NM_020689.4:c.613-4182G>A

Variant names:

• chr20-19649880-G-A
• rs1406968
• NM_020689.4:c.613-4182G>A

Variant summary

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

The NM_020689.4(SLC24A3):​c.613-4182G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.645 in 152,002 control chromosomes in the GnomAD database, including 32,543 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 (32543 hom., cov: 32)
• Consequence: SLC24A3 NM_020689.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400
• Publications: 8 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC24A3	NM_020689.4	c.613-4182G>A		intron_variant	Intron 6 of 16	ENST00000328041.11	NP_065740.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC24A3	ENST00000328041.11	c.613-4182G>A		intron_variant	Intron 6 of 16	1	NM_020689.4	ENSP00000333519.5

Frequencies

GnomAD3 genomes AF: 0.645 AC: 97995 AN: 151884 Hom.: 32508 Cov.: 32

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.645 AC: 98080 AN: 152002 Hom.: 32543 Cov.: 32 AF XY: 0.635 AC XY: 47186 AN XY: 74312

African (AFR) AF: 0.768 AC: 31832 AN: 41454

American (AMR) AF: 0.550 AC: 8409 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1981 AN: 3468

East Asian (EAS) AF: 0.264 AC: 1365 AN: 5170

South Asian (SAS) AF: 0.506 AC: 2431 AN: 4808

European-Finnish (FIN) AF: 0.616 AC: 6498 AN: 10552

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.639 AC: 43444 AN: 67962

Other (OTH) AF: 0.615 AC: 1293 AN: 2104

Alfa AF: 0.632 Hom.: 140621

Bravo AF: 0.648

Asia WGS AF: 0.413 AC: 1438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.36
PhyloP100		0.040
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: rs1406968; hg19: chr20-19630524;