9-89326028-T-C
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_024077.5(SECISBP2):āc.564T>Cā(p.Ser188=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00011 in 1,613,052 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.00048 ( 0 hom., cov: 33)
Exomes š: 0.000071 ( 0 hom. )
Consequence
SECISBP2
NM_024077.5 synonymous
NM_024077.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.308
Genes affected
SECISBP2 (HGNC:30972): (SECIS binding protein 2) The protein encoded by this gene is one of the essential components of the machinery involved in co-translational insertion of selenocysteine (Sec) into selenoproteins. Sec is encoded by the UGA codon, which normally signals translation termination. The recoding of UGA as Sec codon requires a Sec insertion sequence (SECIS) element; present in the 3' untranslated regions of eukaryotic selenoprotein mRNAs. This protein specifically binds to the SECIS element, which is stimulated by a Sec-specific translation elongation factor. Mutations in this gene have been associated with reduction in enzymatic activity of type II iodothyronine deiodinase (a selenoprotein) and abnormal thyroid hormone metabolism. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Aug 2017]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
Variant 9-89326028-T-C is Benign according to our data. Variant chr9-89326028-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 3044063.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.308 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SECISBP2 | NM_024077.5 | c.564T>C | p.Ser188= | synonymous_variant | 4/17 | ENST00000375807.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SECISBP2 | ENST00000375807.8 | c.564T>C | p.Ser188= | synonymous_variant | 4/17 | 1 | NM_024077.5 | P2 |
Frequencies
GnomAD3 genomes AF: 0.000466 AC: 71AN: 152202Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000144 AC: 36AN: 250240Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135364
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GnomAD4 exome AF: 0.0000712 AC: 104AN: 1460732Hom.: 0 Cov.: 31 AF XY: 0.0000633 AC XY: 46AN XY: 726740
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GnomAD4 genome AF: 0.000479 AC: 73AN: 152320Hom.: 0 Cov.: 33 AF XY: 0.000470 AC XY: 35AN XY: 74476
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
SECISBP2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 18, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at