9-89325602-C-T
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_024077.5(SECISBP2):c.358C>T(p.Arg120Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,613,954 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 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.358C>T | p.Arg120Ter | stop_gained | 3/17 | ENST00000375807.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SECISBP2 | ENST00000375807.8 | c.358C>T | p.Arg120Ter | stop_gained | 3/17 | 1 | NM_024077.5 | P2 | |
SECISBP2 | ENST00000339901.8 | c.139C>T | p.Arg47Ter | stop_gained | 3/17 | 1 | A2 | ||
SECISBP2 | ENST00000470305.1 | n.3403C>T | non_coding_transcript_exon_variant | 1/3 | 1 | ||||
SECISBP2 | ENST00000534113.6 | c.154C>T | p.Arg52Ter | stop_gained | 3/17 | 2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152116Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251414Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135874
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461838Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 727218
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152116Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74318
ClinVar
Submissions by phenotype
Thyroid hormone metabolism, abnormal 1 Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Nov 07, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at