rs6081541

Variant names:

• chr20-19232246-A-G
• rs6081541
• NM_020689.4:c.142+19262A>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.142+19262A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,192 control chromosomes in the GnomAD database, including 3,607 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 0.21 (3607 hom., cov: 33)
• Consequence: SLC24A3 NM_020689.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 2 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]

LOC124904879 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.312 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.142+19262A>G		intron	N/A	NP_065740.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC24A3	ENST00000328041.11	TSL:1 MANE Select	c.142+19262A>G		intron	N/A	ENSP00000333519.5

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31378 AN: 152074 Hom.: 3606 Cov.: 33

Gnomad AFR AF: 0.0987

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.206 AC: 31397 AN: 152192 Hom.: 3607 Cov.: 33 AF XY: 0.210 AC XY: 15595 AN XY: 74406

African (AFR) AF: 0.0985 AC: 4091 AN: 41536

American (AMR) AF: 0.230 AC: 3513 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1043 AN: 3470

East Asian (EAS) AF: 0.185 AC: 957 AN: 5182

South Asian (SAS) AF: 0.325 AC: 1568 AN: 4824

European-Finnish (FIN) AF: 0.285 AC: 3021 AN: 10592

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16444 AN: 67980

Other (OTH) AF: 0.224 AC: 474 AN: 2114

Alfa AF: 0.217 Hom.: 501

Bravo AF: 0.196

Asia WGS AF: 0.250 AC: 864 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.64
PhyloP100		-1.5
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: rs6081541; hg19: chr20-19212890;