10-13328315-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_012247.5(SEPHS1):c.751+36G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 1,380,884 control chromosomes in the GnomAD database, including 190,224 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 0.45 ( 17097 hom., cov: 31)
Exomes 𝑓: 0.52 ( 173127 hom. )
Consequence
SEPHS1
NM_012247.5 intron
NM_012247.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.733
Genes affected
SEPHS1 (HGNC:19685): (selenophosphate synthetase 1) This gene encodes an enzyme that synthesizes selenophosphate from selenide and ATP. Selenophosphate is the selenium donor used to synthesize selenocysteine, which is co-translationally incorporated into selenoproteins at in-frame UGA codons. [provided by RefSeq, Sep 2010]
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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 (EAS) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SEPHS1 | ENST00000327347.10 | c.751+36G>A | intron_variant | Intron 7 of 8 | 1 | NM_012247.5 | ENSP00000367893.3 | |||
SEPHS1 | ENST00000545675.5 | c.550+36G>A | intron_variant | Intron 6 of 7 | 1 | ENSP00000441119.2 | ||||
SEPHS1 | ENST00000378614.8 | c.751+36G>A | intron_variant | Intron 7 of 7 | 1 | ENSP00000367877.3 |
Frequencies
GnomAD3 genomes AF: 0.447 AC: 67826AN: 151758Hom.: 17099 Cov.: 31
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GnomAD3 exomes AF: 0.544 AC: 132352AN: 243390Hom.: 38302 AF XY: 0.545 AC XY: 71665AN XY: 131488
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GnomAD4 exome AF: 0.524 AC: 643554AN: 1229008Hom.: 173127 Cov.: 16 AF XY: 0.526 AC XY: 327720AN XY: 622984
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GnomAD4 genome AF: 0.447 AC: 67840AN: 151876Hom.: 17097 Cov.: 31 AF XY: 0.453 AC XY: 33614AN XY: 74212
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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
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at