NM_000548.5(TSC2):c.299C>T (p.Ala100Val) AND not provided

Clinical significance:Conflicting interpretations of pathogenicity, Likely benign(1);Uncertain significance(1) (Last evaluated: Aug 1, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
2 submissions [Details]
Record status:

Allele description [Variation Report for NM_000548.5(TSC2):c.299C>T (p.Ala100Val)]

NM_000548.5(TSC2):c.299C>T (p.Ala100Val)

TSC2:TSC complex subunit 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_000548.5(TSC2):c.299C>T (p.Ala100Val)
  • NC_000016.10:g.2053415C>T
  • NG_005895.1:g.9110C>T
  • NM_000548.5:c.299C>TMANE SELECT
  • NM_001077183.3:c.299C>T
  • NM_001114382.3:c.299C>T
  • NM_001318827.2:c.226-881C>T
  • NM_001318829.2:c.152C>T
  • NM_001318831.2:c.-1-2781C>T
  • NM_001318832.2:c.332C>T
  • NM_001363528.2:c.299C>T
  • NM_001370404.1:c.299C>T
  • NM_001370405.1:c.299C>T
  • NM_021055.3:c.299C>T
  • NP_000539.2:p.Ala100Val
  • NP_001070651.1:p.Ala100Val
  • NP_001107854.1:p.Ala100Val
  • NP_001305758.1:p.Ala51Val
  • NP_001305761.1:p.Ala111Val
  • NP_001350457.1:p.Ala100Val
  • NP_001357333.1:p.Ala100Val
  • NP_001357334.1:p.Ala100Val
  • NP_066399.2:p.Ala100Val
  • LRG_487t1:c.299C>T
  • LRG_487:g.9110C>T
  • NC_000016.9:g.2103416C>T
  • NM_000548.3:c.299C>T
Protein change:
dbSNP: rs375824753
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_001318827.2:c.226-881C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001318831.2:c.-1-2781C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000548.5:c.299C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001077183.3:c.299C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001114382.3:c.299C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001318829.2:c.152C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001318832.2:c.332C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001363528.2:c.299C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370404.1:c.299C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370405.1:c.299C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_021055.3:c.299C>T - missense variant - [Sequence Ontology: SO:0001583]


MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000892153CeGaT Praxis fuer Humangenetik Tuebingencriteria provided, single submitter
Uncertain significance
(Aug 1, 2018)
germlineclinical testing

Citation Link,

SCV000968819GeneDxcriteria provided, single submitter
Likely benign
(May 11, 2018)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes4not providednot providednot providednot providedclinical testing

Details of each submission

From CeGaT Praxis fuer Humangenetik Tuebingen, SCV000892153.8

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided4not providednot providedclinical testingnot provided
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided4not providednot providednot provided

From GeneDx, SCV000968819.1

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


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.

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

Last Updated: Nov 27, 2021

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