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NM_000546.6(TP53):c.248C>T (p.Ala83Val)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(4);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
7 (Most recent: Jul 16, 2021)
Last evaluated:
Nov 20, 2020
Accession:
VCV000127805.11
Variation ID:
127805
Description:
single nucleotide variant
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NM_000546.6(TP53):c.248C>T (p.Ala83Val)

Allele ID
133262
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
17p13.1
Genomic location
17: 7676121 (GRCh38) GRCh38 UCSC
17: 7579439 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_321:g.16430C>T
LRG_321t1:c.248C>T
LRG_321t6:c.-906C>T
... more HGVS
Protein change
A44V, A83V
Other names
p.A83V:GCG>GTG
Canonical SPDI
NC_000017.11:7676120:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (A)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00003
The Genome Aggregation Database (gnomAD) 0.00006
1000 Genomes Project 0.00020
Trans-Omics for Precision Medicine (TOPMed) 0.00004
Links
ClinGen: CA000083
UniProtKB: P04637#VAR_044624
dbSNP: rs201717599
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts May 20, 2020 RCV000115716.11
Uncertain significance 1 criteria provided, single submitter Oct 13, 2016 RCV000409540.1
Likely benign 1 criteria provided, single submitter Nov 20, 2020 RCV001082818.2
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Jul 26, 2020 RCV000679367.6
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
TP53 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
2215 2278

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Oct 13, 2016)
criteria provided, single submitter
Method: clinical testing
Li-Fraumeni syndrome 1
Allele origin: unknown
Counsyl
Accession: SCV000489472.1
Submitted: (Nov 23, 2016)
Evidence details
Likely benign
(Sep 23, 2018)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000187107.7
Submitted: (Nov 30, 2020)
Evidence details
Publications
PubMed (3)
Comment:
Does not segregate with disease in family study (genes with incomplete penetrance);In silico models in agreement (benign)
Likely benign
(Nov 20, 2020)
criteria provided, single submitter
Method: clinical testing
Li-Fraumeni syndrome
Allele origin: germline
Invitae
Accession: SCV000166396.8
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Jul 26, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000149625.14
Submitted: (Jul 16, 2021)
Evidence details
Comment:
In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; This variant is associated with the … (more)
Uncertain significance
(Dec 30, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000806236.1
Submitted: (Jan 29, 2018)
Evidence details
Likely benign
(May 09, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV001134864.2
Submitted: (Mar 06, 2020)
Evidence details
Publications
PubMed (1)
Benign
(May 20, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000910716.2
Submitted: (Jun 11, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Variable population prevalence estimates of germline TP53 variants: A gnomAD-based analysis. de Andrade KC Human mutation 2019 PMID: 30352134
Genome sequencing identifies a basis for everolimus sensitivity. Iyer G Science (New York, N.Y.) 2012 PMID: 22923433
INK4a/ARF locus alterations in human non-Hodgkin's lymphomas mainly occur in tumors with wild-type p53 gene. Pinyol M The American journal of pathology 2000 PMID: 10854221
Frequency and diversity of p53 mutations in childhood rhabdomyosarcoma. Felix CA Cancer research 1992 PMID: 1559227

Text-mined citations for rs201717599...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021