TP53 VCEP in silico data support a benign interpretation because c.215C>G is assigned BP4_moderate in the TP53 PP3/BP4 worksheet with BayesDel -0.108475, and SpliceAI predicts no significant splice effect with a maximum delta score of 0.05.4

BA1 + BP4 Benign
3 vcep_f_u_n_c_t_i_o_n_a_l___w_o_r_k_s_h_e_e_tPMID:10802655 ↗PMID:12567188 ↗PMID:16964264 ↗
4 vcep_p_p_3___b_p_4___c_o_d_e_sspliceai ↗cspec ↗
Gene diagram · NM_000546.5 · variants mapped to exon structure
TP53 NM_000546.5
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 · supports benign
      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= 0.707882; MAF= 70.78822%, 1142226/1613582 alleles, homozygotes = 411964) and has highest observed frequency in the European (non-Finnish) population (AF= 0.747582; MAF= 74.75821%, 882123/1179968 alleles, homozygotes = 329809); grpmax FAF= 0.746273.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 0.662887; MAF= 66.28868%, 186832/281846 alleles, homozygotes = 63926) and has highest observed frequency in the European (non-Finnish) population (AF= 0.73659; MAF= 73.65900%, 94889/128822 alleles, homozygotes = 34940); grpmax FAF= 0.733613.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      71% · 1142226 / 1,613,582
      411964 hom · FAF 75%
      European (non-Finnish)
      882123 / 1,179,968
      75%
      329809 hom
      European (Finnish)
      46913 / 63,994
      73%
      17252 hom
      Ashkenazi Jewish
      21300 / 29,604
      72%
      7644 hom
      Admixed American
      42617 / 59,976
      71%
      15147 hom
      Remaining individuals
      43349 / 62,476
      69%
      15169 hom
      Amish
      611 / 912
      67%
      207 hom
      Middle Eastern
      3519 / 5,810
      61%
      1103 hom
      East Asian
      26984 / 44,862
      60%
      8137 hom
      South Asian
      46205 / 91,050
      51%
      12001 hom
      African/African American
      28605 / 74,930
      38%
      5495 hom
      gnomAD v2.1
      66% · 186832 / 281,846
      63926 hom · FAF 73%
      European (non-Finnish)
      94889 / 128,822
      74%
      34940 hom
      European (Finnish)
      18300 / 25,100
      73%
      6645 hom
      Ashkenazi Jewish
      7414 / 10,366
      72%
      2641 hom
      Admixed American
      25286 / 35,416
      71%
      9030 hom
      Remaining individuals
      4999 / 7,178
      70%
      1753 hom
      East Asian
      11314 / 19,918
      57%
      3235 hom
      South Asian
      15313 / 30,614
      50%
      3897 hom
      African/African American
      9317 / 24,432
      38%
      1785 hom
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Benign (25 clinical laboratories) and as Uncertain significance (1 clinical laboratory) and as Benign by ClinGen TP53 Variant Curation Expert Panel, ClinGen (expert panel).
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.05).
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB has not reviewed this specific variant; no variant-level oncogenicity or biological effect is available. Gene-level context: TP53, a tumor suppressor in the DNA damage pathway, is the most frequently mutated gene in cancer.
      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 not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots