Starting
Initialising…
0%
TP53
Final classification
VUS
TP53 c.919+4A>G · p.?
TP53

NM_000546.6:c.919+4A>G is an intronic variant at the +4 position of intron 8 in TP53, evaluated under the ClinGen TP53 VCEP Specifications v2.4.0. The variant is absent from gnomAD v2.1 and v4.1, supporting PM2_Supporting.

Gene
TP53
Transcript
NM_000546.6
HGVS · transcript:coding
NM_000546.6:c.919+4A>G
Consequence
N/A
GRCh38
chr17:7673697 T>C
GRCh37
chr17:7577015 T>C
Basis Tavtigian et.al., 2020 - Bayesian adaptation of Richards et.al., 2015 v2.4.0 point-based framework: PM2 supporting (+1) + BP4 supporting (-1) = 0 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) + BP4 supporting (-1) = 0 points, which maps to VUS.
Classification rationale
PM2 BP4 VUS
TP53 c.919+4A>G

NM_000546.6:c.919+4A>G is an intronic variant at the +4 position of intron 8 in TP53, evaluated under the ClinGen TP53 VCEP Specifications v2.4.0. The variant is absent from gnomAD v2.1 and v4.1, supporting PM2_Supporting.1 SpliceAI predicts no splicing impact (max delta score 0.00). As an intronic variant outside the ±1,2 canonical splice positions with SpliceAI ≤0.1, BP4_Supporting is met.2 PVS1 is not applicable as the variant lies outside the canonical ±1,2 splice donor/acceptor positions addressed by the VCEP PVS1 flowchart. PS3/BS3 functional codes are not applicable as they address missense variants and small in-frame deletions only. The variant is not located in a VCEP-specified mutational hotspot and has no amino acid change, so PM1 and PM5 are not applicable.3 With one pathogenic supporting code (PM2_Supporting, +1 point) and one benign supporting code (BP4_Supporting, -1 point), the total point value is 0. Under the Tavtigian point-based system adopted by the TP53 VCEP v2.4.0, a score of 0 falls in the range of Uncertain Significance (-1 to 5 points).4

PM2 + BP4 VUS
3 cspec ↗vcep_functional_worksheet
4 cspec ↗final_classification_framework
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
      Absent from gnomAD v4.1.
      v2.1
      Absent from gnomAD v2.1.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      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.
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant is absent from ClinVar.
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
      Functional No data
      No calibrated functional assay or RNA evidence was identified for this variant.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Somatic evidence
      COSMIC
      This variant has not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant does not lie in a statistically significant cancer hotspot.
      COSMIC ↗
      Sources & reference links
      7Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC