1-218346998-C-A
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_003238.6(TGFB2):c.297C>A(p.Tyr99Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. Y99Y) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_003238.6 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TGFB2 | NM_003238.6 | c.297C>A | p.Tyr99Ter | stop_gained | 1/7 | ENST00000366930.9 | |
TGFB2 | NM_001135599.4 | c.297C>A | p.Tyr99Ter | stop_gained | 1/8 | ||
TGFB2 | NR_138148.2 | n.1663C>A | non_coding_transcript_exon_variant | 1/7 | |||
TGFB2 | NR_138149.2 | n.1663C>A | non_coding_transcript_exon_variant | 1/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TGFB2 | ENST00000366930.9 | c.297C>A | p.Tyr99Ter | stop_gained | 1/7 | 1 | NM_003238.6 | P1 | |
TGFB2 | ENST00000366929.4 | c.297C>A | p.Tyr99Ter | stop_gained | 1/8 | 1 | |||
TGFB2 | ENST00000488793.1 | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Loeys-Dietz syndrome 4 Pathogenic:1
Pathogenic, criteria provided, single submitter | research | Baylor-Hopkins Center for Mendelian Genomics, Johns Hopkins University School of Medicine | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at