About TP53
No gene-level summary was recorded for this case.
No variant summary was recorded for this case.
Five-step scale from benign to pathogenic. This variant is likely benign. Select a step to read what it means.
Likely benign.A likely benign classification under the recorded framework.
Gene-level background from the recorded interpretation.
Words with a dotted underline have a short definition. Hover or tap them.No gene-level summary was recorded for this case.
The recorded framework is ClinGen TP53 VCEP v2.4.0. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.
The applied criteria and their strengths are shown as assessed under the stated framework.
This variant is rare in population databases. In gnomAD v4.1, the total allele frequency is 4.34e-06 and the grpmax filtering allele frequency is 2.47e-06, both below the TP53 VCEP PM2 threshold of 3.0e-05; it is also absent from gnomAD-Canada.
Published TP53 functional evidence supports retained protein function. In the TP53 VCEP functional worksheet, p.Gly356Arg is classified as Functional in Kato-class data and noLOF in Giacomelli-class data, with a preliminary functional code of BS3.
Computational evidence supports a benign interpretation. The TP53 VCEP bioinformatic worksheet assigns BP4_moderate for c.1066G>C; BayesDel is -0.347259, which is below the BP4_Moderate threshold of -0.008, and SpliceAI predicts no splice effect (max delta score 0.00). REVEL is also low at 0.138.
Expert panel ClinGen TP53 Variant Curation Expert Panel, ClinGen classified as Likely benign.
TP53 ClinGen VCEP v2.4.0 Tavtigian point-based framework from the CSPEC final-classification ruleset; PM2_Supporting (+1), BS3_Strong (-4), BP4_Moderate (-2), and BP6_Supporting_Benign (-1) yield a total of -6 points.
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1: 7 / 1,613,958 alleles. Recorded AF 4.33716e-06. Recorded homozygote count 0.
This variant is present in gnomAD v2.1 (AF= 3.98721e-06; MAF= 0.00040%, 1/250802 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.82208e-06; MAF= 0.00088%, 1/113352 alleles, homozygotes = 0).
Absent from gnomAD-Canada v1.0.
Recorded SpliceAI maximum delta score: 0.000. Refer to the recorded PP3/BP4 rationale for interpretation.
6 Uncertain significance · 3 Likely benign · 1 Uncertain Significance.
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. TP53, a tumor suppressor in the DNA damage pathway, is the most frequently mutated gene in cancer.
This variant has not previously been reported in somatic cancers (COSMIC).
This variant does not lie in a statistically significant hotspot.
ACMG/AMP criteria under ClinGen TP53 VCEP v2.4.0, with the data and sources behind each one.
28 criteria with recorded statuses: 4 met · 7 not met · 6 not assessed · 11 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
The TP53 c.1066G>C (p.Gly356Arg) variant has been reported in ClinVar, where the ClinGen TP53 Variant Curation Expert Panel classified it as Likely Benign.
This variant is rare in population databases, with gnomAD v4.1 total allele frequency 4.34e-06, grpmax filtering allele frequency 2.47e-06, gnomAD v2.1 total allele frequency 3.99e-06, and no observation in gnomAD-Canada, which supports PM2 at a supporting level but is well below BA1 and BS1 thresholds.
In the TP53 VCEP functional worksheet, p.Gly356Arg is classified as Functional in Kato-class data and noLOF in Giacomelli-class data, supporting BS3 and arguing against PS3.
TP53-specific computational assessment supports a benign interpretation: the TP53 VCEP bioinformatic worksheet assigns BP4_moderate, BayesDel is -0.347259, SpliceAI predicts no splice effect with max delta score 0.00, and REVEL is 0.138.
No criteria match.
TP53 VCEP PM2_Supporting: AF < 0.00003 and no disqualifying ancestry-specific frequency
TP53 VCEP BS3 Strong
TP53 VCEP BP4 Moderate
TP53 VCEP PS1 requires a previously established TP53 VCEP P/LP variant with the same amino acid change
TP53 VCEP PS3 requires non-functional/LOF assay results
TP53 VCEP PM1 hotspot/codon-specific framework
TP53 VCEP PM5 requires prior TP53 VCEP pathogenic or likely pathogenic missense variants at the same residue
TP53 VCEP PP3 requires qualifying damaging bioinformatic evidence
TP53 VCEP BA1 requires FAF ≥ 0.001
TP53 VCEP BS1 requires FAF ≥ 0.0003 and < 0.001
TP53 VCEP PS2 point-based de novo framework
TP53 VCEP PS4 point-based proband framework
TP53 VCEP PP4 low-VAF constitutional mosaicism framework
TP53 VCEP BS2 unaffected older female carrier framework
TP53 VCEP / PVS1 decision tree: not applicable to this missense variant
Not applicable in TP53 VCEP
Not applicable in TP53 VCEP
Not applicable in TP53 VCEP
Not applicable in TP53 VCEP
Not applicable in TP53 VCEP
Not applicable in TP53 VCEP
Not applicable in TP53 VCEP
Not applicable in TP53 VCEP
Not applicable in TP53 VCEP
TP53 VCEP BP7 variant-type restriction
Every interpreted variant in TP53, mapped onto the exon structure of NM_000546.5. Select a row to find it on the plot.
| Protein | Location | Classification | Link |
|---|
| European (non-Finnish)7 / 1,179,982 | 5.9e-06 |
| European (non-Finnish)1 / 113,352 | 8.8e-06 |
This variant is present in gnomAD v4.1 (AF= 4.33716e-06; MAF= 0.00043%, 7/1613958 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 5.93229e-06; MAF= 0.00059%, 7/1179982 alleles, homozygotes = 0); grpmax FAF= 2.47e-06.
This variant is present in gnomAD v2.1 (AF= 3.98721e-06; MAF= 0.00040%, 1/250802 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.82208e-06; MAF= 0.00088%, 1/113352 alleles, homozygotes = 0).
Absent from gnomAD-Canada v1.0.
TP53 VCEP BP4 Moderate
TP53 VCEP PP3 requires qualifying damaging bioinformatic evidence
TP53 VCEP BP7 variant-type restriction
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.138. BayesDel score = -0.347259.
9 paper records listed. No publication is explicitly linked to an applied criterion in the recorded metadata. None of the listed paper records explicitly indicates that the variant is named.
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
This variant is present in gnomAD v4.1 (AF= 4.33716e-06; MAF= 0.00043%, 7/1613958 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 5.93229e-06; MAF= 0.00059%, 7/1179982 alleles, homozygotes = 0); grpmax FAF= 2.47e-06.
This variant is present in gnomAD v2.1 (AF= 3.98721e-06; MAF= 0.00040%, 1/250802 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.82208e-06; MAF= 0.00088%, 1/113352 alleles, homozygotes = 0).
Absent from gnomAD-Canada v1.0.
This variant has been reported in ClinVar as Uncertain significance (6 clinical laboratories) and as Likely benign (3 clinical laboratories) and as Uncertain Significance (1 clinical laboratory) and as Likely Benign by ClinGen TP53 Variant Curation Expert Panel, ClinGen (expert panel). (ClinVarID = 234059)
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.138. BayesDel score = -0.347259.
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. TP53, a tumor suppressor in the DNA damage pathway, is the most frequently mutated gene in cancer.
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
This variant does not lie in a statistically significant hotspot.