rs1036096

Positions:

• chr3-30653599-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000295754.10(TGFBR2):​c.454+3139G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,066 control chromosomes in the GnomAD database, including 2,082 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 0.15 (2082 hom., cov: 31)
• Consequence: TGFBR2 ENST00000295754.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TGFBR2	NM_003242.6	c.454+3139G>A		intron_variant		ENST00000295754.10	NP_003233.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TGFBR2	ENST00000295754.10	c.454+3139G>A		intron_variant		1	NM_003242.6	ENSP00000295754	P1
TGFBR2	ENST00000359013.4	c.529+3139G>A		intron_variant		1		ENSP00000351905
TGFBR2	ENST00000672866.1	n.2050+3139G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23523 AN: 151948 Hom.: 2088 Cov.: 31

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.155 AC: 23520 AN: 152066 Hom.: 2082 Cov.: 31 AF XY: 0.156 AC XY: 11598 AN XY: 74344

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.158

Alfa AF: 0.143 Hom.: 189

Bravo AF: 0.166

Asia WGS AF: 0.263 AC: 915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.64
DANN	Benign	0.64

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: rs1036096; hg19: chr3-30695091;