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TP53
Final classification
VUS
TP53 c.612_623del · p.Glu204_Asp207del
TP53

NM_000546.5:c.612_623del (p.Glu204_Asp207del) is an in-frame deletion of 12 nucleotides in exon 6 of TP53, removing four amino acids (204-207) within the DNA-binding core domain (residues 102-292).

Gene
TP53
Transcript
NM_000546.5
HGVS · transcript:coding
NM_000546.5:c.612_623del
Consequence
N/A
GRCh38
chr17:7674907 GTCATCCAAATAC>G
GRCh37
chr17:7578225 GTCATCCAAATAC>G
Basis ClinGen TP53 Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for TP53 Version 2.4 v2.4 point-based framework: PM2 supporting (+1) = 1 points, which maps to VUS.
ClinGen TP53 Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for TP53 Version 2.4 v2.4 point-based framework: PM2 supporting (+1) = 1 points, which maps to VUS.
Classification rationale
PM2 VUS
TP53 c.612_623del

NM_000546.5:c.612_623del (p.Glu204_Asp207del) is an in-frame deletion of 12 nucleotides in exon 6 of TP53, removing four amino acids (204-207) within the DNA-binding core domain (residues 102-292). The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada (0 alleles across all population databases), meeting PM2_Supporting under the TP53 VCEP (AF < 0.00003).1 The variant is absent from ClinVar and has not been previously classified by any diagnostic laboratory or expert panel.2 The variant is not a null variant (nonsense, frameshift, or canonical splice) and is not addressed by the TP53 VCEP PVS1 decision tree, which covers only truncating and exon-level deletion variants. PVS1 is not applicable.3 No variant-specific functional data are available. The VCEP Functional-worksheet catalogs single amino acid substitutions and deletions but does not include the 4-amino-acid deletion p.Glu204_Asp207del. Two reviewed publications (PMID:11900253, PMID:8023157) discuss p53 structure and function at the gene level but do not mention this specific variant.4 Several criteria (PS2, PS4, PP1, PP4, BS2, BS4) could not be assessed due to absence of proband phenotype, family, or segregation data. Multiple VCEP criteria (PM4, PM6, PP2, PP5, BP1, BP2, BP3, BP5, BP6) are explicitly marked as Not Applicable under the TP53 VCEP v2.4 framework.5 The only applicable and met criterion is PM2_Supporting (absent from population databases). All other assessable criteria are either not applicable, not met, or not assessed due to insufficient data.6

PM2 VUS
3 vcep_pvs1_flowchartpvs1_variant_assessment
4 vcep_functional_worksheet
Gene diagram · NM_000546.5 · variants mapped to exon structure
TP53 NM_000546.5
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 11 assessed
Applied · 1
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
NM_000546.5:c.612_623del is absent from gnomAD v2.1, v4.1, and gnomAD-Canada. The allele frequency of 0 is below the VCEP PM2_Supporting threshold of 0.00003 (0.003%).
Absent from gnomAD v2.1 (0 alleles)gnomAD v4.1 (0 alleles)and gnomAD-Canada v1.0 (0 alleles). AF = 0
Assessed · not applied
Pathogenic
PS1 No variant with the same amino acid change (p.Glu204_Asp207del) has been previously classified as pathogenic or likely pathogenic under the TP53 VCEP specifications.
PS2 No de novo observation data available.
PS3 The TP53 VCEP Functional-worksheet (Supplementary Table S3) catalogs PS3/BS3 assignments for single amino acid substitutions and single amino acid deletions but does not contain an entry for the 4-amino-acid deletion p.Glu204_Asp207del.
PS4 VCEP PS4 uses a point-based system requiring proband-level cancer diagnoses matched to the LFS cancer scoring table.
PP1 No cosegregation data available.
PP4 VCEP PP4 requires observation of the variant at low variant allele fraction (VAF 5-35%) in blood, suggestive of somatic mosaicism or clonal hematopoiesis.
Benign
BA1 NM_000546.5:c.612_623del is absent from gnomAD v2.1, v4.1, and gnomAD-Canada.
BS1 NM_000546.5:c.612_623del is absent from gnomAD v2.1, v4.1, and gnomAD-Canada.
BS2 VCEP BS2 requires ≥2 unrelated females aged ≥60 years without cancer (supporting) from a single source, excluding sarcoma diagnoses at ≥61 years.
BS3 The TP53 VCEP Functional-worksheet does not contain an entry for p.Glu204_Asp207del.
BS4 VCEP BS4 requires lack of segregation in affected family members with LFS-associated cancers.
N/A · 15 PVS1 · PM1 · PM4 · PM5 · PM6 · PP2 · PP3 · PP5 · BP1 · BP2 · BP3 · BP4 · 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 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
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