rs16937883

Positions:

• chr9-20098713-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_017014592.2(SLC24A2):​c.-528-94326T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,240 control chromosomes in the GnomAD database, including 1,223 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 0.12 (1223 hom., cov: 32)
• Consequence: SLC24A2 XM_017014592.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.999

Genes affected

SLC24A2 (HGNC:10976): (solute carrier family 24 member 2) This gene encodes a member of the calcium/cation antiporter superfamily of transport proteins. The encoded protein belongs to the SLC24 branch of exchangers, which can mediate the extrusion of one Ca2+ ion and one K+ ion in exchange for four Na+ ions. This family member is a retinal cone/brain exchanger that can mediate a light-induced decrease in free Ca2+ concentration. This protein may also play a neuroprotective role during ischemic brain injury. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2011]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC24A2	XM_017014592.2	c.-528-94326T>C		intron_variant			XP_016870081.1
		n.20098713A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18227 AN: 152122 Hom.: 1224 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.0300

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0737

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.120 AC: 18236 AN: 152240 Hom.: 1223 Cov.: 32 AF XY: 0.119 AC XY: 8872 AN XY: 74448

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.0303

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.0737

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.124

Alfa AF: 0.105 Hom.: 1157

Bravo AF: 0.124

Asia WGS AF: 0.0720 AC: 248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.4
DANN	Benign	0.75

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs16937883; hg19: chr9-20098711;