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NM_000548.5(TSC2):c.5260-49C>T AND not provided

Germline classification:
Benign (2 submissions)
Last evaluated:
Jun 20, 2018
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000829855.2

Allele description [Variation Report for NM_000548.5(TSC2):c.5260-49C>T]

NM_000548.5(TSC2):c.5260-49C>T

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.5260-49C>T
HGVS:
  • NC_000016.10:g.2088397C>T
  • NG_005895.1:g.44092C>T
  • NG_008617.1:g.54824G>A
  • NM_000548.4:c.5260-49C>T
  • NM_000548.5:c.5260-49C>TMANE SELECT
  • NM_001077183.3:c.5059-49C>T
  • NM_001114382.3:c.5191-49C>T
  • NM_001318827.2:c.4951-49C>T
  • NM_001318829.2:c.4915-49C>T
  • NM_001318831.2:c.4528-49C>T
  • NM_001318832.2:c.5092-49C>T
  • NM_001363528.2:c.5062-49C>T
  • NM_001370404.1:c.5128-49C>T
  • NM_001370405.1:c.5119-49C>T
  • NM_021055.3:c.5131-49C>T
  • LRG_487t1:c.5260-49C>T
  • LRG_487:g.44092C>T
  • NC_000016.9:g.2138398C>T
  • NM_000548.3:c.5260-49C>T
  • p.(=)
Links:
Tuberous sclerosis database (TSC2): TSC2_00150; dbSNP: rs13332221
NCBI 1000 Genomes Browser:
rs13332221
Molecular consequence:
  • NM_000548.5:c.5260-49C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001077183.3:c.5059-49C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001114382.3:c.5191-49C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001318827.2:c.4951-49C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001318829.2:c.4915-49C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001318831.2:c.4528-49C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001318832.2:c.5092-49C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001363528.2:c.5062-49C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001370404.1:c.5128-49C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001370405.1:c.5119-49C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_021055.3:c.5131-49C>T - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000971587GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Benign
(Jun 20, 2018) 		germlineclinical testing

Citation Link,

SCV005297742Breakthrough Genomics, Breakthrough Genomics
criteria provided, single submitter

(ACMG Guidelines, 2015)		Benigngermlinenot provided

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

Help

Summary from all submissions

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

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, SCV000971587.1

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

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

From Breakthrough Genomics, Breakthrough Genomics, SCV005297742.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providednot provided PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024