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TP53
Final classification
Likely Pathogenic
PVS1PM2
TP53
c.599_600del
p.Asn200IlefsTer8
frameshift
This variant

This two-base-pair deletion in TP53 exon 6 produces a frameshift (p.Asn200IlefsTer8) with a premature termination codon at approximately codon 207, upstream of p.Lys351 and predicted to undergo nonsense-mediated decay, satisfying PVS1 at very strong strength per the TP53 VCEP decision tree.

Transcript
NM_000546.6
HGVS · transcript:coding
NM_000546.6:c.599_600del
GRCh38
chr17:7674930 AAT>A
GRCh37
chr17:7578248 AAT>A
Basis ClinGen TP53 Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for TP53 Version 2.4 v2.4 point-based framework: PVS1 very strong (+8) + PM2 supporting (+1) = 9 points, which maps to Likely Pathogenic.
ClinGen TP53 Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for TP53 Version 2.4 v2.4 point-based framework: PVS1 very strong (+8) + PM2 supporting (+1) = 9 points, which maps to Likely Pathogenic.
Classification rationale
PVS1PM2 Likely Pathogenic
TP53 c.599_600del frameshift

This two-base-pair deletion in TP53 exon 6 produces a frameshift (p.Asn200IlefsTer8) with a premature termination codon at approximately codon 207, upstream of p.Lys351 and predicted to undergo nonsense-mediated decay, satisfying PVS1 at very strong strength per the TP53 VCEP decision tree.1 The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, meeting PM2_Supporting at an allele frequency below 0.003%.2 Absence from population databases is consistent with a pathogenic role and does not satisfy any benign frequency criterion (BA1, BS1).3 No variant-specific functional, segregation, de novo, or clinical observations were identified, and none of the reviewed publications mentions NM_000546.6:c.599_600del; therefore no additional pathogenic or benign criteria are met.4

PVS1 + PM2 Likely Pathogenic
Gene diagram · NM_000546.6 · variants mapped to exon structure
TP53 NM_000546.6
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 11 assessed
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
Applied · 2
Strength Supporting Moderate Strong Very strong
PVS1 very strong Pathogenic
This 2-base-pair deletion in exon 6 produces a frameshift (p.Asn200IlefsTer8) with a premature termination codon at approximately codon 207, upstream of p.Lys351 and predicted to undergo nonsense-mediated decay, meeting PVS1 at very strong strength per the TP53 VCEP decision tree.
Frameshift variant (c.599_600del) with PTC at p.Asn200IlefsTer8 (~codon 207).PTC located in exon 6upstream of p.Lys351
PM2 supporting Pathogenic
The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, satisfying PM2_Supporting (allele frequency below 0.003%).
Absent from gnomAD v2.1 (exome).Absent from gnomAD v4.1 (exome).Absent from gnomAD-Canada v1.0 (genomes).
Assessed · not applied · 11 not met · 0 not assessed
Pathogenic
PS2 No de novo observation of this variant was identified; no proband or confirmed parental testing data are available to tally de novo points.
PS3 No functional data exist for this frameshift variant.
PS4 No affected-proband observations were identified; the variant is absent from ClinVar and COSMIC, and no case-control prevalence data are available to tally PS4 points.
PM1 This frameshift at codon 200 does not fall within a TP53 VCEP-defined hotspot codon (175, 245, 248, 249, 273, 282), which applies only to missense variants, and it is not a cancerhotspots.org missense change with qualifying somatic occurrences.
PP1 No cosegregation data are available for this variant.
PP4 No proband phenotype or variant allele fraction (VAF) data are available to satisfy the TP53 VCEP PP4 rule, which requires somatic VAF observations (5-35%).
Benign
BA1 The variant is absent from gnomAD and does not reach the stand-alone benign allele frequency threshold (>=0.1%).
BS1 The variant is absent from gnomAD and does not meet the strong benign allele frequency threshold (>=0.0003).
BS2 No unaffected adult (cancer-free female >=60 years) observations are available for this variant.
BS3 No functional data demonstrate a benign (normal function) effect for this frameshift variant; it is not present in the TP53 VCEP functional worksheet and no reviewed publication tested it.
BS4 No segregation data are available to assess lack of segregation among affected family members.
N/A · 15 PS1 · PM3 · PM4 · PM5 · PM6 · PP2 · PP3 · PP5 · BP1 · BP2 · BP3 · BP4 · BP5 · BP6 · BP7
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.
🇨🇦 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 = 0.05).
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 · 5 PMIDs not cited in assessment
11753428 ↗ A novel mechanism of tumorigenesis involving pH-dependent destabilization of a mutant p53 tetramer. ONCOKB
11900253 ↗ Rescuing the function of mutant p53. ONCOKB
16007150 ↗ The relationship among p53 oligomer formation, structure and transcriptional activity using a comprehensive missense mutation library. ONCOKB
19336573 ↗ High incidence of protein-truncating TP53 mutations in BRCA1-related breast cancer. ONCOKB
21467160 ↗ Prognostic significance of truncating TP53 mutations in head and neck squamous cell carcinoma. ONCOKB