NM_000546.6(TP53):c.96+41_97-54del AND Hereditary cancer-predisposing syndrome

Germline classification:: Benign (2 submissions)
Last evaluated:: Jun 18, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000161045.5

Allele description [Variation Report for NM_000546.6(TP53):c.96+41_97-54del]

NM_000546.6(TP53):c.96+41_97-54del

Gene:

TP53:tumor protein p53 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

17p13.1

Genomic location:

Preferred name:

NM_000546.6(TP53):c.96+41_97-54del

HGVS:

NC_000017.11:g.7676335TCCAGGTCCCCAGCCC[1]
NG_017013.2:g.16194ACCTGGAGGGCTGGGG[1]
NM_000546.6:c.96+41_97-54delMANE SELECT
NM_001126112.3:c.96+41_97-54del
NM_001126113.3:c.96+41_97-54del
NM_001126114.3:c.96+41_97-54del
NM_001126118.2:c.-22+41_-21-54del
NM_001276695.3:c.-22+41_-21-54del
NM_001276696.3:c.-22+41_-21-54del
NM_001276760.3:c.-22+41_-21-54del
NM_001276761.3:c.-22+41_-21-54del
LRG_321t1:c.96+41_97-54del
LRG_321:g.16194ACCTGGAGGGCTGGGG[1]
NC_000017.10:g.7579653TCCAGGTCCCCAGCCC[1]
NC_000017.10:g.7579669_7579684delTCCAGGTCCCCAGCCC
NM_000546.4:c.96+16_96+31delGGGCTGGGGACCTGGA
NM_000546.5:c.96+41_97-54del

Links:

dbSNP: rs59758982

NCBI 1000 Genomes Browser:

rs59758982

Molecular consequence:

NM_000546.6:c.96+41_97-54del - intron variant - [Sequence Ontology: SO:0001627]
NM_001126112.3:c.96+41_97-54del - intron variant - [Sequence Ontology: SO:0001627]
NM_001126113.3:c.96+41_97-54del - intron variant - [Sequence Ontology: SO:0001627]
NM_001126114.3:c.96+41_97-54del - intron variant - [Sequence Ontology: SO:0001627]
NM_001126118.2:c.-22+41_-21-54del - intron variant - [Sequence Ontology: SO:0001627]
NM_001276695.3:c.-22+41_-21-54del - intron variant - [Sequence Ontology: SO:0001627]
NM_001276696.3:c.-22+41_-21-54del - intron variant - [Sequence Ontology: SO:0001627]
NM_001276760.3:c.-22+41_-21-54del - intron variant - [Sequence Ontology: SO:0001627]
NM_001276761.3:c.-22+41_-21-54del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Chain A, PUTATIVE GDP-FUCOSE PROTEIN O-FUCOSYLTRANSFERASE 1
Chain A, PUTATIVE GDP-FUCOSE PROTEIN O-FUCOSYLTRANSFERASE 1
gi|346652124|pdb|3ZY5|A

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002582432	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Jun 18, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002582432

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign
(Jun 18, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From GeneDx, SCV000211775.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The variant is found in HEREDICANCER,COLO-HEREDIC,BR-OV-HEREDIC panel(s).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Genome-Nilou Lab, SCV002582432.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Flagged submissions

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000211775	GeneDx	flagged submission Reason: This record appears to be redundant with a more recent record from the same submitter. Notes: SCV000211775 appears to be redundant with SCV001849336. (GeneDx Variant Classification (06012015))	Benign (Oct 15, 2013)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000211775

GeneDx

flagged submission

Reason: This record appears to be redundant with a more recent record from the same submitter.

Notes: SCV000211775 appears to be redundant with SCV001849336.

(GeneDx Variant Classification (06012015))

Benign
(Oct 15, 2013)

germline

clinical testing

Citation Link

Last Updated: Dec 24, 2023

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