rs9843942

Positions:

• chr3-30688144-G-A
• chr3-30688144-G-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_003242.6(TGFBR2):​c.1397-240G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 152,044 control chromosomes in the GnomAD database, including 14,828 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.43 (14828 hom., cov: 33)
• Consequence: TGFBR2 NM_003242.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.474

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BP6: Variant 3-30688144-G-A is Benign according to our data. Variant chr3-30688144-G-A is described in ClinVar as [Benign]. Clinvar id is 678626.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TGFBR2	NM_003242.6	c.1397-240G>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.1397-240G>A		intron_variant		1	NM_003242.6	ENSP00000295754	P1

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65716 AN: 151928 Hom.: 14794 Cov.: 33

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.433 AC: 65801 AN: 152044 Hom.: 14828 Cov.: 33 AF XY: 0.434 AC XY: 32262 AN XY: 74302

Gnomad4 AFR AF: 0.552

Gnomad4 AMR AF: 0.487

Gnomad4 ASJ AF: 0.453

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.478

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.366

Gnomad4 OTH AF: 0.417

Alfa AF: 0.379 Hom.: 14920

Bravo AF: 0.452

Asia WGS AF: 0.439 AC: 1530 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 18, 2018

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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.30
DANN	Benign	0.49
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs9843942; hg19: chr3-30729636;