16-29664607-C-T
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_003123.6(SPN):c.879C>T(p.Gly293=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0886 in 1,602,388 control chromosomes in the GnomAD database, including 11,764 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.079 ( 952 hom., cov: 31)
Exomes 𝑓: 0.090 ( 10812 hom. )
Consequence
SPN
NM_003123.6 synonymous
NM_003123.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.59
Genes affected
SPN (HGNC:11249): (sialophorin) This gene encodes a highly sialylated glycoprotein that functions in antigen-specific activation of T cells, and is found on the surface of thymocytes, T lymphocytes, monocytes, granulocytes, and some B lymphocytes. It contains a mucin-like extracellular domain, a transmembrane region and a carboxy-terminal intracellular region. The extracellular domain has a high proportion of serine and threonine residues, allowing extensive O-glycosylation, and has one potential N-glycosylation site, while the carboxy-terminal region has potential phosphorylation sites that may mediate transduction of activation signals. Different glycoforms of this protein have been described. In stimulated immune cells, proteolytic cleavage of the extracellular domain occurs in some cell types, releasing a soluble extracellular fragment. Defects in expression of this gene are associated with Wiskott-Aldrich syndrome. [provided by RefSeq, Sep 2017]
QPRT (HGNC:9755): (quinolinate phosphoribosyltransferase) This gene encodes a key enzyme in catabolism of quinolinate, an intermediate in the tryptophan-nicotinamide adenine dinucleotide pathway. Quinolinate acts as a most potent endogenous exitotoxin to neurons. Elevation of quinolinate levels in the brain has been linked to the pathogenesis of neurodegenerative disorders such as epilepsy, Alzheimer's disease, and Huntington's disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 16-29664607-C-T is Benign according to our data. Variant chr16-29664607-C-T is described in ClinVar as [Benign]. Clinvar id is 3059616.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPN | NM_003123.6 | c.879C>T | p.Gly293= | synonymous_variant | 2/2 | ENST00000652691.1 | |
SPN | NM_001030288.4 | c.879C>T | p.Gly293= | synonymous_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPN | ENST00000652691.1 | c.879C>T | p.Gly293= | synonymous_variant | 2/2 | NM_003123.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0788 AC: 11971AN: 151922Hom.: 948 Cov.: 31
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GnomAD3 exomes AF: 0.142 AC: 32698AN: 230572Hom.: 3756 AF XY: 0.144 AC XY: 18168AN XY: 125824
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GnomAD4 exome AF: 0.0897 AC: 130032AN: 1450348Hom.: 10812 Cov.: 32 AF XY: 0.0959 AC XY: 69170AN XY: 720930
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GnomAD4 genome AF: 0.0788 AC: 11979AN: 152040Hom.: 952 Cov.: 31 AF XY: 0.0851 AC XY: 6324AN XY: 74306
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
SPN-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 21, 2019 | This variant is classified as 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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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DG_spliceai
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at