rs4899329

Variant names:

• chr14-70153925-C-A
• rs4899329
• NM_182932.3:c.1784+12714G>T

Your query was ambiguous. Multiple possible variants found:

• chr14-70153925-C-A
• chr14-70153925-C-G
• chr14-70153925-C-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.1784+12714G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.652 in 152,192 control chromosomes in the GnomAD database, including 33,477 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 0.65 (33477 hom., cov: 33)
• Consequence: SLC8A3 NM_182932.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.141
• Publications: 3 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=-0.52).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.936 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_182932.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC8A3	NM_182932.3	MANE Select	c.1784+12714G>T		intron	N/A	NP_891977.1	P57103-2
	SLC8A3	NM_183002.3		c.1784+12714G>T		intron	N/A	NP_892114.1	P57103-1
	SLC8A3	NM_033262.5		c.1784+12714G>T		intron	N/A	NP_150287.1	P57103-7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC8A3	ENST00000356921.7	TSL:1 MANE Select	c.1784+12714G>T		intron	N/A	ENSP00000349392.3	P57103-2
	SLC8A3	ENST00000381269.6	TSL:1	c.1784+12714G>T		intron	N/A	ENSP00000370669.2	P57103-1
	SLC8A3	ENST00000528359.6	TSL:1	c.1784+12714G>T		intron	N/A	ENSP00000433531.1	P57103-7

Frequencies

GnomAD3 genomes AF: 0.652 AC: 99177 AN: 152074 Hom.: 33462 Cov.: 33

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.958

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.652 AC: 99239 AN: 152192 Hom.: 33477 Cov.: 33 AF XY: 0.654 AC XY: 48687 AN XY: 74396

African (AFR) AF: 0.784 AC: 32584 AN: 41546

American (AMR) AF: 0.568 AC: 8691 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.657 AC: 2282 AN: 3472

East Asian (EAS) AF: 0.958 AC: 4955 AN: 5170

South Asian (SAS) AF: 0.840 AC: 4045 AN: 4818

European-Finnish (FIN) AF: 0.523 AC: 5539 AN: 10594

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.573 AC: 38976 AN: 67980

Other (OTH) AF: 0.640 AC: 1353 AN: 2114

Alfa AF: 0.606 Hom.: 84890

Bravo AF: 0.657

Asia WGS AF: 0.876 AC: 3048 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	6.1
DANN	Benign	0.89
PhyloP100		0.14
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4899329; hg19: chr14-70620642;