rs11669203

Variant names:

• chr19-7914916-G-C
• rs11669203
• NM_001419781.1:c.60G>C

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_001419781.1(TGFBR3L):​c.60G>C​(p.Gly20Gly) variant causes a synonymous 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_001419781.1 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.386
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP7: Synonymous conserved (PhyloP=0.386 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001419781.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TGFBR3L	NM_001419781.1	MANE Select	c.60G>C	p.Gly20Gly	synonymous	Exon 1 of 7	NP_001406710.1	H3BV60-1
	TGFBR3L	NM_001195259.2		c.-1352G>C		5_prime_UTR	Exon 1 of 6	NP_001182188.1	H3BV60-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TGFBR3L	ENST00000713907.1	MANE Select	c.60G>C	p.Gly20Gly	synonymous	Exon 1 of 7	ENSP00000519206.1	H3BV60-1
	TGFBR3L	ENST00000713908.1		c.60G>C	p.Gly20Gly	synonymous	Exon 1 of 6	ENSP00000519207.1	A0AAQ5BH11
	TGFBR3L	ENST00000869760.1		c.60G>C	p.Gly20Gly	synonymous	Exon 1 of 7	ENSP00000539819.1

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

African (AFR) AF: 0.0621 AC: 2582 AN: 41550

American (AMR) AF: 0.142 AC: 2167 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 387 AN: 3470

East Asian (EAS) AF: 0.133 AC: 687 AN: 5164

South Asian (SAS) AF: 0.118 AC: 569 AN: 4824

European-Finnish (FIN) AF: 0.202 AC: 2140 AN: 10602

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14570 AN: 67970

Other (OTH) AF: 0.153 AC: 323 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.3
DANN	Benign	0.60
PhyloP100		0.39
PromoterAI		0.011	Neutral

Splicing

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

Other links and lift over

dbSNP: rs11669203; hg19: chr19-7979801;