chr10-13333906-T-C
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_012247.5(SEPHS1):c.471A>G(p.Thr157=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 1,612,738 control chromosomes in the GnomAD database, including 298,423 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.64 ( 31262 hom., cov: 32)
Exomes 𝑓: 0.60 ( 267161 hom. )
Consequence
SEPHS1
NM_012247.5 synonymous
NM_012247.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.77
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 -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
?
Variant 10-13333906-T-C is Benign according to our data. Variant chr10-13333906-T-C is described in ClinVar as [Benign]. Clinvar id is 1181340.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-2.77 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEPHS1 | NM_012247.5 | c.471A>G | p.Thr157= | synonymous_variant | 5/9 | ENST00000327347.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEPHS1 | ENST00000327347.10 | c.471A>G | p.Thr157= | synonymous_variant | 5/9 | 1 | NM_012247.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.639 AC: 97010AN: 151932Hom.: 31242 Cov.: 32
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GnomAD3 exomes AF: 0.638 AC: 160300AN: 251240Hom.: 51993 AF XY: 0.630 AC XY: 85542AN XY: 135806
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GnomAD4 exome AF: 0.603 AC: 880336AN: 1460688Hom.: 267161 Cov.: 37 AF XY: 0.603 AC XY: 437924AN XY: 726706
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GnomAD4 genome ? AF: 0.638 AC: 97071AN: 152050Hom.: 31262 Cov.: 32 AF XY: 0.639 AC XY: 47494AN XY: 74302
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 16, 2020 | - - |
Computational 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