rs3773650

chr3-30676937-A-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_003242.6(TGFBR2):c.1396+2691A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.833 in 152,224 control chromosomes in the GnomAD database, including 53,222 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.83 (53222 hom., cov: 34)
• Consequence: TGFBR2 NM_003242.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.685

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.923 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TGFBR2	NM_003242.6	c.1396+2691A>C		intron_variant		ENST00000295754.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TGFBR2	ENST00000295754.10	c.1396+2691A>C		intron_variant		1	NM_003242.6	P1
TGFBR2	ENST00000359013.4	c.1471+2691A>C		intron_variant		1
TGFBR2	ENST00000672866.1	n.2992+2691A>C		intron_variant, non_coding_transcript_variant
TGFBR2	ENST00000673203.1	n.274+2691A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.833 AC: 126722 AN: 152106 Hom.: 53157 Cov.: 34

Gnomad AFR AF: 0.931

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.856

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.808

Gnomad OTH AF: 0.834

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.833 AC: 126846 AN: 152224 Hom.: 53222 Cov.: 34 AF XY: 0.826 AC XY: 61439 AN XY: 74406

Gnomad4 AFR AF: 0.931

Gnomad4 AMR AF: 0.856

Gnomad4 ASJ AF: 0.763

Gnomad4 EAS AF: 0.696

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.750

Gnomad4 NFE AF: 0.808

Gnomad4 OTH AF: 0.830

Alfa AF: 0.805 Hom.: 28788

Bravo AF: 0.853

Asia WGS AF: 0.723 AC: 2515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
Cadd	Benign	18
Dann	Benign	0.72

Splicing

Name	Calibrated prediction	Score	Prediction
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

Other links and lift over

dbSNP: rs3773650; hg19: chr3-30718429;