chr3-30606875-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The XM_047449400.1(LOC105377015):c.50C>T(p.Pro17Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000222 in 1,349,260 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 4/5 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
XM_047449400.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC105377015 | XM_047449400.1 | c.50C>T | p.Pro17Leu | missense_variant | 1/2 | ||
TGFBR2 | NM_003242.6 | c.-9G>A | 5_prime_UTR_variant | 1/7 | ENST00000295754.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TGFBR2 | ENST00000295754.10 | c.-9G>A | 5_prime_UTR_variant | 1/7 | 1 | NM_003242.6 | P1 | ||
TGFBR2 | ENST00000359013.4 | c.-9G>A | 5_prime_UTR_variant | 1/8 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000188 AC: 3AN: 159648Hom.: 0 AF XY: 0.0000341 AC XY: 3AN XY: 88022
GnomAD4 exome AF: 0.00000222 AC: 3AN: 1349260Hom.: 0 Cov.: 30 AF XY: 0.00000452 AC XY: 3AN XY: 663104
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Loeys-Dietz syndrome 2 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | All of Us Research Program, National Institutes of Health | Jun 08, 2023 | This variant causes a G to A nucleotide substitution at the -9 position in the 5' untranslated region in the TGFBR2 protein. To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with TGFBR2-related disorders in the literature. This variant has been identified in 3/159648 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at