rs17878444

Positions:

• chr1-91772335-A-AATCCCATTTTTGTTTAGG

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_003243.5(TGFBR3):​c.247-13603_247-13586dupCCTAAACAAAAATGGGAT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.41 (13640 hom., cov: 0)
• Consequence: TGFBR3 NM_003243.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.21

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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TGFBR3	NM_003243.5	c.247-13603_247-13586dupCCTAAACAAAAATGGGAT		intron_variant		ENST00000212355.9	NP_003234.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TGFBR3	ENST00000212355.9	c.247-13586_247-13585insCCTAAACAAAAATGGGAT		intron_variant		1	NM_003243.5	ENSP00000212355.4

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62394 AN: 151218 Hom.: 13596 Cov.: 0

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.413 AC: 62495 AN: 151338 Hom.: 13640 Cov.: 0 AF XY: 0.413 AC XY: 30522 AN XY: 73922

Gnomad4 AFR AF: 0.535

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.391

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.474

Gnomad4 FIN AF: 0.347

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.406

Alfa AF: 0.377 Hom.: 1030

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17878444; hg19: chr1-92237892;