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NM_000546.6:c.-89A>G
p.? · TP53
0%
complete
Final classification
VUS
TP53
c.-89A>G
p.?
unknown · exon 1

TP53 encodes the p53 tumor suppressor protein, a transcription factor that responds to cellular stress such as DNA damage by switching on genes that trigger cell cycle arrest, DNA repair, senescence, or programmed cell death. In healthy cells, p53 is kept at low levels by constant degradation, but stress signals stabilize and activate it to protect against damaged cells surviving and dividing. Inherited mutations in TP53 cause Li-Fraumeni syndrome, a condition marked by a high risk of developing multiple cancers at a young age. TP53 is the most commonly mutated gene across human cancers, and loss of its normal function promotes tumor growth, spread, drug resistance, and genomic instability.

This variant

TP53 encodes a stress-activated tumor suppressor whose inherited disruption causes Li-Fraumeni syndrome, making TP53 variation clinically relevant to inherited cancer risk.

Transcript
NM_000546.6
HGVS · transcript:coding
NM_000546.6:c.-89A>G
GRCh38
chr17:7687437 T>C
GRCh37
chr17:7590755 T>C
VUS: no adjudicated criteria contribute points under the ClinGen TP53 VCEP v2.4 point-based framework, yielding a total of 0 points.
Classification rationale
VUS
TP53 c.-89A>G unknown · exon 1

All three requested criteria are not applicable because NM_000546.6:c.-89A>G is a 5′-UTR single-nucleotide variant with p.? and no qualifying protein-length or null-variant consequence. The governing TP53 VCEP PVS1 files were searched for c.-89A>G and the requested p.? notations; no exact pre-assigned entry was found. The ClinGen TP53 VCEP v2.4 framework governs all four requested criteria. PS2, PP1, and BS4 cannot be assessed because the case contains no proband, parental, pedigree, relative-genotype, phenotype, or meiosis evidence. PM6 is not applicable because the TP53 VCEP explicitly dropped PM6 and directs de novo evidence to PS2. The governing Table-of-LFS-Cancers-and-Points-for-PS2-and-PP1-Code-Application.pdf was searched under c.-89A>G, c.89A>G, p.Asn30Ser, and p.?; no variant-specific entry was found. All three requested computational criteria are not_applicable because NM_000546.6:c.-89A>G is a 5' UTR variant with protein consequence p.?, not a missense, synonymous, intronic, or splice-region variant within the applicable TP53 VCEP rules. The ClinGen TP53 VCEP v2.4 framework governs all four requested criteria. Population frequency evidence does not meet BA1, BS1, or PM2 because the relevant gnomAD v4.1 frequencies exceed the TP53 PM2 limit but remain below the TP53 BS1 and BA1 limits. BS2 is not assessable because no individual-level unaffected older female carrier data are available.

LYFE Sciences is an AI system, and it can make mistakes. Criteria may be applied incorrectly, sources may be misread, and a confident-looking classification can still be wrong. Double-check every criterion and its underlying evidence before relying on any call.
Gene diagram · NM_000546.6 · variants mapped to exon structure
TP53 NM_000546.6
Fetching transcript structure from UCSC…
Applied criteria · 0 applied · 9 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 · 0

No criteria were applied for this variant.

Assessed · not applied · 3 not met · 6 not assessed
Pathogenic
PS2 Not assessed: no proband phenotype or confirmed maternity-and-paternity de novo observation is available to calculate the TP53 VCEP PS2 points.
PS4 Not assessed: no proband phenotype, tumor pathology, or PS4 point total is available to compare with the 1-point Supporting threshold.
PM2 Not met: gnomAD v4.1 total AF is 0.0000551821, above the TP53 VCEP PM2 limit of 0.00003.
PP1 Not assessed: no informative relatives or meioses are available to compare variant carriage with LFS-associated cancer status.
PP4 Not assessed: no multigene-panel VAF observation is available to compare with the TP53 PP4 5-35% Supporting range.
Benign
BA1 Not met: the highest eligible non-founder gnomAD v4.1 FAF is 0.000084030, below the TP53 VCEP BA1 threshold of 0.001.
BS1 Not met: the highest eligible non-founder gnomAD v4.1 FAF is 0.000084030, below the TP53 VCEP BS1 lower threshold of 0.0003.
BS2 Not assessed: no source provides the required count of unrelated female carriers aged at least 60 years without cancer.
BS4 Not assessed: no affected family members with documented non-carriage of the variant are available for the TP53 VCEP BS4 Strong rule.
N/A · 19 PVS1 · PS1 · PS3 · PM1 · PM3 · PM4 · PM5 · PM6 · PP2 · PP3 · PP5 · BS3 · 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
This variant is present in gnomAD v4.1 (AF= 5.51821e-05; MAF= 0.00552%, 22/398680 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.40299e-05; MAF= 0.00840%, 19/226110 alleles, homozygotes = 0); grpmax FAF= 5.467e-05.
v2.1
This variant is present in gnomAD v2.1 (AF= 0.000223001; MAF= 0.02230%, 7/31390 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 0.000453779; MAF= 0.04538%, 7/15426 alleles, homozygotes = 0); grpmax FAF= 0.00021217.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.0055% · 22 / 398,680
0 hom · FAF 0.0055%
European (non-Finnish)
19 / 226,110
0.0084%
European (Finnish)
2 / 31,446
0.0064%
Remaining individuals
1 / 18,490
0.0054%
+ 7 not observed (Admixed American, Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
gnomAD v2.1
0.022% · 7 / 31,390
0 hom · FAF 0.021%
European (non-Finnish)
7 / 15,426
0.045%
+ 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian)
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 = 0.07).
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
8Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC