rs16980240

Positions:

• chr20-19241692-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
SLC24A3	NM_020689.4	c.142+28708C>T		intron_variant		ENST00000328041.11	NP_065740.2
LOC124904879	XR_007067551.1	n.7795C>T		non_coding_transcript_exon_variant	2/2
LOC124904879	XR_007067552.1	n.11343C>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC24A3	ENST00000328041.11	c.142+28708C>T		intron_variant		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

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.0884

Gnomad4 ASJ AF: 0.0684

Gnomad4 EAS AF: 0.0316

Gnomad4 SAS AF: 0.0701

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.115

Alfa AF: 0.130 Hom.: 2922

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs16980240; hg19: chr20-19222336;