rs902

Variant names:

• chr1-91682670-C-G
• rs902
• NM_003243.5:c.*1069G>C

Your query was ambiguous. Multiple possible variants found:

• chr1-91682670-C-G
• chr1-91682670-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003243.5(TGFBR3):​c.*1069G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.775 in 453,748 control chromosomes in the GnomAD database, including 137,443 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 0.79 (47878 hom., cov: 29)
  • Exomes 𝑓: 0.77 (89565 hom.)
• Consequence: TGFBR3 NM_003243.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.513
• Publications: 13 publications found

Genes affected

TGFBR3 (HGNC:11774): (transforming growth factor beta receptor 3) This locus encodes the transforming growth factor (TGF)-beta type III receptor. The encoded receptor is a membrane proteoglycan that often functions as a co-receptor with other TGF-beta receptor superfamily members. Ectodomain shedding produces soluble TGFBR3, which may inhibit TGFB signaling. Decreased expression of this receptor has been observed in various cancers. Alternatively spliced transcript variants encoding different isoforms have been identified for this gene.[provided by RefSeq, Sep 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.962 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003243.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TGFBR3	NM_003243.5	MANE Select	c.*1069G>C		3_prime_UTR	Exon 17 of 17	NP_003234.2
	TGFBR3	NM_001195683.2		c.*1069G>C		3_prime_UTR	Exon 17 of 17	NP_001182612.1
	TGFBR3	NM_001195684.1		c.*1069G>C		3_prime_UTR	Exon 18 of 18	NP_001182613.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TGFBR3	ENST00000212355.9	TSL:1 MANE Select	c.*1069G>C		3_prime_UTR	Exon 17 of 17	ENSP00000212355.4
	TGFBR3	ENST00000525962.5	TSL:1	c.*1069G>C		3_prime_UTR	Exon 16 of 16	ENSP00000436127.1
	TGFBR3	ENST00000370399.6	TSL:1	c.*1069G>C		3_prime_UTR	Exon 18 of 18	ENSP00000359426.2

Frequencies

GnomAD3 genomes AF: 0.790 AC: 119988 AN: 151834 Hom.: 47811 Cov.: 29

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.985

Gnomad SAS AF: 0.815

Gnomad FIN AF: 0.793

Gnomad MID AF: 0.755

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.777

GnomAD2 exomes AF: 0.785 AC: 102470 AN: 130460 AF XY: 0.784

Gnomad AFR exome AF: 0.875

Gnomad AMR exome AF: 0.772

Gnomad ASJ exome AF: 0.741

Gnomad EAS exome AF: 0.991

Gnomad FIN exome AF: 0.790

Gnomad NFE exome AF: 0.739

Gnomad OTH exome AF: 0.754

GnomAD4 exome AF: 0.767 AC: 231592 AN: 301796 Hom.: 89565 Cov.: 0 AF XY: 0.770 AC XY: 132420 AN XY: 171996

African (AFR) AF: 0.868 AC: 7426 AN: 8554

American (AMR) AF: 0.771 AC: 21015 AN: 27274

Ashkenazi Jewish (ASJ) AF: 0.743 AC: 8009 AN: 10786

East Asian (EAS) AF: 0.991 AC: 9128 AN: 9210

South Asian (SAS) AF: 0.803 AC: 47923 AN: 59650

European-Finnish (FIN) AF: 0.778 AC: 9625 AN: 12366

Middle Eastern (MID) AF: 0.749 AC: 861 AN: 1150

European-Non Finnish (NFE) AF: 0.736 AC: 116863 AN: 158764

Other (OTH) AF: 0.765 AC: 10742 AN: 14042

GnomAD4 genome AF: 0.790 AC: 120112 AN: 151952 Hom.: 47878 Cov.: 29 AF XY: 0.794 AC XY: 58996 AN XY: 74256

African (AFR) AF: 0.868 AC: 35997 AN: 41472

American (AMR) AF: 0.770 AC: 11754 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2540 AN: 3470

East Asian (EAS) AF: 0.985 AC: 5083 AN: 5162

South Asian (SAS) AF: 0.815 AC: 3897 AN: 4782

European-Finnish (FIN) AF: 0.793 AC: 8369 AN: 10554

Middle Eastern (MID) AF: 0.757 AC: 221 AN: 292

European-Non Finnish (NFE) AF: 0.736 AC: 49969 AN: 67938

Other (OTH) AF: 0.779 AC: 1641 AN: 2106

Alfa AF: 0.756 Hom.: 7730

Bravo AF: 0.792

Asia WGS AF: 0.891 AC: 3102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.50
PhyloP100		-0.51
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs902; hg19: chr1-92148227;