9-89328674-C-T
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_024077.5(SECISBP2):c.589C>T(p.Arg197Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000205 in 1,613,620 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_024077.5 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 |
---|---|---|---|---|---|---|---|
SECISBP2 | NM_024077.5 | c.589C>T | p.Arg197Ter | stop_gained | 5/17 | ENST00000375807.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SECISBP2 | ENST00000375807.8 | c.589C>T | p.Arg197Ter | stop_gained | 5/17 | 1 | NM_024077.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152172Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251342Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135862
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1461448Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 727072
GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152172Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74336
ClinVar
Submissions by phenotype
not provided Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Oct 18, 2017 | The R197X variant in the SECISBP2 gene has been reported previously in an individual with SBP2 deficiency who also harbored an additional variant in the SECISBP2 gene (Dumitrescu and Refetoff, 2015). This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The R197X variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016). We interpret R197X as a likely pathogenic variant. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at