rs12459087
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1
The NM_015063.3(SLC8A2):c.267C>T(p.Ile89=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 1,614,138 control chromosomes in the GnomAD database, including 9,127 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 0.076 ( 595 hom., cov: 32)
Exomes 𝑓: 0.10 ( 8532 hom. )
Consequence
SLC8A2
NM_015063.3 synonymous
NM_015063.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.424
Genes affected
SLC8A2 (HGNC:11069): (solute carrier family 8 member A2) Predicted to enable calcium:cation antiporter activity involved in regulation of postsynaptic cytosolic calcium ion concentration and calcium:sodium antiporter activity. Predicted to be involved in several processes, including inorganic cation transmembrane transport; learning or memory; and regulation of short-term neuronal synaptic plasticity. Predicted to act upstream of or within several processes, including modulation of chemical synaptic transmission; regulation of action potential firing pattern; and response to ischemia. Part of presynapse. Biomarker of Alzheimer's disease. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.39).
BP7
?
Synonymous conserved (PhyloP=-0.424 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC8A2 | NM_015063.3 | c.267C>T | p.Ile89= | synonymous_variant | 2/10 | ENST00000236877.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC8A2 | ENST00000236877.11 | c.267C>T | p.Ile89= | synonymous_variant | 2/10 | 1 | NM_015063.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0765 AC: 11648AN: 152174Hom.: 595 Cov.: 32
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GnomAD3 exomes AF: 0.0898 AC: 22562AN: 251378Hom.: 1193 AF XY: 0.0934 AC XY: 12688AN XY: 135898
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GnomAD4 exome AF: 0.104 AC: 152173AN: 1461846Hom.: 8532 Cov.: 34 AF XY: 0.104 AC XY: 75738AN XY: 727226
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GnomAD4 genome ? AF: 0.0765 AC: 11646AN: 152292Hom.: 595 Cov.: 32 AF XY: 0.0759 AC XY: 5651AN XY: 74466
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at