3-30691909-TTATATATATA-TTATATATATATA
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The ENST00000295754.10(TGFBR2):c.*328_*329dup variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.075 ( 1092 hom., cov: 0)
Exomes 𝑓: 0.012 ( 7 hom. )
Consequence
TGFBR2
ENST00000295754.10 3_prime_UTR
ENST00000295754.10 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.163
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 Benign. Variant got -10 ACMG points.
BP6
Variant 3-30691909-T-TTA is Benign according to our data. Variant chr3-30691909-T-TTA is described in ClinVar as [Benign]. Clinvar id is 1231162.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TGFBR2 | NM_003242.6 | c.*328_*329dup | 3_prime_UTR_variant | 7/7 | ENST00000295754.10 | NP_003233.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TGFBR2 | ENST00000295754.10 | c.*328_*329dup | 3_prime_UTR_variant | 7/7 | 1 | NM_003242.6 | ENSP00000295754 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0751 AC: 11064AN: 147250Hom.: 1093 Cov.: 0
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GnomAD4 exome AF: 0.0116 AC: 1151AN: 98988Hom.: 7 Cov.: 0 AF XY: 0.0105 AC XY: 517AN XY: 49106
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GnomAD4 genome AF: 0.0752 AC: 11071AN: 147286Hom.: 1092 Cov.: 0 AF XY: 0.0725 AC XY: 5200AN XY: 71712
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 25, 2021 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at