17-17792961-C-T
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_030665.4(RAI1):c.13C>T(p.Arg5Ter) 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 Likely pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. R5R) has been classified as Likely benign.
Frequency
Consequence
NM_030665.4 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 |
---|---|---|---|---|---|---|---|
RAI1 | NM_030665.4 | c.13C>T | p.Arg5Ter | stop_gained | 3/6 | ENST00000353383.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAI1 | ENST00000353383.6 | c.13C>T | p.Arg5Ter | stop_gained | 3/6 | 1 | NM_030665.4 | P1 | |
RAI1 | ENST00000395774.1 | c.13C>T | p.Arg5Ter | stop_gained | 2/2 | 2 | |||
RAI1 | ENST00000471135.2 | c.13C>T | p.Arg5Ter | stop_gained | 4/4 | 3 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome Cov.: 43
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Smith-Magenis syndrome Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet | Aug 01, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.