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NM_000548.5(TSC2):c.482-1G>A AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 10, 2016
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:
RCV000521778.1

Allele description

NM_000548.5(TSC2):c.482-1G>A

Gene:
TSC2:TSC complex subunit 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16p13.3
Genomic location:
Preferred name:
NM_000548.5(TSC2):c.482-1G>A
HGVS:
  • NC_000016.10:g.2055401G>A
  • NG_005895.1:g.11096G>A
  • NM_000548.5:c.482-1G>AMANE SELECT
  • NM_001077183.3:c.482-1G>A
  • NM_001114382.3:c.482-1G>A
  • NM_001318827.2:c.371-1G>A
  • NM_001318829.2:c.335-1G>A
  • NM_001318831.2:c.-1-795G>A
  • NM_001318832.2:c.515-1G>A
  • NM_001363528.2:c.482-1G>A
  • NM_001370404.1:c.482-1G>A
  • NM_001370405.1:c.482-1G>A
  • NM_001406663.1:c.482-1G>A
  • NM_001406664.1:c.482-1G>A
  • NM_001406665.1:c.482-1G>A
  • NM_001406667.1:c.572-1G>A
  • NM_001406668.1:c.572-1G>A
  • NM_001406670.1:c.371-1G>A
  • NM_001406671.1:c.482-1G>A
  • NM_001406673.1:c.482-1G>A
  • NM_001406675.1:c.335-1G>A
  • NM_001406676.1:c.335-1G>A
  • NM_001406677.1:c.425-1G>A
  • NM_001406678.1:c.371-1G>A
  • NM_001406679.1:c.335-1G>A
  • NM_001406680.1:c.-335-1G>A
  • NM_001406681.1:c.37-18G>A
  • NM_001406682.1:c.-1-795G>A
  • NM_001406683.1:c.-335-1G>A
  • NM_001406684.1:c.-1-795G>A
  • NM_001406685.1:c.-1-795G>A
  • NM_001406686.1:c.-1-795G>A
  • NM_001406687.1:c.-335-1G>A
  • NM_001406688.1:c.-1-795G>A
  • NM_001406689.1:c.-950-1G>A
  • NM_001406690.1:c.-950-1G>A
  • NM_001406691.1:c.-950-1G>A
  • NM_001406692.1:c.-950-1G>A
  • NM_001406693.1:c.-1166-1G>A
  • NM_001406694.1:c.-831-1G>A
  • NM_001406695.1:c.-831-1G>A
  • NM_001406696.1:c.-938-1G>A
  • NM_001406697.1:c.-950-1G>A
  • NM_001406698.1:c.-1126-1G>A
  • NM_021055.3:c.482-1G>A
  • LRG_487t1:c.482-1G>A
  • LRG_487:g.11096G>A
  • NC_000016.9:g.2105402G>A
  • NM_000548.3:c.482-1G>A
Links:
dbSNP: rs137854306
NCBI 1000 Genomes Browser:
rs137854306
Molecular consequence:
  • NM_001318831.2:c.-1-795G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406681.1:c.37-18G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406682.1:c.-1-795G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406684.1:c.-1-795G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406685.1:c.-1-795G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406686.1:c.-1-795G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001406688.1:c.-1-795G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000548.5:c.482-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001077183.3:c.482-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001114382.3:c.482-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001318827.2:c.371-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001318829.2:c.335-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001318832.2:c.515-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001363528.2:c.482-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001370404.1:c.482-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001370405.1:c.482-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406663.1:c.482-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406664.1:c.482-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406665.1:c.482-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406667.1:c.572-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406668.1:c.572-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406670.1:c.371-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406671.1:c.482-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406673.1:c.482-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406675.1:c.335-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406676.1:c.335-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406677.1:c.425-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406678.1:c.371-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406679.1:c.335-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406680.1:c.-335-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406683.1:c.-335-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406687.1:c.-335-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406689.1:c.-950-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406690.1:c.-950-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406691.1:c.-950-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406692.1:c.-950-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406693.1:c.-1166-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406694.1:c.-831-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406695.1:c.-831-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406696.1:c.-938-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406697.1:c.-950-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001406698.1:c.-1126-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_021055.3:c.482-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000618184GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Pathogenic
(Aug 10, 2016) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000618184.2

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

Description

The c.482-1 G>A splice site variant in the TSC2 gene destroys the canonical splice acceptor site for intron 5. It is predicted to cause abnormal gene splicing, either leading to an abnormal message that is subject to nonsense-mediated mRNA decay, or to an abnormal protein product if the message is used for protein translation. It was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. Although this pathogenic variant has not been previously reported to our knowledge, its presence is consistent with a diagnosis of tuberous sclerosis

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

Last Updated: Jun 10, 2023