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NM_000548.5(TSC2):c.3814+1G>C AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jul 6, 2022
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:
RCV003114236.3

Allele description [Variation Report for NM_000548.5(TSC2):c.3814+1G>C]

NM_000548.5(TSC2):c.3814+1G>C

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.3814+1G>C
HGVS:
  • NC_000016.10:g.2081799G>C
  • NG_005895.1:g.37494G>C
  • NM_000548.5:c.3814+1G>CMANE SELECT
  • NM_001077183.3:c.3682+1G>C
  • NM_001114382.3:c.3814+1G>C
  • NM_001318827.2:c.3574+1G>C
  • NM_001318829.2:c.3538+1G>C
  • NM_001318831.2:c.3082+1G>C
  • NM_001318832.2:c.3715+1G>C
  • NM_001363528.2:c.3685+1G>C
  • NM_001370404.1:c.3682+1G>C
  • NM_001370405.1:c.3685+1G>C
  • NM_001406663.1:c.3811+1G>C
  • NM_001406664.1:c.3811+1G>C
  • NM_001406665.1:c.3682+1G>C
  • NM_001406667.1:c.3775+1G>C
  • NM_001406668.1:c.3772+1G>C
  • NM_001406670.1:c.3703+1G>C
  • NM_001406671.1:c.3673+1G>C
  • NM_001406673.1:c.3670+1G>C
  • NM_001406675.1:c.3667+1G>C
  • NM_001406676.1:c.3664+1G>C
  • NM_001406677.1:c.3625+1G>C
  • NM_001406678.1:c.3571+1G>C
  • NM_001406679.1:c.3535+1G>C
  • NM_001406680.1:c.3214+1G>C
  • NM_001406681.1:c.3223+1G>C
  • NM_001406682.1:c.3214+1G>C
  • NM_001406683.1:c.3214+1G>C
  • NM_001406684.1:c.3211+1G>C
  • NM_001406685.1:c.3085+1G>C
  • NM_001406686.1:c.3085+1G>C
  • NM_001406687.1:c.3082+1G>C
  • NM_001406688.1:c.3082+1G>C
  • NM_001406689.1:c.2470+1G>C
  • NM_001406690.1:c.2341+1G>C
  • NM_001406691.1:c.2338+1G>C
  • NM_001406692.1:c.2341+1G>C
  • NM_001406693.1:c.2341+1G>C
  • NM_001406694.1:c.2341+1G>C
  • NM_001406695.1:c.2338+1G>C
  • NM_001406696.1:c.2338+1G>C
  • NM_001406697.1:c.2338+1G>C
  • NM_001406698.1:c.2080+1G>C
  • NM_021055.3:c.3685+1G>C
  • LRG_487t1:c.3814+1G>C
  • LRG_487:g.37494G>C
  • NC_000016.9:g.2131800G>C
  • NM_000548.3:c.3814+1G>C
  • p.?
Links:
Tuberous sclerosis database (TSC2): TSC2_02376; dbSNP: rs397514902
NCBI 1000 Genomes Browser:
rs397514902
Molecular consequence:
  • NM_000548.5:c.3814+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001077183.3:c.3682+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001114382.3:c.3814+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001318827.2:c.3574+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001318829.2:c.3538+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001318831.2:c.3082+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001318832.2:c.3715+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001363528.2:c.3685+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001370404.1:c.3682+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001370405.1:c.3685+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406663.1:c.3811+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406664.1:c.3811+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406665.1:c.3682+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406667.1:c.3775+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406668.1:c.3772+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406670.1:c.3703+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406671.1:c.3673+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406673.1:c.3670+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406675.1:c.3667+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406676.1:c.3664+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406677.1:c.3625+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406678.1:c.3571+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406679.1:c.3535+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406680.1:c.3214+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406681.1:c.3223+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406682.1:c.3214+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406683.1:c.3214+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406684.1:c.3211+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406685.1:c.3085+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406686.1:c.3085+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406687.1:c.3082+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406688.1:c.3082+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406689.1:c.2470+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406690.1:c.2341+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406691.1:c.2338+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406692.1:c.2341+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406693.1:c.2341+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406694.1:c.2341+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406695.1:c.2338+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406696.1:c.2338+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406697.1:c.2338+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001406698.1:c.2080+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_021055.3:c.3685+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003799711ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2021)		Likely pathogenic
(Jul 6, 2022) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV003799711.2

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

Description

The TSC2 c.3814+1G>C variant (rs397514902), to our knowledge, is not reported in the medical literature but is reported in ClinVar (Variation ID: 65032). This variant is absent from the Genome Aggregation Database, indicating it is not a common polymorphism. This variant disrupts the canonical splice donor site of intron 31, which is likely to negatively impact gene function. Based on available information, this variant is considered to be likely pathogenic.

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

Last Updated: Jun 2, 2024