9-20287950-T-C

Variant names:

• chr9-20287950-T-C
• rs7026582
• XM_017014592.2:c.-529+13276A>G

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+13276A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.616 in 152,050 control chromosomes in the GnomAD database, including 30,698 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 0.62 (30698 hom., cov: 32)
• Consequence: SLC24A2 XM_017014592.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.61
• 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93513 AN: 151932 Hom.: 30639 Cov.: 32

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.927

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.624

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

GnomAD4 genome AF: 0.616 AC: 93631 AN: 152050 Hom.: 30698 Cov.: 32 AF XY: 0.622 AC XY: 46197 AN XY: 74294

African (AFR) AF: 0.790 AC: 32764 AN: 41486

American (AMR) AF: 0.679 AC: 10384 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.604 AC: 2096 AN: 3470

East Asian (EAS) AF: 0.927 AC: 4808 AN: 5188

South Asian (SAS) AF: 0.828 AC: 3987 AN: 4816

European-Finnish (FIN) AF: 0.461 AC: 4854 AN: 10526

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.482 AC: 32741 AN: 67962

Other (OTH) AF: 0.628 AC: 1325 AN: 2110

Alfa AF: 0.545 Hom.: 44483

Bravo AF: 0.634

Asia WGS AF: 0.861 AC: 2996 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	11
DANN	Benign	0.91
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs7026582; hg19: chr9-20287948; COSMIC: COSV60341039;