rs11669203

chr19-7914916-G-C

Variant summary

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

The NM_001195259.2(TGFBR3L):c.-1352G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,194 control chromosomes in the GnomAD database, including 2,184 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 (2184 hom., cov: 32)
• Consequence: TGFBR3L NM_001195259.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.386

Genes affected

TGFBR3L (HGNC:44152): (transforming growth factor beta receptor 3 like) Predicted to enable glycosaminoglycan binding activity; transforming growth factor beta-activated receptor activity; and type II transforming growth factor beta receptor binding activity. Predicted to contribute to transforming growth factor beta binding activity. Predicted to be involved in several processes, including blood vessel morphogenesis; regulation of transforming growth factor beta receptor signaling pathway; and transforming growth factor beta receptor signaling pathway. Predicted to be integral component of membrane. Predicted to be active in cell surface and extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TGFBR3L	NM_001195259.2	c.-1352G>C		5_prime_UTR_variant	1/6	ENST00000565886.2
TGFBR3L	XM_011527610.3	c.-1352G>C		5_prime_UTR_variant	1/4
TGFBR3L	XM_011527613.3	c.-1352G>C		5_prime_UTR_variant	1/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TGFBR3L	ENST00000565886.2	c.-1352G>C		5_prime_UTR_variant	1/6	5	NM_001195259.2	P1

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23584 AN: 152076 Hom.: 2188 Cov.: 32

Gnomad AFR AF: 0.0622

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.155 AC: 23574 AN: 152194 Hom.: 2184 Cov.: 32 AF XY: 0.152 AC XY: 11313 AN XY: 74396

Gnomad4 AFR AF: 0.0621

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.153

Alfa AF: 0.187 Hom.: 393

Bravo AF: 0.146

Asia WGS AF: 0.123 AC: 427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	7.3
Dann	Benign	0.60

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11669203; hg19: chr19-7979801;