NM_000546.5(TP53):c.782+10C>T AND not specified

Clinical significance:Benign/Likely benign (Last evaluated: Oct 22, 2020)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000422316.2

Allele description [Variation Report for NM_000546.5(TP53):c.782+10C>T]

NM_000546.5(TP53):c.782+10C>T

Gene:
TP53:tumor protein p53 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17p13.1
Genomic location:
Preferred name:
NM_000546.5(TP53):c.782+10C>T
HGVS:
  • NC_000017.11:g.7674171G>A
  • NG_017013.2:g.18380C>T
  • NM_000546.5:c.782+10C>T
  • NM_001126112.2:c.782+10C>T
  • NM_001126113.2:c.782+10C>T
  • NM_001126114.2:c.782+10C>T
  • NM_001126115.1:c.386+10C>T
  • NM_001126116.1:c.386+10C>T
  • NM_001126117.1:c.386+10C>T
  • NM_001126118.1:c.665+10C>T
  • NM_001276695.2:c.665+10C>T
  • NM_001276696.2:c.665+10C>T
  • NM_001276697.2:c.305+10C>T
  • NM_001276698.2:c.305+10C>T
  • NM_001276699.2:c.305+10C>T
  • NM_001276760.2:c.665+10C>T
  • NM_001276761.2:c.665+10C>T
  • LRG_321t1:c.782+10C>T
  • LRG_321t2:c.782+10C>T
  • LRG_321t3:c.782+10C>T
  • LRG_321t4:c.782+10C>T
  • LRG_321t5:c.386+10C>T
  • LRG_321t6:c.386+10C>T
  • LRG_321t7:c.386+10C>T
  • LRG_321t8:c.665+10C>T
  • LRG_321:g.18380C>T
  • NC_000017.10:g.7577489G>A
  • NM_000546.4:c.782+10C>T
Links:
dbSNP: rs200277687
NCBI 1000 Genomes Browser:
rs200277687
Molecular consequence:
  • NM_000546.5:c.782+10C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001126112.2:c.782+10C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001126113.2:c.782+10C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001126114.2:c.782+10C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001126115.1:c.386+10C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001126116.1:c.386+10C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001126117.1:c.386+10C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001126118.1:c.665+10C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001276695.2:c.665+10C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001276696.2:c.665+10C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001276697.2:c.305+10C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001276698.2:c.305+10C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001276699.2:c.305+10C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001276760.2:c.665+10C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001276761.2:c.665+10C>T - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000514942GeneDxcriteria provided, single submitter
Benign
(Mar 19, 2015)
germlineclinical testing

Citation Link,

SCV001442709Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Likely benign
(Oct 22, 2020)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

TP53 mutations in human cancer: database reassessment and prospects for the next decade.

Leroy B, Anderson M, Soussi T.

Hum Mutat. 2014 Jun;35(6):672-88. doi: 10.1002/humu.22552. Review.

PubMed [citation]
PMID:
24665023

Identification and characterization of TP53 gene Allele Dropout in Li-Fraumeni syndrome and Oral cancer cohorts.

Haque MM, Kowtal P, Sarin R.

Sci Rep. 2018 Aug 3;8(1):11705. doi: 10.1038/s41598-018-30238-7.

PubMed [citation]
PMID:
30076369
PMCID:
PMC6076284

Details of each submission

From GeneDx, SCV000514942.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001442709.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

Variant summary: TP53 c.782+10C>T alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 4/4 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 1.6e-05 in 251330 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.782+10C>T in individuals affected with Li-Fraumeni Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as benign/likely benign. Based on the evidence outlined above, the variant was classified as likely benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jun 14, 2021

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