rs16980240

Variant names:

• chr20-19241692-C-T
• rs16980240
• NM_020689.4:c.142+28708C>T

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+28708C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 151,338 control chromosomes in the GnomAD database, including 1,311 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 0.13 (1311 hom., cov: 33)
• Consequence: SLC24A3 NM_020689.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 5 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC24A3	NM_020689.4	c.142+28708C>T		intron_variant	Intron 1 of 16	ENST00000328041.11	NP_065740.2
LOC124904879	XR_007067551.1	n.7795C>T		non_coding_transcript_exon_variant	Exon 2 of 2
LOC124904879	XR_007067552.1	n.11343C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC24A3	ENST00000328041.11	c.142+28708C>T		intron_variant	Intron 1 of 16	1	NM_020689.4	ENSP00000333519.5

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19838 AN: 151218 Hom.: 1312 Cov.: 33

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.0886

Gnomad ASJ AF: 0.0684

Gnomad EAS AF: 0.0315

Gnomad SAS AF: 0.0703

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.131 AC: 19852 AN: 151338 Hom.: 1311 Cov.: 33 AF XY: 0.131 AC XY: 9670 AN XY: 74056

African (AFR) AF: 0.161 AC: 6671 AN: 41440

American (AMR) AF: 0.0884 AC: 1348 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.0684 AC: 237 AN: 3466

East Asian (EAS) AF: 0.0316 AC: 164 AN: 5190

South Asian (SAS) AF: 0.0701 AC: 338 AN: 4820

European-Finnish (FIN) AF: 0.155 AC: 1638 AN: 10570

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9031 AN: 67290

Other (OTH) AF: 0.115 AC: 242 AN: 2106

Alfa AF: 0.131 Hom.: 6191

Bravo AF: 0.128

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.28
DANN	Benign	0.85
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: rs16980240; hg19: chr20-19222336;