rs321227

Variant names:

• chr9-20215409-G-A
• rs321227
• XM_017014592.2:c.-529+85817C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-20215409-G-A
• chr9-20215409-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_017014592.2(SLC24A2):​c.-529+85817C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 151,854 control chromosomes in the GnomAD database, including 17,355 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 0.45 (17355 hom., cov: 31)
• Consequence: SLC24A2 XM_017014592.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400
• Publications: 7 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC24A2	XM_017014592.2	c.-529+85817C>T		intron_variant	Intron 2 of 14		XP_016870081.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68326 AN: 151736 Hom.: 17358 Cov.: 31

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.450 AC: 68328 AN: 151854 Hom.: 17355 Cov.: 31 AF XY: 0.443 AC XY: 32885 AN XY: 74194

African (AFR) AF: 0.263 AC: 10871 AN: 41386

American (AMR) AF: 0.366 AC: 5588 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.575 AC: 1992 AN: 3466

East Asian (EAS) AF: 0.140 AC: 723 AN: 5180

South Asian (SAS) AF: 0.301 AC: 1446 AN: 4808

European-Finnish (FIN) AF: 0.550 AC: 5780 AN: 10508

Middle Eastern (MID) AF: 0.524 AC: 153 AN: 292

European-Non Finnish (NFE) AF: 0.592 AC: 40187 AN: 67928

Other (OTH) AF: 0.451 AC: 953 AN: 2114

Alfa AF: 0.368 Hom.: 1171

Bravo AF: 0.430

Asia WGS AF: 0.202 AC: 702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.54
PhyloP100		-0.040

Splicing

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

Other links and lift over

dbSNP: rs321227; hg19: chr9-20215407;