NM_000548.5(TSC2):c.4662+16C>G AND Tuberous sclerosis 2

Germline classification:: Likely benign (1 submission)
Last evaluated:: Jun 27, 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:: RCV002202318.6

Allele description [Variation Report for NM_000548.5(TSC2):c.4662+16C>G]

NM_000548.5(TSC2):c.4662+16C>G

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.4662+16C>G

HGVS:

NC_000016.10:g.2085338C>G
NG_005895.1:g.41033C>G
NM_000548.5:c.4662+16C>GMANE SELECT
NM_001077183.3:c.4461+16C>G
NM_001114382.3:c.4593+16C>G
NM_001318827.2:c.4353+16C>G
NM_001318829.2:c.4317+16C>G
NM_001318831.2:c.3930+16C>G
NM_001318832.2:c.4494+16C>G
NM_001363528.2:c.4464+16C>G
NM_001370404.1:c.4530+16C>G
NM_001370405.1:c.4533+16C>G
NM_021055.3:c.4533+16C>G
LRG_487:g.41033C>G
NC_000016.9:g.2135339C>G

Links:

dbSNP: rs45517356

NCBI 1000 Genomes Browser:

rs45517356

Molecular consequence:

NM_000548.5:c.4662+16C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001077183.3:c.4461+16C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001114382.3:c.4593+16C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001318827.2:c.4353+16C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001318829.2:c.4317+16C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001318831.2:c.3930+16C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001318832.2:c.4494+16C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001363528.2:c.4464+16C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001370404.1:c.4530+16C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001370405.1:c.4533+16C>G - intron variant - [Sequence Ontology: SO:0001627]
NM_021055.3:c.4533+16C>G - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Tuberous sclerosis 2 (TSC2)
Identifiers:: MONDO: MONDO:0013199; MedGen: C1860707; Orphanet: 805; OMIM: 613254

Recent activity

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Homo sapiens phospholipase D family member 6 (PLD6), mRNA; nuclear gene for mito...
Homo sapiens phospholipase D family member 6 (PLD6), mRNA; nuclear gene for mitochondrial product
gi|1519245464|ref|NM_178836.4|

Nucleotide
Homo sapiens zinc finger with KRAB and SCAN domains 3 (ZKSCAN3), transcript vari...
Homo sapiens zinc finger with KRAB and SCAN domains 3 (ZKSCAN3), transcript variant 3, mRNA
gi|1675178444|ref|NM_001242895.2|

Nucleotide
602876729F1 NCI_CGAP_Mam2 Mus musculus cDNA clone IMAGE:5008590 5', mRNA sequenc...
602876729F1 NCI_CGAP_Mam2 Mus musculus cDNA clone IMAGE:5008590 5', mRNA sequence
gi|14498626|gnl|dbEST|8837271|gb|BI 6.1|

Nucleotide
Homo sapiens genomic DNA; cDNA DKFZp761M10121 (from clone DKFZp761M10121)
Homo sapiens genomic DNA; cDNA DKFZp761M10121 (from clone DKFZp761M10121)
gi|6807798|emb|AL137313.1|

Nucleotide
Pramel59 PRAME like 59 [Mus musculus]
Pramel59 PRAME like 59 [Mus musculus]
Gene ID:622894

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002353906	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jun 27, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002353906

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jun 27, 2023)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002353906.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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