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NM_000368.5(TSC1):c.2626-4del AND Tuberous sclerosis syndrome

Germline classification:
Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:
Jan 11, 2024
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:
RCV000042234.17

Allele description [Variation Report for NM_000368.5(TSC1):c.2626-4del]

NM_000368.5(TSC1):c.2626-4del

Gene:
TSC1:TSC complex subunit 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
9q34.13
Genomic location:
Preferred name:
NM_000368.5(TSC1):c.2626-4del
HGVS:
  • NC_000009.11:g.135773001del
  • NC_000009.12:g.132897631del
  • NG_012386.1:g.52020del
  • NM_000368.5:c.2626-4delMANE SELECT
  • NM_001162426.2:c.2623-4del
  • NM_001162427.2:c.2473-4del
  • NM_001362177.2:c.2263-4del
  • LRG_486:g.52020del
  • NC_000009.11:g.135773001del
  • NC_000009.11:g.135773001delA
  • NC_000009.11:g.135773002del
  • NC_000009.11:g.135773018del
  • NM_000368.3:c.2626-4delT
  • NM_000368.4:c.2626-4delT
  • NM_000368.5:c.2626-4delTMANE SELECT
  • p.(=)
Links:
Tuberous sclerosis database (TSC1): TSC1_00277; dbSNP: rs5901000
NCBI 1000 Genomes Browser:
rs5901000
Molecular consequence:
  • NM_000368.5:c.2626-4del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001162426.2:c.2623-4del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001162427.2:c.2473-4del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001362177.2:c.2263-4del - intron variant - [Sequence Ontology: SO:0001627]
Observations:
1

Condition(s)

Name:
Tuberous sclerosis syndrome (TSC)
Synonyms:
Tuberous sclerosis
Identifiers:
MONDO: MONDO:0001734; MedGen: C0041341; OMIM: PS191100

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000066020Tuberous sclerosis database (TSC1)
no classification provided

(Tuberous Sclerosis Database Assertion Criteria 2015)		not providedgermlinecuration

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

Citation Link,

SCV000478204Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification 20161018)		Benign
(Jun 14, 2016) 		germlineclinical testing

ICSL_Variant_Classification_20161018.pdf,

Citation Link,

SCV004834397All of Us Research Program, National Institutes of Health
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain Significance
(Jan 11, 2024) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedcuration
not providedgermlineunknown1not providednot provided108544not providedclinical testing

Citations

PubMed

Genotype/phenotype correlation in 325 individuals referred for a diagnosis of tuberous sclerosis complex in the United States.

Au KS, Williams AT, Roach ES, Batchelor L, Sparagana SP, Delgado MR, Wheless JW, Baumgartner JE, Roa BB, Wilson CM, Smith-Knuppel TK, Cheung MY, Whittemore VH, King TM, Northrup H.

Genet Med. 2007 Feb;9(2):88-100.

PubMed [citation]
PMID:
17304050

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 Tuberous sclerosis database (TSC1), SCV000066020.3

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

From Illumina Laboratory Services, Illumina, SCV000478204.2

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

From All of Us Research Program, National Institutes of Health, SCV004834397.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknown108544not providednot provided1not providednot providednot provided

Last Updated: Sep 29, 2024