Variant rs12459087 details in Genebe, Genetics Data Aggregator

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.Ile89Ile) 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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.424

Variant links:

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]

SLC8A2 links:

SLC8A2 (HGNC:):

SLC8A2 links:

Genome browser will be placed here

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	Protein	UniProt
SLC8A2	NM_015063.3 linkuse as main transcript	c.267C>T	p.Ile89Ile	synonymous_variant	2/10	ENST00000236877.11	NP_055878.1	Q9UPR5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC8A2	ENST00000236877.11 linkuse as main transcript	c.267C>T	p.Ile89Ile	synonymous_variant	2/10	1	NM_015063.3	ENSP00000236877.5		Q9UPR5

Frequencies

GnomAD3 genomes

AF:

0.0765

AC:

11648

AN:

152174

Hom.:

595

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0194

Gnomad AMI

AF:

0.160

Gnomad AMR

AF:

0.0627

Gnomad ASJ

AF:

0.0605

Gnomad EAS

AF:

0.0644

Gnomad SAS

AF:

0.109

Gnomad FIN

AF:

0.105

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.109

Gnomad OTH

AF:

0.0635

GnomAD3 exomes

AF:

0.0898

AC:

22562

AN:

251378

Hom.:

1193

AF XY:

0.0934

AC XY:

12688

AN XY:

135898

show subpopulations

Gnomad AFR exome

AF:

0.0172

Gnomad AMR exome

AF:

0.0451

Gnomad ASJ exome

AF:

0.0579

Gnomad EAS exome

AF:

0.0723

Gnomad SAS exome

AF:

0.109

Gnomad FIN exome

AF:

0.108

Gnomad NFE exome

AF:

0.111

Gnomad OTH exome

AF:

0.0850

GnomAD4 exome

AF:

0.104

AC:

152173

AN:

1461846

Hom.:

8532

Cov.:

AF XY:

0.104

AC XY:

75738

AN XY:

727226

show subpopulations

Gnomad4 AFR exome

AF:

0.0159

Gnomad4 AMR exome

AF:

0.0470

Gnomad4 ASJ exome

AF:

0.0584

Gnomad4 EAS exome

AF:

0.0505

Gnomad4 SAS exome

AF:

0.109

Gnomad4 FIN exome

AF:

0.109

Gnomad4 NFE exome

AF:

0.112

Gnomad4 OTH exome

AF:

0.0947

GnomAD4 genome

AF:

0.0765

AC:

11646

AN:

152292

Hom.:

595

Cov.:

AF XY:

0.0759

AC XY:

5651

AN XY:

74466

show subpopulations

Gnomad4 AFR

AF:

0.0193

Gnomad4 AMR

AF:

0.0626

Gnomad4 ASJ

AF:

0.0605

Gnomad4 EAS

AF:

0.0644

Gnomad4 SAS

AF:

0.108

Gnomad4 FIN

AF:

0.105

Gnomad4 NFE

AF:

0.109

Gnomad4 OTH

AF:

0.0629

Alfa

AF:

0.0993

Hom.:

1337

Bravo

AF:

0.0717

Asia WGS

AF:

0.0920

AC:

323

AN:

3478

EpiCase

AF:

0.101

EpiControl

AF:

0.100

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.39

CADD

Benign

6.3

DANN

Benign

0.88

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over