chr1-91708703-A-G
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1
The NM_003243.5(TGFBR3):āc.2247T>Cā(p.Thr749=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.938 in 1,614,092 control chromosomes in the GnomAD database, including 711,345 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Genomes: š 0.94 ( 66664 hom., cov: 31)
Exomes š: 0.94 ( 644681 hom. )
Consequence
TGFBR3
NM_003243.5 synonymous
NM_003243.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.68
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
BP6
Variant 1-91708703-A-G is Benign according to our data. Variant chr1-91708703-A-G is described in ClinVar as [Benign]. Clinvar id is 3060406.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=2.68 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.935 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TGFBR3 | NM_003243.5 | c.2247T>C | p.Thr749= | synonymous_variant | 14/17 | ENST00000212355.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TGFBR3 | ENST00000212355.9 | c.2247T>C | p.Thr749= | synonymous_variant | 14/17 | 1 | NM_003243.5 | P3 |
Frequencies
GnomAD3 genomes AF: 0.935 AC: 142250AN: 152146Hom.: 66606 Cov.: 31
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GnomAD3 exomes AF: 0.933 AC: 234439AN: 251350Hom.: 109695 AF XY: 0.933 AC XY: 126757AN XY: 135846
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GnomAD4 exome AF: 0.939 AC: 1372215AN: 1461828Hom.: 644681 Cov.: 66 AF XY: 0.939 AC XY: 682563AN XY: 727216
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GnomAD4 genome AF: 0.935 AC: 142368AN: 152264Hom.: 66664 Cov.: 31 AF XY: 0.936 AC XY: 69670AN XY: 74444
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
TGFBR3-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
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DANN
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at