rs4987017
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005410.4(SELENOP):c.*818T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00596 in 1,110,286 control chromosomes in the GnomAD database, including 270 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.026 ( 169 hom., cov: 33)
Exomes 𝑓: 0.0028 ( 101 hom. )
Consequence
SELENOP
NM_005410.4 3_prime_UTR
NM_005410.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.823
Genes affected
CCDC152 (HGNC:34438): (coiled-coil domain containing 152)
SELENOP (HGNC:10751): (selenoprotein P) This gene encodes a selenoprotein that is predominantly expressed in the liver and secreted into the plasma. This selenoprotein is unique in that it contains multiple selenocysteine (Sec) residues per polypeptide (10 in human), and accounts for most of the selenium in plasma. It has been implicated as an extracellular antioxidant, and in the transport of selenium to extra-hepatic tissues via apolipoprotein E receptor-2 (apoER2). Mice lacking this gene exhibit neurological dysfunction, suggesting its importance in normal brain function. Sec is encoded by the UGA codon, which normally signals translation termination. The 3' UTRs of selenoprotein mRNAs contain a conserved stem-loop structure, designated the Sec insertion sequence (SECIS) element, that is necessary for the recognition of UGA as a Sec codon, rather than as a stop signal. The mRNA for this selenoprotein contains two SECIS elements. The use of alternative polyadenylation sites, one located in between the two SECIS elements, results in two populations of mRNAs containing either both (predominant) or just the upstream SECIS element (PMID:27881738). Alternatively spliced transcript variants have also been found for this gene. [provided by RefSeq, Oct 2018]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.087 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC152 | NM_001134848.2 | c.*121A>G | 3_prime_UTR_variant | 9/9 | ENST00000361970.10 | ||
SELENOP | NM_005410.4 | c.*818T>C | 3_prime_UTR_variant | 5/5 | ENST00000514985.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC152 | ENST00000361970.10 | c.*121A>G | 3_prime_UTR_variant | 9/9 | 1 | NM_001134848.2 | P1 | ||
SELENOP | ENST00000514985.6 | c.*818T>C | 3_prime_UTR_variant | 5/5 | 1 | NM_005410.4 | P1 | ||
CCDC152 | ENST00000388827.4 | c.*121A>G | 3_prime_UTR_variant | 7/7 | 2 | ||||
SELENOP | ENST00000512980.5 | n.4156T>C | non_coding_transcript_exon_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0258 AC: 3932AN: 152140Hom.: 168 Cov.: 33
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GnomAD4 exome AF: 0.00280 AC: 2682AN: 958028Hom.: 101 Cov.: 12 AF XY: 0.00241 AC XY: 1177AN XY: 488096
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GnomAD4 genome ? AF: 0.0259 AC: 3936AN: 152258Hom.: 169 Cov.: 33 AF XY: 0.0247 AC XY: 1840AN XY: 74456
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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