rs11466512

chr3-30671634-T-Achr3-30671634-T-Cchr3-30671634-T-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_003242.6(TGFBR2):c.455-4T>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 1,613,682 control chromosomes in the GnomAD database, including 77,185 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.26 ( 5767 hom., cov: 33)

Exomes 𝑓: 0.31 ( 71418 hom. )

Consequence

TGFBR2
NM_003242.6 splice_region, splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.0003021

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:17

Conservation

PhyloP100: 0.564

Variant links:

Genes affected

TGFBR2 (HGNC:11773): (transforming growth factor beta receptor 2) The protein encoded by this gene is a transmembrane protein that has a protein kinase domain, forms a heterodimeric complex with TGF-beta receptor type-1, and binds TGF-beta. This receptor/ligand complex phosphorylates proteins, which then enter the nucleus and regulate the transcription of genes related to cell proliferation, cell cycle arrest, wound healing, immunosuppression, and tumorigenesis. Mutations in this gene have been associated with Marfan Syndrome, Loeys-Deitz Aortic Aneurysm Syndrome, and the development of various types of tumors. Alternatively spliced transcript variants encoding different isoforms have been characterized. [provided by RefSeq, Aug 2017]

TGFBR2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 3-30671634-T-A is Benign according to our data. Variant chr3-30671634-T-A is described in ClinVar as [Benign]. Clinvar id is 44658.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-30671634-T-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TGFBR2	NM_003242.6 linkuse as main transcript	c.455-4T>A		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000295754.10

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
TGFBR2	ENST00000295754.10 linkuse as main transcript	c.455-4T>A	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	1	NM_003242.6	P1	P37173-1
TGFBR2	ENST00000359013.4 linkuse as main transcript	c.530-4T>A	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant	1			P37173-2
TGFBR2	ENST00000672866.1 linkuse as main transcript	n.2051-4T>A	splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.264

AC:

40090

AN:

152018

Hom.:

5768

Cov.:

show subpopulations

Gnomad AFR

AF:

0.153

Gnomad AMI

AF:

0.423

Gnomad AMR

AF:

0.354

Gnomad ASJ

AF:

0.214

Gnomad EAS

AF:

0.317

Gnomad SAS

AF:

0.226

Gnomad FIN

AF:

0.281

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.307

Gnomad OTH

AF:

0.276

GnomAD3 exomes

AF:

0.300

AC:

75434

AN:

251114

Hom.:

12291

AF XY:

0.293

AC XY:

39743

AN XY:

135712

show subpopulations

Gnomad AFR exome

AF:

0.149

Gnomad AMR exome

AF:

0.443

Gnomad ASJ exome

AF:

0.201

Gnomad EAS exome

AF:

0.317

Gnomad SAS exome

AF:

0.213

Gnomad FIN exome

AF:

0.286

Gnomad NFE exome

AF:

0.311

Gnomad OTH exome

AF:

0.297

GnomAD4 exome

AF:

0.308

AC:

450865

AN:

1461546

Hom.:

71418

Cov.:

AF XY:

0.305

AC XY:

221547

AN XY:

727080

show subpopulations

Gnomad4 AFR exome

AF:

0.148

Gnomad4 AMR exome

AF:

0.438

Gnomad4 ASJ exome

AF:

0.206

Gnomad4 EAS exome

AF:

0.324

Gnomad4 SAS exome

AF:

0.218

Gnomad4 FIN exome

AF:

0.287

Gnomad4 NFE exome

AF:

0.320

Gnomad4 OTH exome

AF:

0.291

GnomAD4 genome

AF:

0.264

AC:

40103

AN:

152136

Hom.:

5767

Cov.:

AF XY:

0.260

AC XY:

19315

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.153

Gnomad4 AMR

AF:

0.354

Gnomad4 ASJ

AF:

0.214

Gnomad4 EAS

AF:

0.316

Gnomad4 SAS

AF:

0.226

Gnomad4 FIN

AF:

0.281

Gnomad4 NFE

AF:

0.307

Gnomad4 OTH

AF:

0.275

Alfa

AF:

0.250

Hom.:

1704

Bravo

AF:

0.270

Asia WGS

AF:

0.264

AC:

920

AN:

3478

EpiCase

AF:

0.300

EpiControl

AF:

0.305

ClinVar

Significance: Benign

Submissions summary: Benign:17

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:8

Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Benign, criteria provided, single submitter	clinical testing	Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan	Jan 24, 2024	This variant is classified as Benign based on local population frequency. This variant was detected in 53% of patients studied by a panel of primary immunodeficiencies. Number of patients: 47. Only high quality variants are reported. -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, Amsterdam University Medical Center	-	- -
Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Sep 19, 2011	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 20, 2012	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. -

Familial thoracic aortic aneurysm and aortic dissection

Benign:4

Benign, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Mar 09, 2018	- -
Benign, criteria provided, single submitter	clinical testing	Invitae	Feb 01, 2024	- -
Benign, criteria provided, single submitter	clinical testing	CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario	May 09, 2019	- -
Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jun 14, 2016	- -

Marfan syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Nov 30, 2023

- -

Loeys-Dietz syndrome 2

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

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. -

Cardiovascular phenotype

Benign:1

Benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Feb 10, 2015

General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance -

Thoracic aortic aneurysm

Benign:1

Benign, no assertion criteria provided

clinical testing

Cohesion Phenomics

Sep 23, 2022

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

Cadd

Benign

8.3

Dann

Benign

0.53

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00030

dbscSNV1_RF

Benign

0.022

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over