rs9310940

Positions:

• chr3-30680726-T-G

Variant summary

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

The NM_003242.6(TGFBR2):​c.1396+6480T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 151,966 control chromosomes in the GnomAD database, including 21,157 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 0.52 (21157 hom., cov: 31)
• Consequence: TGFBR2 NM_003242.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.616

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=-0.69).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TGFBR2	NM_003242.6	c.1396+6480T>G		intron_variant		ENST00000295754.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TGFBR2	ENST00000295754.10	c.1396+6480T>G		intron_variant		1	NM_003242.6	P1
TGFBR2	ENST00000359013.4	c.1471+6480T>G		intron_variant		1
TGFBR2	ENST00000672866.1	n.2992+6480T>G		intron_variant, non_coding_transcript_variant
TGFBR2	ENST00000673203.1	n.274+6480T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79627 AN: 151848 Hom.: 21137 Cov.: 31

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.524 AC: 79694 AN: 151966 Hom.: 21157 Cov.: 31 AF XY: 0.526 AC XY: 39070 AN XY: 74298

Gnomad4 AFR AF: 0.455

Gnomad4 AMR AF: 0.661

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.553

Gnomad4 SAS AF: 0.450

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.541

Gnomad4 OTH AF: 0.530

Alfa AF: 0.532 Hom.: 6942

Bravo AF: 0.536

Asia WGS AF: 0.499 AC: 1731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	5.5
DANN	Benign	0.81
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs9310940; hg19: chr3-30722218;