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NM_003722.5(TP63):c.580-11A>T AND not provided

Germline classification:
Benign (2 submissions)
Last evaluated:
Jul 24, 2021
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:
RCV001355643.3

Allele description [Variation Report for NM_003722.5(TP63):c.580-11A>T]

NM_003722.5(TP63):c.580-11A>T

Gene:
TP63:tumor protein p63 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3q28
Genomic location:
Preferred name:
NM_003722.5(TP63):c.580-11A>T
HGVS:
  • NC_000003.12:g.189864221A>T
  • NG_007550.3:g.272476A>T
  • NM_001114978.2:c.580-11A>T
  • NM_001114979.2:c.580-11A>T
  • NM_001114980.2:c.298-11A>T
  • NM_001114981.2:c.298-11A>T
  • NM_001114982.2:c.298-11A>T
  • NM_001329144.2:c.580-11A>T
  • NM_001329145.2:c.298-11A>T
  • NM_001329146.2:c.43-11A>T
  • NM_001329148.2:c.580-11A>T
  • NM_001329149.2:c.298-11A>T
  • NM_001329150.2:c.43-11A>T
  • NM_001329964.2:c.574-11A>T
  • NM_003722.5:c.580-11A>TMANE SELECT
  • LRG_428t1:c.580-11A>T
  • LRG_428:g.272476A>T
  • NC_000003.11:g.189582010A>T
Links:
dbSNP: rs148217164
NCBI 1000 Genomes Browser:
rs148217164
Molecular consequence:
  • NM_001114978.2:c.580-11A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001114979.2:c.580-11A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001114980.2:c.298-11A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001114981.2:c.298-11A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001114982.2:c.298-11A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001329144.2:c.580-11A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001329145.2:c.298-11A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001329146.2:c.43-11A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001329148.2:c.580-11A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001329149.2:c.298-11A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001329150.2:c.43-11A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001329964.2:c.574-11A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_003722.5:c.580-11A>T - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001550586Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria provided
Likely benignunknownclinical testing

SCV001988743GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Benign
(Jul 24, 2021) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineyesnot providednot 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), SCV001550586.1

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

Description

The TP63 c.574-11A>T variant was not identified in the literature nor was it identified in ClinVar, Cosmic or LOVD 3.0. The variant was identified in dbSNP (ID: rs148217164) and in control databases in 99 of 282638 chromosomes at a frequency of 0.00035 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 95 of 24962 chromosomes (freq: 0.003806), Latino in 3 of 35438 chromosomes (freq: 0.000085) and European (non-Finnish) in 1 of 128962 chromosomes (freq: 0.000008); it was not observed in the Ashkenazi Jewish, East Asian, European (Finnish), Other or South Asian populations. The c.574-11A>T 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, only 2 of 4 in silico or computational prediction software programs (MaxEntScan, GeneSplicer) predict a greater than 10% 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 providednot providednot providednot providednot provided

From GeneDx, SCV001988743.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 28, 2024