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TP53
Final classification
Likely Pathogenic
TP53 c.610G>T · p.Glu204Ter
TP53

NM_000546.6:c.610G>T (p.Glu204Ter) is a nonsense variant in exon 6 of TP53, producing a premature termination codon at position 204 that is predicted to undergo nonsense-mediated decay, satisfying PVS1 at very strong strength per the TP53 VCEP PVS1 flowchart.

Gene
TP53
Transcript
NM_000546.6
HGVS · transcript:coding
NM_000546.6:c.610G>T
Consequence
N/A
GRCh38
chr17:7674921 C>A
GRCh37
chr17:7578239 C>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.610G>T

NM_000546.6:c.610G>T (p.Glu204Ter) is a nonsense variant in exon 6 of TP53, producing a premature termination codon at position 204 that is predicted to undergo nonsense-mediated decay, satisfying PVS1 at very strong strength per the TP53 VCEP PVS1 flowchart.1 The variant is absent from all gnomAD population databases (v2.1, v4.1, Canada v1.0), meeting PM2 at supporting strength under the VCEP threshold of <0.00003.2 The variant has been observed as a recurrent somatic mutation in COSMIC (n=100, COSV52679869) and is classified as Pathogenic by two clinical laboratories in ClinVar (ClinVarID 977783), consistent with a deleterious truncating effect.3 No proband phenotype data, segregation information, de novo observations, or VAF data are available to support PS2, PS4, PP1, or PP4 scoring under the VCEP point-based system.4 The VCEP functional (PS3/BS3) and in silico (PP3/BP4/BP7) criteria are limited to missense variants, in-frame deletions, synonymous variants, and intronic variants by the framework specifications and do not apply to nonsense variants. The truncating consequence is fully captured by PVS1.5 Under the Tavtigian point-based classification system used by the TP53 VCEP, PVS1 (very strong = 8 points) plus PM2 (supporting = 1 point) yields a total of 9 points, which falls in the Likely Pathogenic range (6-9 points).6

PVS1 + PM2 Likely Pathogenic
1 vcep_pvs1_flowchartcspec ↗pvs1_variant_assessment
5 cspec ↗vcep_flowchart_for_application_of_functional_rule_codesvcep_functional_worksheetvcep_flowchart_for_application_of_pp3_2c_bp4_2c_and_bp7vcep_pp3_bp4_codes
6 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 applied · 9 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PVS1 very strong Pathogenic
NM_000546.6:c.610G>T is a nonsense variant producing a premature termination codon at p.Glu204Ter. The PTC is upstream of p.Lys351 (codon 351) and is located in exon 6, not in exon 11 or the 3'-most 50 nucleotides of exon 10, and is therefore predicted to undergo nonsense-mediated decay. Per the TP53 VCEP PVS1 flowchart (Figure 1, version 2.4), nonsense variants upstream of p.Lys351 predicted to undergo NMD are assigned PVS1 at very strong strength.
Nonsense variant p.Glu204Ter (E204*) at codon 204upstream of the NMD-escape boundary at p.Lys351PTC in exon 6 — not in exon 11 or the 3'-most 50 nt of exon 10 — predicted to trigger NMD
PM2 supporting Pathogenic
The variant is absent from gnomAD v2.1 (exomes), gnomAD v4.1 (exomes), and gnomAD-Canada v1.0 (genomes), yielding an allele frequency of 0. This is below the VCEP PM2_Supporting threshold of <0.00003 (0.003%). No single genetic ancestry group has multiple alleles with frequency >0.00004.
gnomAD v2.1: absent (AF = 0)gnomAD v4.1: absent (AF = 0)gnomAD-Canada v1.0: absent (AF = 0)
Assessed · not applied
Pathogenic
PS2 No de novo observation data are available for this variant.
PS4 The VCEP PS4 point-based scoring system requires proband-level cancer phenotype data (strongly associated LFS cancers = 4 points, moderately associated = 2 points per proband).
PM1 The TP53 VCEP PM1 rules are explicitly limited to missense variants: (1) missense variants within codons 175, 245, 248, 249, 273, or 282 (moderate), or (2) missense variants at cancerhotspots.org with ≥10 somatic occurrences for the same amino acid change (moderate) or 2-9 occurrences (supporting).
PP1 No cosegregation data are available for this variant.
PP4 The VCEP PP4 criterion requires observation of the variant with a variant allele fraction (VAF) of 5-35% (supporting) or at least 2 independent observations with VAF 5-25% (moderate) to address potential clonal hematopoiesis/somatic mosaicism.
Benign
BA1 The VCEP BA1 rule requires a filtering allele frequency (FAF) ≥0.001 (0.1%) in a single continental subpopulation with ≥2,000 alleles tested and ≥2 alleles present.
BS1 The VCEP BS1 rule requires a filtering allele frequency (FAF) ≥0.0003 (0.03%) but <0.001 in a single continental subpopulation with ≥2,000 alleles tested and ≥2 alleles present.
BS2 The VCEP BS2 rule requires ≥2 unrelated females who have reached at least 60 years of age without cancer (supporting), 4-7 (moderate), or ≥8 (strong), all from a single source.
BS4 The VCEP BS4 rule requires lack of segregation in affected family members diagnosed with LFS-associated cancers.
N/A · 17 PS1 · PS3 · PM3 · PM4 · PM5 · PM6 · PP2 · PP3 · PP5 · BS3 · 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 has been reported in ClinVar as Pathogenic (2 clinical laboratories). (ClinVarID = 977783)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). BayesDel score = 0.66.
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 previously been reported in somatic cancers (COSMIC; COSV52679869, n = 100 times).
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 · 9 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
17392385 ↗ American Cancer Society guidelines for breast screening with MRI as an adjunct to mammography. CLINVAR
20301471 ↗ Wilms Tumor Predisposition. CLINVAR
24493721 ↗ American Society of Clinical Oncology Expert Statement: collection and use of a cancer family history for oncology providers. CLINVAR
23619274 ↗ American College of Medical Genetics and Genomics technical standards and guidelines: microarray analysis for chromosome abnormalities in neoplastic disorders. CLINVAR