rs2383113

Positions:

• chr9-19678271-A-C
• chr9-19678271-A-G
• chr9-19678271-A-T

Variant summary

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

The NM_020344.4(SLC24A2):​c.931-55972T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.642 in 152,084 control chromosomes in the GnomAD database, including 33,269 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 0.64 (33269 hom., cov: 32)
• Consequence: SLC24A2 NM_020344.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.546

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC24A2	NM_020344.4	c.931-55972T>G		intron_variant		ENST00000341998.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC24A2	ENST00000341998.7	c.931-55972T>G		intron_variant		1	NM_020344.4	P3
SLC24A2	ENST00000286344.4	c.931-55972T>G		intron_variant		1		A1

Frequencies

GnomAD3 genomes AF: 0.642 AC: 97585 AN: 151966 Hom.: 33244 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.942

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.642 AC: 97647 AN: 152084 Hom.: 33269 Cov.: 32 AF XY: 0.648 AC XY: 48155 AN XY: 74352

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.741

Gnomad4 ASJ AF: 0.620

Gnomad4 EAS AF: 0.942

Gnomad4 SAS AF: 0.713

Gnomad4 FIN AF: 0.729

Gnomad4 NFE AF: 0.726

Gnomad4 OTH AF: 0.655

Alfa AF: 0.704 Hom.: 49485

Bravo AF: 0.636

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	0.45

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: rs2383113; hg19: chr9-19678269;