NM_000546.6(TP53):c.74+9A>C AND Li-Fraumeni syndrome 1

Germline classification:: Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:: Apr 11, 2023
Review status:: criteria provided, conflicting classifications

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:: RCV000410984.11

Allele description [Variation Report for NM_000546.6(TP53):c.74+9A>C]

NM_000546.6(TP53):c.74+9A>C

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

17p13.1

Genomic location:

Preferred name:

NM_000546.6(TP53):c.74+9A>C

HGVS:

NC_000017.11:g.7676512T>G
NG_017013.2:g.16039A>C
NM_000546.6:c.74+9A>CMANE SELECT
NM_001126112.3:c.74+9A>C
NM_001126113.3:c.74+9A>C
NM_001126114.3:c.74+9A>C
NM_001126118.2:c.-152A>C
NM_001276695.3:c.-44+9A>C
NM_001276696.3:c.-44+9A>C
NM_001276760.3:c.-44+9A>C
NM_001276761.3:c.-44+9A>C
LRG_321t1:c.74+9A>C
LRG_321:g.16039A>C
NC_000017.10:g.7579830T>G
NM_000546.5:c.74+9A>C

Links:

dbSNP: rs1057517593

NCBI 1000 Genomes Browser:

rs1057517593

Molecular consequence:

NM_001126118.2:c.-152A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000546.6:c.74+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001126112.3:c.74+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001126113.3:c.74+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001126114.3:c.74+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001276695.3:c.-44+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001276696.3:c.-44+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001276760.3:c.-44+9A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001276761.3:c.-44+9A>C - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Li-Fraumeni syndrome 1 (LFS)
Identifiers:: Gene: 553989; MedGen: C1835398; Orphanet: 524; OMIM: 151623

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Rattus norvegicus psa mRNA for puromycin-sensitive aminopeptidase, partial cds
gi|17221642|dbj|AB062596.1|

Nucleotide
Homo sapiens cDNA FLJ13449 fis, clone PLACE1003025
Homo sapiens cDNA FLJ13449 fis, clone PLACE1003025
gi|10435465|dbj|AK023511.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000489244	Counsyl	criteria provided, single submitter (Counsyl Autosomal Dominant Disease Classification criteria (2015))	Likely benign (Sep 7, 2016)	unknown	clinical testing	Counsyl Autosomal Dominant Disease Classification criteria (2015), Citation Link,
SCV001283246	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Uncertain significance (Apr 27, 2017)	germline	clinical testing	Citation Link,
SCV004017889	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Likely benign (Apr 11, 2023)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000489244

Counsyl

criteria provided, single submitter

(Counsyl Autosomal Dominant Disease Classification criteria (2015))

Likely benign
(Sep 7, 2016)

unknown

clinical testing

Counsyl Autosomal Dominant Disease Classification criteria (2015),

Citation Link,

SCV001283246

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Uncertain significance
(Apr 27, 2017)

germline

clinical testing

Citation Link,

SCV004017889

Myriad Genetics, Inc.

criteria provided, single submitter

(Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))

Likely benign
(Apr 11, 2023)

unknown

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Counsyl, SCV000489244.2

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

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

From Illumina Laboratory Services, Illumina, SCV001283246.1

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

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.

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

From Myriad Genetics, Inc., SCV004017889.1

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

Description

This variant is considered likely benign. This variant is intronic and is not expected to impact mRNA splicing.

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

Last Updated: Nov 10, 2024

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