rs7146198

Variant names:

• chr14-70177452-A-C
• rs7146198
• NM_182932.3:c.-62-8968T>G

Your query was ambiguous. Multiple possible variants found:

• chr14-70177452-A-C
• chr14-70177452-A-G
• chr14-70177452-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_182932.3(SLC8A3):​c.-62-8968T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.857 in 152,226 control chromosomes in the GnomAD database, including 55,960 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 0.86 (55960 hom., cov: 33)
• Consequence: SLC8A3 NM_182932.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276
• Publications: 5 publications found

Genes affected

SLC8A3 (HGNC:11070): (solute carrier family 8 member A3) This gene encodes a member of the sodium/calcium exchanger integral membrane protein family. Na+/Ca2+ exchange proteins are involved in maintaining Ca2+ homeostasis in a wide variety of cell types. The protein is regulated by intracellular calcium ions and is found in both the plasma membrane and intracellular organellar membranes, where exchange of Na+ for Ca2+ occurs in an electrogenic manner. Alternative splicing has been observed for this gene and multiple variants have been described. [provided by RefSeq, Aug 2013]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.866 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC8A3	NM_182932.3	c.-62-8968T>G		intron_variant	Intron 1 of 6	ENST00000356921.7	NP_891977.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC8A3	ENST00000356921.7	c.-62-8968T>G		intron_variant	Intron 1 of 6	1	NM_182932.3	ENSP00000349392.3

Frequencies

GnomAD3 genomes AF: 0.857 AC: 130310 AN: 152108 Hom.: 55908 Cov.: 33

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.747

Gnomad AMR AF: 0.878

Gnomad ASJ AF: 0.867

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.859

Gnomad FIN AF: 0.875

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.859

Gnomad OTH AF: 0.845

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.857 AC: 130419 AN: 152226 Hom.: 55960 Cov.: 33 AF XY: 0.856 AC XY: 63741 AN XY: 74434

African (AFR) AF: 0.862 AC: 35776 AN: 41518

American (AMR) AF: 0.879 AC: 13437 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.867 AC: 3007 AN: 3468

East Asian (EAS) AF: 0.702 AC: 3629 AN: 5172

South Asian (SAS) AF: 0.860 AC: 4150 AN: 4828

European-Finnish (FIN) AF: 0.875 AC: 9269 AN: 10594

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.859 AC: 58435 AN: 68032

Other (OTH) AF: 0.846 AC: 1789 AN: 2114

Alfa AF: 0.856 Hom.: 76582

Bravo AF: 0.854

Asia WGS AF: 0.821 AC: 2857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.73
DANN	Benign	0.62
PhyloP100		-0.28
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs7146198; hg19: chr14-70644169;