NM_003242.6(TGFBR2):c.455-4T>A AND Loeys-Dietz syndrome 2

Germline classification:: Benign (1 submission)
Last evaluated:: Jan 13, 2018
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:: RCV000322117.13

Allele description [Variation Report for NM_003242.6(TGFBR2):c.455-4T>A]

NM_003242.6(TGFBR2):c.455-4T>A

Gene:

TGFBR2:transforming growth factor beta receptor 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p24.1

Genomic location:

Preferred name:

NM_003242.6(TGFBR2):c.455-4T>A

HGVS:

NC_000003.12:g.30671634T>A
NG_007490.1:g.70133T>A
NM_001024847.3:c.530-4T>A
NM_001407126.1:c.638-4T>A
NM_001407127.1:c.563-4T>A
NM_001407128.1:c.482-4T>A
NM_001407129.1:c.458-4T>A
NM_001407130.1:c.455-4T>A
NM_001407132.1:c.350-4T>A
NM_001407133.1:c.350-4T>A
NM_001407134.1:c.350-4T>A
NM_001407135.1:c.350-4T>A
NM_001407136.1:c.350-4T>A
NM_001407137.1:c.170-4T>A
NM_001407138.1:c.95-4T>A
NM_001407139.1:c.530-16753T>A
NM_003242.6:c.455-4T>AMANE SELECT
LRG_779t1:c.530-4T>A
LRG_779t2:c.455-4T>A
LRG_779:g.70133T>A
NC_000003.11:g.30713126T>A
NM_001024847.2:c.530-4T>A
NM_003242.5:c.455-4T>A
NM_003242.6:c.455-4T>A
c.455-4T>A

Links:

dbSNP: rs11466512

NCBI 1000 Genomes Browser:

rs11466512

Molecular consequence:

NM_001024847.3:c.530-4T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407126.1:c.638-4T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407127.1:c.563-4T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407128.1:c.482-4T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407129.1:c.458-4T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407130.1:c.455-4T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407132.1:c.350-4T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407133.1:c.350-4T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407134.1:c.350-4T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407135.1:c.350-4T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407136.1:c.350-4T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407137.1:c.170-4T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407138.1:c.95-4T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407139.1:c.530-16753T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_003242.6:c.455-4T>A - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Loeys-Dietz syndrome 2 (LDS2)
Synonyms:: Loeys-Dietz syndrome type 1B; MARFAN SYNDROME, TYPE II; Loeys-Dietz syndrome type 2B; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0012427; MedGen: C2674574; Orphanet: 558; OMIM: 610168

Recent activity

Clear Turn Off Turn On

essv16109678 (0)
PopSet
Homo sapiens zinc finger protein 313 (ZNF313), mRNA
Homo sapiens zinc finger protein 313 (ZNF313), mRNA
gi|19923549|ref|NM_018683.2|

Nucleotide
Luciobarbus graecus isolate Ex09A3 cytochrome oxidase subunit I gene, partial cd...
Luciobarbus graecus isolate Ex09A3 cytochrome oxidase subunit I gene, partial cds; mitochondrial
gi|610493488|gb|KJ554075.1|

Nucleotide
Rehmannia glutinosa UDP-glucose glucosyltransferase 1 (UGT1) mRNA, complete cds.
Rehmannia glutinosa UDP-glucose glucosyltransferase 1 (UGT1) mRNA, complete cds.
PopSet: 2813237085

PopSet

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000442838	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Benign (Jan 13, 2018)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000442838

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Benign
(Jan 13, 2018)

germline

clinical testing

Citation Link

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

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000442838.3

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

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

#	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: Nov 10, 2024

ClinVar

Relating variation to medicine