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Variant interpretation report

TP53 c.344A>G, p.(His115Arg)

NM_000546.5:c.344A>G NP_000537.3:p.(His115Arg) View identifiers
Classification
Likely benign

Variant description:

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.

In plain language

Gene-level background from the recorded interpretation.

About TP53

No gene-level summary was recorded for this case.

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.
01The reasoning

How it was classified

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.

Recorded applied criteria

The applied criteria and their strengths are shown as assessed under the stated framework.

Pathogenic evidence criteria: 1 Benign evidence criteria: 3
Pathogenic criteria applied · 1
PM2Supporting
PM2 · supporting

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.

Benign criteria applied · 3
BS3Strong
BS3 · strong

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.

BP4Supporting
BP4 · supporting

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.

BP6Supporting
BP6 · supporting

Expert panel ClinGen TP53 Variant Curation Expert Panel, ClinGen classified as Likely benign.

Recorded classification: Likely benign

TP53 VCEP v2.4.0 Tavtigian point framework: BS3_Strong (-4) + BP4_Supporting (-1) + PM2_Supporting (+1) = -4 points.

02The sources

Evidence at a glance

Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.

SpliceAI score
0.030 maximum delta

Recorded SpliceAI maximum delta score: 0.030. Refer to the recorded PP3/BP4 rationale for interpretation.

Functional evidence
Statement 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.

COSMIC
Cancer Hotspots
Somatic evidence
Not assessed

No COSMIC evidence statement is recorded in this case.

Cancer Hotspots

This variant does not lie in a statistically significant hotspot.

For specialists

Technical detail

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.

Met Not met Not assessed Not applicable

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.

Met · 4

PM2 SupportingThis 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. Details ▾Hide ▴
Rule
TP53 VCEP PM2 is applied at Supporting strength for variants with allele frequency <0.00003 in large population datasets.
Evidence considered
  • Absent from gnomAD v2.1
  • Absent from gnomAD v4.1
Sources
BS3 StrongPublished 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. Details ▾Hide ▴
Rule
TP53 VCEP BS3 applies at Strong strength when Kato data are functional and the majority of eligible assays show no loss of function.
Evidence considered
  • Functional worksheet row for H115R: Functional in Kato
  • noLOF in Giacomelli
  • noLOF in Kotler
  • preliminary code BS3
Sources
vcep_functional_worksheetvcep_flowchart_for_application_of_functional_rule_codesPMID:12826609 ↗PMID:29979965 ↗
BP4 SupportingAvailable 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. Details ▾Hide ▴
Rule
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.
Evidence considered
  • PP3/BP4 worksheet row for c.344A>G assigns BP4
  • BayesDel 0.0464313
  • SpliceAI max delta 0.03
  • REVEL 0.484
Sources
cspec ↗vcep_pp3_bp4_codesvcep_flowchart_for_application_of_pp3_2c_bp4_2c_and_bp7bayesdelspliceai ↗revel
BP6 SupportingExpert panel ClinGen TP53 Variant Curation Expert Panel, ClinGen classified as Likely benign. Details ▾Hide ▴
Rule
Not applicable per TP53 VCEP and SVI guidance.
Evidence considered
  • TP53 VCEP marks BP6 as not applicable
  • ClinVar expert panel classification
Sources

Not met · 5 · evaluated, threshold not reached

PS3 Available TP53 functional evidence does not support a damaging effect sufficient for PS3. The TP53 functional worksheet lists p.His115Arg as Functional in Kato data, with no loss of function in Giacomelli and Kotler data, and assigns a preliminary benign functional code instead of PS3. Details ▾Hide ▴
Rule
TP53 VCEP PS3 requires non-functional or partially functional assay results meeting the specified cross-assay pattern.
Evidence considered
  • Functional worksheet row for H115R: Functional / noLOF / noLOF / BS3
Sources
vcep_functional_worksheetvcep_flowchart_for_application_of_functional_rule_codesPMID:12826609 ↗PMID:29979965 ↗
PM1 This missense change is not at one of the TP53 codons predefined for PM1 application, and reviewed hotspot evidence did not show a statistically significant somatic hotspot or recurrent exact amino acid change count sufficient for TP53 PM1. Details ▾Hide ▴
Rule
TP53 VCEP PM1 applies to codons 175, 245, 248, 249, 273, and 282, or to exact amino acid changes with qualifying cancerhotspots.org recurrence.
Evidence considered
  • TP53 VCEP PM1 codon list excludes codon 115
  • Cancer Hotspots review did not identify a significant hotspot row for H115
Sources
PP3 Available computational evidence does not support a damaging prediction 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 SpliceAI predicts no significant splice effect with a maximum delta score of 0.03 below the 0.2 threshold. REVEL is 0.484 but TP53 VCEP PP3/BP4 uses BayesDel with splice review rather than REVEL for code assignment. Details ▾Hide ▴
Rule
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.
Evidence considered
  • PP3/BP4 worksheet row for c.344A>G assigns BP4
  • BayesDel 0.0464313
  • SpliceAI max delta 0.03
  • REVEL 0.484
Sources
cspec ↗vcep_pp3_bp4_codesvcep_flowchart_for_application_of_pp3_2c_bp4_2c_and_bp7bayesdelspliceai ↗revel
BA1 This variant is absent from gnomAD v2.1 and gnomAD v4.1 and therefore does not meet the TP53 VCEP BA1 threshold of filtering allele frequency at or above 0.001. Details ▾Hide ▴
Rule
TP53 VCEP BA1 requires FAF >=0.001 in a qualifying continental subpopulation.
Evidence considered
  • Absent from gnomAD v2.1
  • Absent from gnomAD v4.1
Sources
BS1 This variant is absent from gnomAD v2.1 and gnomAD v4.1 and therefore does not meet the TP53 VCEP BS1 threshold of filtering allele frequency at or above 0.0003. Details ▾Hide ▴
Rule
TP53 VCEP BS1 requires FAF >=0.0003 but <0.001 in a qualifying continental subpopulation.
Evidence considered
  • Absent from gnomAD v2.1
  • Absent from gnomAD v4.1
Sources

Not assessed · 8 · no assessment recorded

PS1 No reviewed evidence identified an established TP53 VCEP Pathogenic or Likely Pathogenic variant that creates the same amino acid change, so PS1 was not assessed. Details ▾Hide ▴
Rule
TP53 VCEP PS1 requires the same amino acid change as a TP53 VCEP-classified pathogenic or likely pathogenic variant.
Evidence considered
  • ClinVar record was reviewed for the current variant
Still missing
  • Direct same-amino-acid comparator review was not established from the reviewed sources.
Sources
PS2 No confirmed de novo observations with appropriate parental confirmation were identified, so PS2 was not assessed. Details ▾Hide ▴
Rule
TP53 VCEP PS2 uses Li-Fraumeni syndrome point thresholds for confirmed de novo observations.
Evidence considered
  • TP53 VCEP PS2 point-based thresholds were reviewed
Still missing
  • No proband-level de novo data were identified.
Sources
cspec ↗vcep_table_of_lfs_cancers_and_points_for_ps2_and_pp1_code_application
PS4 No proband-based Li-Fraumeni syndrome point total was identified for this variant, so PS4 was not assessed. Details ▾Hide ▴
Rule
TP53 VCEP PS4 requires PM2_Supporting plus sufficient affected-individual points.
Evidence considered
  • Population rarity reviewed
  • TP53 VCEP PS4 point thresholds reviewed
Still missing
  • No affected proband count or phenotype point total was established.
  • TP53 VCEP requires PM2_Supporting before PS4 can be applied
  • but qualifying case-level observations were not identified.
Sources
PM5 TP53 uses classic same-residue missense PM5 logic, but no validated previously classified pathogenic or likely pathogenic same-residue comparator was established from the reviewed materials, so PM5 was not assessed. Details ▾Hide ▴
Rule
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.
Evidence considered
  • PM5 candidate artifact was reviewed but did not provide a usable comparator determination
Still missing
  • No confirmed TP53 VCEP same-residue pathogenic or likely pathogenic comparator was identified.
Sources
cspec ↗pm5_candidatesclinvar ↗
PP1 No segregation data were identified to show cosegregation with Li-Fraumeni syndrome-associated cancers, so PP1 was not assessed. Details ▾Hide ▴
Rule
TP53 VCEP PP1 requires 3 or more informative meioses meeting phenotype criteria.
Evidence considered
  • TP53 VCEP PP1 meiosis thresholds reviewed
Still missing
  • No informative meiosis count or family segregation data were identified.
Sources
cspec ↗vcep_table_of_lfs_cancers_and_points_for_ps2_and_pp1_code_application
PP4 No low-variant-allele-fraction constitutional mosaicism evidence or other qualifying TP53-specific phenotype data were identified, so PP4 was not assessed. Details ▾Hide ▴
Rule
TP53 VCEP PP4 is reserved for specific low-VAF clinical observation contexts.
Evidence considered
  • TP53 VCEP PP4 criteria reviewed
Still missing
  • No qualifying VAF-based clinical observation data were identified.
Sources
BS2 No single-source series of unaffected females age 60 years or older carrying this variant was identified, so BS2 was not assessed. Details ▾Hide ▴
Rule
TP53 VCEP BS2 requires 2 or more unrelated older unaffected female carriers from a single source, depending on strength level.
Evidence considered
  • TP53 VCEP BS2 thresholds reviewed
Still missing
  • No qualifying unaffected carrier dataset was identified.
Sources
BS4 No lack-of-segregation data in affected relatives with Li-Fraumeni syndrome-associated cancers were identified, so BS4 was not assessed. Details ▾Hide ▴
Rule
TP53 VCEP BS4 requires lack of segregation in affected family members with relevant cancers.
Evidence considered
  • TP53 VCEP BS4 criterion reviewed
Still missing
  • No informative non-segregation data were identified.
Sources
Not applicable · 11· recorded as not applicable Show reasons ▾Hide reasons ▴
PVS1 N/AThis variant is a missense substitution, and available evidence does not indicate a nonsense, frameshift, canonical +/-1,2 splice, or other TP53 null-variant mechanism required for PVS1 application. Details ▾Hide ▴
Rule
TP53 VCEP PVS1 flowchart; missense variants without qualifying splicing/null evidence do not meet PVS1.
Evidence considered
  • TP53 VCEP includes PVS1 for null-variant mechanisms
  • Variant-level PVS1 scaffold does not place c.344A>G in a PVS1-eligible bucket
Sources
pvs1_gene_contextpvs1_variant_assessmentcspec ↗vcep_pvs1_flowchart
PM3 VCEPPM3 is not applicable in the TP53 VCEP framework for this disorder context. Details ▾Hide ▴
VCEP rule
Not applicable per TP53 VCEP.
Evidence considered
  • TP53 VCEP marks PM3 as not applicable
Sources
PM4 VCEPPM4 is not applicable because this variant is a missense substitution and the TP53 VCEP does not use PM4 in this context. Details ▾Hide ▴
VCEP rule
Not applicable per TP53 VCEP.
Evidence considered
  • TP53 VCEP marks PM4 as not applicable
Sources
PM6 VCEPPM6 is not applicable in the TP53 VCEP framework. Details ▾Hide ▴
VCEP rule
Not applicable per TP53 VCEP.
Evidence considered
  • TP53 VCEP marks PM6 as not applicable
Sources
PP2 VCEPPP2 is not applicable in the TP53 VCEP framework. Details ▾Hide ▴
VCEP rule
Not applicable per TP53 VCEP.
Evidence considered
  • TP53 VCEP marks PP2 as not applicable
Sources
PP5 VCEPPP5 is not for use in the TP53 VCEP framework. Details ▾Hide ▴
VCEP rule
Not applicable per TP53 VCEP and SVI guidance.
Evidence considered
  • TP53 VCEP marks PP5 as not applicable
Sources
BP1 VCEPBP1 is not applicable in the TP53 VCEP framework. Details ▾Hide ▴
VCEP rule
Not applicable per TP53 VCEP.
Evidence considered
  • TP53 VCEP marks BP1 as not applicable
Sources
BP2 VCEPBP2 is not applicable in the TP53 VCEP framework. Details ▾Hide ▴
VCEP rule
Not applicable per TP53 VCEP.
Evidence considered
  • TP53 VCEP marks BP2 as not applicable
Sources
BP3 VCEPBP3 is not applicable because this variant is not an in-frame indel in a repetitive region, and the TP53 VCEP does not use BP3 here. Details ▾Hide ▴
VCEP rule
Not applicable per TP53 VCEP.
Evidence considered
  • TP53 VCEP marks BP3 as not applicable
Sources
BP5 VCEPBP5 is not applicable in the TP53 VCEP framework. Details ▾Hide ▴
VCEP rule
Not applicable per TP53 VCEP.
Evidence considered
  • TP53 VCEP marks BP5 as not applicable
Sources
BP7 N/ABP7 is intended for synonymous or certain intronic variants and is not applicable to this missense substitution. Details ▾Hide ▴
Rule
TP53 VCEP BP7 applies to synonymous or qualifying intronic variants with no splice impact.
Evidence considered
  • Variant is missense
  • not synonymous or intronic
Sources
cspec ↗vcep_flowchart_for_application_of_pp3_2c_bp4_2c_and_bp7

Identifiers

Gene
TP53
Transcript
NM_000546.5
Coding (HGVS c.)
NM_000546.5:c.344A>G
Protein (HGVS p.)
NP_000537.3:p.(His115Arg)
GRCh38
chr17:7676025 T>C
GRCh37
chr17:7579343 T>C
ClinVar
406595, 182925

Gene diagram

Every interpreted variant in TP53, mapped onto the exon structure of NM_000546.5. Select a row to find it on the plot.

TP53NM_000546.5
Fetching transcript structure from UCSC…
gnomAD v4.1 Allele count data not recorded
gnomAD v2.1 Allele count data not recorded

Statements

gnomAD v4.1

Absent from gnomAD v4.1.

gnomAD v2.1

Absent from gnomAD v2.1.

SpliceAI and Pangolin

SpliceAI acceptor lossat +228 bp
0.000
SpliceAI acceptor gainat +43 bp
0.030
SpliceAI donor lossat +169 bp
0.020
SpliceAI donor gainat -31 bp
0.000
Pangolin splice lossmagnitude shown
-0.000
Pangolin splice gain
0.040

Other predictors

REVEL
0.484
BayesDel
0.046

How the predictions were used

BP4 SupportingAvailable 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. Details ▾Hide ▴
Rule
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.
Evidence considered
  • PP3/BP4 worksheet row for c.344A>G assigns BP4
  • BayesDel 0.0464313
  • SpliceAI max delta 0.03
  • REVEL 0.484
Sources
cspec ↗vcep_pp3_bp4_codesvcep_flowchart_for_application_of_pp3_2c_bp4_2c_and_bp7bayesdelspliceai ↗revel
PP3 Available computational evidence does not support a damaging prediction 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 SpliceAI predicts no significant splice effect with a maximum delta score of 0.03 below the 0.2 threshold. REVEL is 0.484 but TP53 VCEP PP3/BP4 uses BayesDel with splice review rather than REVEL for code assignment. Details ▾Hide ▴
Rule
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.
Evidence considered
  • PP3/BP4 worksheet row for c.344A>G assigns BP4
  • BayesDel 0.0464313
  • SpliceAI max delta 0.03
  • REVEL 0.484
Sources
cspec ↗vcep_pp3_bp4_codesvcep_flowchart_for_application_of_pp3_2c_bp4_2c_and_bp7bayesdelspliceai ↗revel
BP7 N/ABP7 is intended for synonymous or certain intronic variants and is not applicable to this missense substitution. Details ▾Hide ▴
Rule
TP53 VCEP BP7 applies to synonymous or qualifying intronic variants with no splice impact.
Evidence considered
  • Variant is missense
  • not synonymous or intronic
Sources
cspec ↗vcep_flowchart_for_application_of_pp3_2c_bp4_2c_and_bp7

Statement

In silico

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.

Recorded publications

  • Rescuing the function of mutant p53.
    No paper-specific finding is recorded.
    PMID 11900253 ↗
  • Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations.
    No paper-specific finding is recorded.
    PMID 8023157 ↗
  • p53 mutants exhibiting enhanced transcriptional activation and altered promoter selectivity are revealed using a sensitive, yeast-based functional assay.
    Inga A et al. · 2001
    No paper-specific finding is recorded.
    PMID 11313981 ↗
  • Understanding the function-structure and function-mutation relationships of p53 tumor suppressor protein by high-resolution missense mutation analysis.
    Kato S et al. · 2003
    No paper-specific finding is recorded.
    PMID 12826609 ↗
  • Mutational analysis of the p53 core domain L1 loop.
    Zupnick A et al. · 2006
    No paper-specific finding is recorded.
    PMID 16687402 ↗
  • Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.
    No paper-specific finding is recorded.
    PMID 25741868 ↗
  • Higher-than-expected population prevalence of potentially pathogenic germline TP53 variants in individuals unselected for cancer history.
    de Andrade KC et al. · 2017
    No paper-specific finding is recorded.
    PMID 28861920 ↗
  • A Systematic p53 Mutation Library Links Differential Functional Impact to Cancer Mutation Pattern and Evolutionary Conservation.
    Kotler E et al. · 2018
    No paper-specific finding is recorded.
    PMID 29979965 ↗
  • Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
    No paper-specific finding is recorded.
    PMID 28492532 ↗

Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.

All source links

Statements for reports

The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.

gnomAD v4.1

Absent from gnomAD v4.1.

gnomAD v2.1

Absent from gnomAD v2.1.

ClinVar

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)

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.03). REVEL score = 0.484. BayesDel score = 0.0464313.

Functional

OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.

Somatic

This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).

Cancer Hotspots

This variant does not lie in a statistically significant hotspot.