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 absent from gnomAD v2.1 and gnomAD v4.1, which is below the TP53 VCEP PM2_Supporting threshold of less than 0.00003 overall allele frequency and supports rarity in population databases.
Published TP53 functional evidence supports normal or near-normal protein function rather than loss of function. In the TP53 functional worksheet, p.His115Arg is listed as Functional in Kato data and noLOF in both Giacomelli and Kotler data, and the pre-assigned TP53 VCEP functional code is BS3.
Available computational evidence supports a benign interpretation under TP53 VCEP rules. The TP53 PP3/BP4 worksheet assigns BP4 for c.344A>G, BayesDel is 0.0464313 which is below the TP53 PP3 threshold of 0.16 and within the BP4-supporting range, and SpliceAI predicts no significant splice effect with a maximum delta score of 0.03 below the 0.2 threshold. REVEL is 0.484 and does not override the TP53 VCEP-specific BP4 assignment.
Expert panel ClinGen TP53 Variant Curation Expert Panel, ClinGen classified as Likely benign.
TP53 VCEP v2.4.0 Tavtigian point framework: BS3_Strong (-4) + BP4_Supporting (-1) + PM2_Supporting (+1) = -4 points.
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1 allele counts were not recorded for this variant.
Absent from gnomAD v2.1.
Recorded SpliceAI maximum delta score: 0.030. Refer to the recorded PP3/BP4 rationale for interpretation.
A ClinVar laboratory submission summary was not recorded.
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.
No COSMIC evidence statement is recorded in this case.
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 · 5 not met · 8 not assessed · 11 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
The TP53 c.344A>G (p.His115Arg) variant has not been observed in somatic cancers in COSMIC and has been reported in ClinVar, where the ClinGen TP53 Variant Curation Expert Panel classifies it as Likely Benign.
This variant is absent from gnomAD v2.1 and gnomAD v4.1, which is below the TP53 VCEP PM2_Supporting threshold of less than 0.00003 and supports rarity in population databases.
In TP53 functional studies summarized by the TP53 VCEP functional worksheet, p.His115Arg was functional in Kato data and showed no loss of function in Giacomelli and Kotler data, supporting BS3.
TP53-specific in silico assessment assigns BP4 because BayesDel is 0.0464313, below the TP53 PP3 threshold of 0.16, and SpliceAI predicts no meaningful splice effect with a maximum delta score of 0.03 below the 0.2 threshold; REVEL is 0.484.
No criteria match.
TP53 VCEP PM2 is applied at Supporting strength for variants with allele frequency <0.00003 in large population datasets.
TP53 VCEP BS3 applies at Strong strength when Kato data are functional and the majority of eligible assays show no loss of function.
TP53 VCEP BP4_Supporting for missense variants applies when BayesDel is <0.16 and >-0.008 with no predicted splicing impact, defined as SpliceAI <0.2.
TP53 VCEP PS3 requires non-functional or partially functional assay results meeting the specified cross-assay pattern.
TP53 VCEP PM1 applies to codons 175, 245, 248, 249, 273, and 282, or to exact amino acid changes with qualifying cancerhotspots.org recurrence.
TP53 VCEP PP3 for missense variants requires qualifying aGVGD class with BayesDel >=0.16, or predicted splice impact with SpliceAI >=0.2 in the relevant contexts.
TP53 VCEP BA1 requires FAF >=0.001 in a qualifying continental subpopulation.
TP53 VCEP BS1 requires FAF >=0.0003 but <0.001 in a qualifying continental subpopulation.
TP53 VCEP PS1 requires the same amino acid change as a TP53 VCEP-classified pathogenic or likely pathogenic variant.
TP53 VCEP PS2 uses Li-Fraumeni syndrome point thresholds for confirmed de novo observations.
TP53 VCEP PS4 requires PM2_Supporting plus sufficient affected-individual points.
TP53 VCEP PM5 requires a different missense variant at the same residue previously classified as Pathogenic, or in limited circumstances Likely Pathogenic, under TP53 VCEP rules.
TP53 VCEP PP1 requires 3 or more informative meioses meeting phenotype criteria.
TP53 VCEP PP4 is reserved for specific low-VAF clinical observation contexts.
TP53 VCEP BS2 requires 2 or more unrelated older unaffected female carriers from a single source, depending on strength level.
TP53 VCEP BS4 requires lack of segregation in affected family members with relevant cancers.
TP53 VCEP PVS1 flowchart; missense variants without qualifying splicing/null evidence do not meet PVS1.
Not applicable per TP53 VCEP.
Not applicable per TP53 VCEP.
Not applicable per TP53 VCEP.
Not applicable per TP53 VCEP.
Not applicable per TP53 VCEP and SVI guidance.
Not applicable per TP53 VCEP.
Not applicable per TP53 VCEP.
Not applicable per TP53 VCEP.
Not applicable per TP53 VCEP.
TP53 VCEP BP7 applies to synonymous or qualifying intronic variants with no splice impact.
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 |
|---|
Absent from gnomAD v4.1.
Absent from gnomAD v2.1.
TP53 VCEP BP4_Supporting for missense variants applies when BayesDel is <0.16 and >-0.008 with no predicted splicing impact, defined as SpliceAI <0.2.
TP53 VCEP PP3 for missense variants requires qualifying aGVGD class with BayesDel >=0.16, or predicted splice impact with SpliceAI >=0.2 in the relevant contexts.
TP53 VCEP BP7 applies to synonymous or qualifying intronic variants with no splice impact.
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.03). REVEL score = 0.484. BayesDel score = 0.0464313.
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.
Absent from gnomAD v4.1.
Absent from gnomAD v2.1.
This variant has been reported in ClinVar as Uncertain significance (3 clinical laboratories) and as Likely benign (2 clinical laboratories) and as Uncertain Significance (1 clinical laboratory) and as Likely Benign by ClinGen TP53 Variant Curation Expert Panel, ClinGen (expert panel). (ClinVarID = 182925)
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.03). REVEL score = 0.484. BayesDel score = 0.0464313.
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.
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.