9-19678271-A-C

Variant names:

• chr9-19678271-A-C
• rs2383113
• NM_020344.4:c.931-55972T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020344.4. 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
	SLC24A2	NM_020344.4	MANE Select	c.931-55972T>G		intron	N/A	NP_065077.1
	SLC24A2	NM_001375850.1		c.931-55972T>G		intron	N/A	NP_001362779.1
	SLC24A2	NM_001193288.3		c.931-55972T>G		intron	N/A	NP_001180217.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC24A2	ENST00000341998.7	TSL:1 MANE Select	c.931-55972T>G		intron	N/A	ENSP00000344801.1
	SLC24A2	ENST00000286344.4	TSL:1	c.931-55972T>G		intron	N/A	ENSP00000286344.3

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

African (AFR) AF: 0.400 AC: 16560 AN: 41436

American (AMR) AF: 0.741 AC: 11302 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.620 AC: 2153 AN: 3470

East Asian (EAS) AF: 0.942 AC: 4877 AN: 5176

South Asian (SAS) AF: 0.713 AC: 3440 AN: 4824

European-Finnish (FIN) AF: 0.729 AC: 7733 AN: 10606

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.726 AC: 49334 AN: 67998

Other (OTH) AF: 0.655 AC: 1383 AN: 2110

Alfa AF: 0.696 Hom.: 61908

Bravo AF: 0.636

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.45
PhyloP100		-0.55
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: rs2383113; hg19: chr9-19678269;