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TP53
Final classification
VUS
TP53 c.431_436del · p.Gln144_Trp146delinsArg
TP53

NM_000546.6:c.431_436del (p.Gln144_Trp146delinsArg) is a 6-bp in-frame deletion in exon 5 of TP53, removing two amino acids (Q144 and W146) in the DNA-binding core domain L2 loop region and inserting arginine.

Gene
TP53
Transcript
NM_000546.6
HGVS · transcript:coding
NM_000546.6:c.431_436del
Consequence
N/A
GRCh38
chr17:7675175 CACAGCT>C
GRCh37
chr17:7578493 CACAGCT>C
Basis Tavtigian et.al., 2020 - Bayesian adaptation of Richards et.al., 2015 v2.4.0 point-based framework: PM2 supporting (+1) = 1 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) = 1 points, which maps to VUS.
Classification rationale
PM2 VUS
TP53 c.431_436del

NM_000546.6:c.431_436del (p.Gln144_Trp146delinsArg) is a 6-bp in-frame deletion in exon 5 of TP53, removing two amino acids (Q144 and W146) in the DNA-binding core domain L2 loop region and inserting arginine. This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, consistent with PM2_Supporting (allele frequency < 0.003%).1 The variant has not been reported in ClinVar and has not been observed in COSMIC.2 SpliceAI predicts no splicing impact (max delta score = 0.00).3 The variant is not covered by the VCEP PVS1 framework (in-frame deletion, not a null variant), nor by VCEP PP3/BP4 in silico rules (multi-amino-acid deletion, not a missense or single-AA deletion).4 No variant-specific functional assay data from eligible studies (Kato, Kotler, Giacomelli, Funk, Kawaguchi) are available; the VCEP Functional worksheet does not contain this variant. OncoKB infers a Likely Loss-of-function but this is a somatic curation and not a direct germline functional assay.5 No proband data, segregation data, de novo observations, or cancer-phenotype data were available for this variant. Only one criterion met: PM2_Supporting. All other applicable criteria are either not met, not assessed due to absent data, or not applicable per VCEP specifications.

PM2 VUS
4 vcep_pvs1_flowchartvcep_pp3_bp4_codes
5 vcep_functional_worksheetoncokb ↗
Gene diagram · NM_000546.6 · variants mapped to exon structure
TP53 NM_000546.6
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 13 assessed
Applied · 1
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
NM_000546.6:c.431_436del is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0. This satisfies the VCEP PM2_Supporting rule requiring an allele frequency below 0.00003 (0.003%).
Absent from gnomAD v2.1 (exomes)Absent from gnomAD v4.1 (exomes)Absent from gnomAD-Canada v1.0 (genomes)
Assessed · not applied
Pathogenic
PS1 VCEP PS1 requires a same-residue missense variant previously classified as pathogenic or likely pathogenic by TP53 VCEP specifications.
PS2 No de novo observation data available for this variant.
PS3 This 2-amino-acid in-frame deletion (p.Gln144_Trp146delinsArg) is not listed in the VCEP Functional worksheet (Supplementary Table S3), which covers single amino acid substitutions and single amino acid deletions.
PS4 No proband data available.
PP1 No cosegregation data available.
PP3 This variant is a 2-amino-acid in-frame deletion, which is not covered by the VCEP PP3 rules.
PP4 VCEP PP4 requires observation of the variant with a variant allele fraction (VAF) of 5-35%.
Benign
BA1 VCEP BA1 requires a filtering allele frequency ≥ 0.001 (0.1%) in a gnomAD continental subpopulation.
BS1 VCEP BS1 requires a filtering allele frequency ≥ 0.0003 (0.03%) but < 0.001 in a gnomAD continental subpopulation.
BS2 VCEP BS2 requires observation of the variant in unrelated females who have reached at least 60 years of age without cancer.
BS3 This 2-amino-acid in-frame deletion is not listed in the VCEP Functional worksheet.
BS4 VCEP BS4 requires lack of segregation in affected family members with LFS-associated cancers.
BP4 This is a 2-amino-acid in-frame deletion, which is not covered by the VCEP BP4 rules.
N/A · 13 PVS1 · PM1 · PM4 · PM5 · PM6 · PP2 · PP5 · BP1 · BP2 · BP3 · BP5 · BP6 · BP7
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
Absent from gnomAD-Canada v1.0.
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 / OncoKB screenshot
Functional Likely Oncogenic
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Hotspot
COSMIC
This variant lies in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant lies in a statistically significant hotspot.
Sources & reference links
9Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 2 PMIDs not cited in assessment
11900253 ↗ Rescuing the function of mutant p53. ONCOKB
8023157 ↗ Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations. ONCOKB