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NM_000546.6(TP53):c.891C>T (p.His297=) AND Malignant tumor of breast

Germline classification:
Likely benign (1 submission)
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV001356137.4

Allele description [Variation Report for NM_000546.6(TP53):c.891C>T (p.His297=)]

NM_000546.6(TP53):c.891C>T (p.His297=)

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.891C>T (p.His297=)
HGVS:
  • NC_000017.11:g.7673729G>A
  • NG_017013.2:g.18822C>T
  • NM_000546.6:c.891C>TMANE SELECT
  • NM_001126112.3:c.891C>T
  • NM_001126113.3:c.891C>T
  • NM_001126114.3:c.891C>T
  • NM_001126115.2:c.495C>T
  • NM_001126116.2:c.495C>T
  • NM_001126117.2:c.495C>T
  • NM_001126118.2:c.774C>T
  • NM_001276695.3:c.774C>T
  • NM_001276696.3:c.774C>T
  • NM_001276697.3:c.414C>T
  • NM_001276698.3:c.414C>T
  • NM_001276699.3:c.414C>T
  • NM_001276760.3:c.774C>T
  • NM_001276761.3:c.774C>T
  • NP_000537.3:p.His297=
  • NP_000537.3:p.His297=
  • NP_001119584.1:p.His297=
  • NP_001119585.1:p.His297=
  • NP_001119586.1:p.His297=
  • NP_001119587.1:p.His165=
  • NP_001119588.1:p.His165=
  • NP_001119589.1:p.His165=
  • NP_001119590.1:p.His258=
  • NP_001263624.1:p.His258=
  • NP_001263625.1:p.His258=
  • NP_001263626.1:p.His138=
  • NP_001263627.1:p.His138=
  • NP_001263628.1:p.His138=
  • NP_001263689.1:p.His258=
  • NP_001263690.1:p.His258=
  • LRG_321t1:c.891C>T
  • LRG_321:g.18822C>T
  • LRG_321p1:p.His297=
  • NC_000017.10:g.7577047G>A
  • NM_000546.4:c.891C>T
  • NM_000546.5:c.891C>T
  • p.H297H
  • p.His297His
Links:
dbSNP: rs750578863
NCBI 1000 Genomes Browser:
rs750578863
Molecular consequence:
  • NM_000546.6:c.891C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001126112.3:c.891C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001126113.3:c.891C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001126114.3:c.891C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001126115.2:c.495C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001126116.2:c.495C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001126117.2:c.495C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001126118.2:c.774C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001276695.3:c.774C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001276696.3:c.774C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001276697.3:c.414C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001276698.3:c.414C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001276699.3:c.414C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001276760.3:c.774C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001276761.3:c.774C>T - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
1

Condition(s)

Name:
Malignant tumor of breast
Synonyms:
Malignant breast neoplasm; Cancer breast
Identifiers:
MONDO: MONDO:0007254; MedGen: C0006142

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001551211Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria provided
Likely benignunknownclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyes1not providednot providednot providednot providedclinical testing

Details of each submission

From Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV001551211.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The TP53 p.His297= variant was not identified in the literature nor was it identified in the Cosmic, LOVD 3.0, UMD TP53 Mutation Database, or Database of germline p53 mutations databases. The variant was identified in dbSBP (ID: rs750578863) as “With Likely benign allele,” ClinVar (as likely benign by Ambry Genetics and GeneDx), Clinvitae, and IARC TP53 Database. The variant was identified in control databases in 4 of 277226 chromosomes at a frequency of 0.000014 in the following populations: African in 2 of 24024 chromosomes (freq: 0.00008), Latino in 1 of 34420 chromosomes (freq. 0.00003), and European (Non-Finnish) in 1 of 126726 chromosomes (freq. 0.000008) increasing the likelihood that this may be a low frequency benign variant in certain populations of origin (Genome Aggregation Consortium Feb 27, 2017). The p.His297= variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. In addition, in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Oct 13, 2024