1-91828164-G-A

Position:

• chr1-91828164-G-A

Variant summary

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

The NM_003243.5(TGFBR3):​c.62-30693C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 151,952 control chromosomes in the GnomAD database, including 3,857 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 0.22 (3857 hom., cov: 32)
• Consequence: TGFBR3 NM_003243.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TGFBR3	NM_003243.5	c.62-30693C>T		intron_variant		ENST00000212355.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TGFBR3	ENST00000212355.9	c.62-30693C>T		intron_variant		1	NM_003243.5	P3

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33686 AN: 151832 Hom.: 3856 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.222 AC: 33707 AN: 151952 Hom.: 3857 Cov.: 32 AF XY: 0.222 AC XY: 16495 AN XY: 74266

Gnomad4 AFR AF: 0.252

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.363

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.204

Alfa AF: 0.137 Hom.: 286

Bravo AF: 0.220

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.45
DANN	Benign	0.68

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: rs12132114; hg19: chr1-92293721;