rs10819639

Positions:

• chr9-99132079-T-G

Variant summary

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

The NM_004612.4(TGFBR1):​c.344-430T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 152,018 control chromosomes in the GnomAD database, including 3,319 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 0.20 (3319 hom., cov: 31)
• Consequence: TGFBR1 NM_004612.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.81

Genes affected

TGFBR1 (HGNC:11772): (transforming growth factor beta receptor 1) The protein encoded by this gene forms a heteromeric complex with type II TGF-beta receptors when bound to TGF-beta, transducing the TGF-beta signal from the cell surface to the cytoplasm. The encoded protein is a serine/threonine protein kinase. Mutations in this gene have been associated with Loeys-Dietz aortic aneurysm syndrome (LDAS). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2008]

TGFBR1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TGFBR1	NM_004612.4	c.344-430T>G		intron_variant		ENST00000374994.9	NP_004603.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TGFBR1	ENST00000374994.9	c.344-430T>G		intron_variant		1	NM_004612.4	ENSP00000364133.4

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30359 AN: 151900 Hom.: 3318 Cov.: 31

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.0150

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.200 AC: 30379 AN: 152018 Hom.: 3319 Cov.: 31 AF XY: 0.194 AC XY: 14378 AN XY: 74304

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.0154

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.251

Gnomad4 OTH AF: 0.209

Alfa AF: 0.229 Hom.: 528

Bravo AF: 0.193

Asia WGS AF: 0.103 AC: 359 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.1
DANN	Benign	0.28

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: rs10819639; hg19: chr9-101894361;