rs4016180
Positions:
- chr3-30691909-TTATATATATA-T
- chr3-30691909-TTATATATATA-TTATA
- chr3-30691909-TTATATATATA-TTATATA
- chr3-30691909-TTATATATATA-TTATATATA
- chr3-30691909-TTATATATATA-TTATATATATATA
- chr3-30691909-TTATATATATA-TTATATATATATATA
- chr3-30691909-TTATATATATA-TTATATATATATATATA
- chr3-30691909-TTATATATATA-TTATATATATATATATATA
- chr3-30691909-TTATATATATA-TTATATATATATATATATATA
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_003242.6(TGFBR2):c.*320_*329del variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.0000323 in 247,442 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000034 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000030 ( 1 hom. )
Consequence
TGFBR2
NM_003242.6 3_prime_UTR
NM_003242.6 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.96
Genes affected
TGFBR2 (HGNC:11773): (transforming growth factor beta receptor 2) The protein encoded by this gene is a transmembrane protein that has a protein kinase domain, forms a heterodimeric complex with TGF-beta receptor type-1, and binds TGF-beta. This receptor/ligand complex phosphorylates proteins, which then enter the nucleus and regulate the transcription of genes related to cell proliferation, cell cycle arrest, wound healing, immunosuppression, and tumorigenesis. Mutations in this gene have been associated with Marfan Syndrome, Loeys-Deitz Aortic Aneurysm Syndrome, and the development of various types of tumors. Alternatively spliced transcript variants encoding different isoforms have been characterized. [provided by RefSeq, Aug 2017]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
?
High AC in GnomAd4 at 5 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TGFBR2 | NM_003242.6 | c.*320_*329del | 3_prime_UTR_variant | 7/7 | ENST00000295754.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TGFBR2 | ENST00000295754.10 | c.*320_*329del | 3_prime_UTR_variant | 7/7 | 1 | NM_003242.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000339 AC: 5AN: 147324Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.0000300 AC: 3AN: 100118Hom.: 1 AF XY: 0.00 AC XY: 0AN XY: 49628
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GnomAD4 genome ? AF: 0.0000339 AC: 5AN: 147324Hom.: 0 Cov.: 0 AF XY: 0.0000279 AC XY: 2AN XY: 71690
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at