Starting
Initialising…
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TP53
Final classification
Likely pathogenic
TP53 c.833C>A · p.Pro278His
TP53

TP53 p.Pro278His has abnormal functional evidence, and the TP53 VCEP functional worksheet assigns PS3 for this amino acid substitution.

Gene
TP53
Transcript
NM_000546.6
HGVS · transcript:coding
NM_000546.6:c.833C>A
Consequence
N/A
GRCh38
chr17:7673787 G>T
GRCh37
chr17:7577105 G>T
Basis Fallback generic ACMG/AMP combination rules were used because the workspace explicitly retrieved TP53 VCEP criterion specifications and noted a Tavtigian points-based system, but did not explicitly retrieve the TP53 VCEP final point-to-classification thresholds. Under the generic ACMG/AMP fallback, PS3 + PP3_Moderate + PM2_Supporting supports Likely Pathogenic.
Fallback generic ACMG/AMP combination rules were used because the workspace explicitly retrieved TP53 VCEP criterion specifications and noted a Tavtigian points-based system, but did not explicitly retrieve the TP53 VCEP final point-to-classification thresholds. Under the generic ACMG/AMP fallback, PS3 + PP3_Moderate + PM2_Supporting supports Likely Pathogenic.
Classification rationale
PS3PM2PP3 Likely pathogenic
TP53 c.833C>A

TP53 p.Pro278His has abnormal functional evidence, and the TP53 VCEP functional worksheet assigns PS3 for this amino acid substitution.1 TP53 in silico assessment assigns c.833C>A as PP3_Moderate, with BayesDel 0.607821 and Class C65 supporting a deleterious missense effect.2 SpliceAI predicts a max delta score of 0.00, which is below the TP53 splice-impact threshold of 0.2 and does not indicate a predicted splice effect.3 The variant is absent from gnomAD v4.1, and absence from population databases is consistent with the TP53 PM2_Supporting threshold of less than 0.00003.4 Using the generic ACMG/AMP combination rules as a fallback because explicit TP53 VCEP final Tavtigian score thresholds were not explicitly retrieved, PS3 with PP3_Moderate and PM2_Supporting supports a Likely Pathogenic classification.5

PS3 + PM2 + PP3 Likely pathogenic
1 vcep_f_u_n_c_t_i_o_n_a_l___w_o_r_k_s_h_e_e_t
2 vcep_p_p_3___b_p_4___c_o_d_e_s
5 generic_acmg_combination_rules
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 · supports pathogenic
      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 (4 clinical laboratories) and as Likely pathogenic (1 clinical laboratory) and as Pathogenic (1 clinical laboratory).
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
      Functional / OncoKB screenshot
      Functional
      OncoKB classifies this variant as Likely Oncogenic; biological effect: Likely Loss-of-function.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence
      COSMIC
      This variant has previously been reported in somatic cancers (COSMIC; COSV52665769, n = 29 times).
      Hotspots
      This variant does not lie in a statistically significant cancer 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:29979965
      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
      6Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB