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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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 v4.9

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;