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NM_000368.5(TSC1):c.2626-5_2626-4del AND Lymphangiomyomatosis

Germline classification:
Benign (1 submission)
Last evaluated:
Mar 30, 2023
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:
RCV002221210.2

Allele description [Variation Report for NM_000368.5(TSC1):c.2626-5_2626-4del]

NM_000368.5(TSC1):c.2626-5_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.2626-5_2626-4del
HGVS:
  • NC_000009.12:g.132897630_132897631del
  • NG_012386.1:g.52019_52020del
  • NM_000368.5:c.2626-5_2626-4delMANE SELECT
  • NM_001162426.2:c.2623-5_2623-4del
  • NM_001162427.2:c.2473-5_2473-4del
  • NM_001362177.2:c.2263-5_2263-4del
  • LRG_486:g.52019_52020del
  • NC_000009.11:g.135773001_135773002delAA
  • NC_000009.11:g.135773017_135773018del
  • NM_000368.4:c.2626-5_2626-4delTT
  • NM_000368.5:c.2626-5_2626-4delTTMANE SELECT
Links:
dbSNP: rs5901000
NCBI 1000 Genomes Browser:
rs5901000
Molecular consequence:
  • NM_000368.5:c.2626-5_2626-4del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001162426.2:c.2623-5_2623-4del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001162427.2:c.2473-5_2473-4del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001362177.2:c.2263-5_2263-4del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Lymphangiomyomatosis (LAM)
Synonyms:
Lymphangioleiomyomatosis; Lymphangioleiomyomatosis, somatic
Identifiers:
MONDO: MONDO:0011705; MedGen: C0751674; Orphanet: 538; OMIM: 606690

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002498689Molecular Genetics, Royal Melbourne Hospital

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)		Benign
(Mar 30, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

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

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 Molecular Genetics, Royal Melbourne Hospital, SCV002498689.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

Population allele frequency is 4.7% (rs118203716, 4,915/103,824 alleles in gnomAD v2.1). Based on classification scheme RMH ACMG Guidelines v1.1.1, this variant is classified as Benign. Following criteria are met: BA1.

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

Last Updated: Jan 13, 2025