NM_020689.4:c.143-20127A>G

Variant names:

• chr20-19260832-A-G
• rs4814836
• NM_020689.4:c.143-20127A>G

Variant summary

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

The NM_020689.4(SLC24A3):​c.143-20127A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 152,118 control chromosomes in the GnomAD database, including 5,726 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 0.25 (5726 hom., cov: 33)
• Consequence: SLC24A3 NM_020689.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.791
• Publications: 7 publications found

Genes affected

SLC24A3 (HGNC:10977): (solute carrier family 24 member 3) Plasma membrane sodium/calcium exchangers are an important component of intracellular calcium homeostasis and electrical conduction. Potassium-dependent sodium/calcium exchangers such as SLC24A3 are believed to transport 1 intracellular calcium and 1 potassium ion in exchange for 4 extracellular sodium ions (Kraev et al., 2001 [PubMed 11294880]).[supplied by OMIM, Mar 2008]

SLC24A3-AS1 (HGNC:40540): (SLC24A3 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.751 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020689.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC24A3	NM_020689.4	MANE Select	c.143-20127A>G		intron	N/A	NP_065740.2
	SLC24A3-AS1	NR_024564.1		n.1037+877T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC24A3	ENST00000328041.11	TSL:1 MANE Select	c.143-20127A>G		intron	N/A	ENSP00000333519.5
	SLC24A3-AS1	ENST00000319682.2	TSL:2	n.1037+877T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37447 AN: 152000 Hom.: 5725 Cov.: 33

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.772

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.266

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

GnomAD4 genome AF: 0.246 AC: 37474 AN: 152118 Hom.: 5726 Cov.: 33 AF XY: 0.253 AC XY: 18774 AN XY: 74352

African (AFR) AF: 0.246 AC: 10203 AN: 41498

American (AMR) AF: 0.401 AC: 6122 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 729 AN: 3470

East Asian (EAS) AF: 0.771 AC: 3961 AN: 5140

South Asian (SAS) AF: 0.183 AC: 885 AN: 4824

European-Finnish (FIN) AF: 0.176 AC: 1866 AN: 10602

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12826 AN: 67988

Other (OTH) AF: 0.268 AC: 566 AN: 2112

Alfa AF: 0.221 Hom.: 8103

Bravo AF: 0.271

Asia WGS AF: 0.446 AC: 1548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.3
DANN	Benign	0.54
PhyloP100		0.79
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: rs4814836; hg19: chr20-19241476;