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NM_000548.5(TSC2):c.4626C>A (p.Thr1542=) AND Hereditary cancer-predisposing syndrome

Germline classification:
Likely benign (1 submission)
Last evaluated:
Feb 4, 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:
RCV003169363.2

Allele description [Variation Report for NM_000548.5(TSC2):c.4626C>A (p.Thr1542=)]

NM_000548.5(TSC2):c.4626C>A (p.Thr1542=)

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.4626C>A (p.Thr1542=)
HGVS:
  • NC_000016.10:g.2085286C>A
  • NG_005895.1:g.40981C>A
  • NM_000548.5:c.4626C>AMANE SELECT
  • NM_001077183.3:c.4425C>A
  • NM_001114382.3:c.4557C>A
  • NM_001318827.2:c.4317C>A
  • NM_001318829.2:c.4281C>A
  • NM_001318831.2:c.3894C>A
  • NM_001318832.2:c.4458C>A
  • NM_001363528.2:c.4428C>A
  • NM_001370404.1:c.4494C>A
  • NM_001370405.1:c.4497C>A
  • NM_021055.3:c.4497C>A
  • NP_000539.2:p.Thr1542=
  • NP_001070651.1:p.Thr1475=
  • NP_001107854.1:p.Thr1519=
  • NP_001305756.1:p.Thr1439=
  • NP_001305758.1:p.Thr1427=
  • NP_001305760.1:p.Thr1298=
  • NP_001305761.1:p.Thr1486=
  • NP_001350457.1:p.Thr1476=
  • NP_001357333.1:p.Thr1498=
  • NP_001357334.1:p.Thr1499=
  • NP_066399.2:p.Thr1499=
  • LRG_487t1:c.4626C>A
  • LRG_487:g.40981C>A
  • NC_000016.9:g.2135287C>A
  • NM_000548.3:c.4626C>A
Links:
dbSNP: rs1164781795
NCBI 1000 Genomes Browser:
rs1164781795
Molecular consequence:
  • NM_000548.5:c.4626C>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001077183.3:c.4425C>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001114382.3:c.4557C>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001318827.2:c.4317C>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001318829.2:c.4281C>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001318831.2:c.3894C>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001318832.2:c.4458C>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001363528.2:c.4428C>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001370404.1:c.4494C>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001370405.1:c.4497C>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_021055.3:c.4497C>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Hereditary cancer-predisposing syndrome
Synonyms:
Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003863470Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely benign
(Feb 4, 2023) 		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 Ambry Genetics, SCV003863470.2

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

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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

Last Updated: Sep 29, 2024