rs1131243
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_003243.5(TGFBR3):c.*19G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000182 in 1,261,744 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000089 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000018 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
TGFBR3
NM_003243.5 3_prime_UTR
NM_003243.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.122
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 -8 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BS2
?
High AC in GnomAdExome4 at 23 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TGFBR3 | NM_003243.5 | c.*19G>C | 3_prime_UTR_variant | 17/17 | ENST00000212355.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TGFBR3 | ENST00000212355.9 | c.*19G>C | 3_prime_UTR_variant | 17/17 | 1 | NM_003243.5 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 13AN: 145198Hom.: 0 Cov.: 32 FAILED QC
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32
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GnomAD4 exome AF: 0.0000182 AC: 23AN: 1261744Hom.: 0 Cov.: 31 AF XY: 0.0000241 AC XY: 15AN XY: 622120
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.0000895 AC: 13AN: 145330Hom.: 0 Cov.: 32 AF XY: 0.0000847 AC XY: 6AN XY: 70826
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Data not reliable, filtered out with message: AS_VQSR
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ClinVar
Not reported inComputational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at