chr9-20220840-C-T

Variant names:

• chr9-20220840-C-T
• rs321225
• XM_017014592.2:c.-529+80386G>A

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+80386G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.458 in 151,938 control chromosomes in the GnomAD database, including 17,627 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 0.46 (17627 hom., cov: 31)
• Consequence: SLC24A2 XM_017014592.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.525
• Publications: 1 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.582 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: 0.459 AC: 69638 AN: 151820 Hom.: 17630 Cov.: 31

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.458 AC: 69638 AN: 151938 Hom.: 17627 Cov.: 31 AF XY: 0.451 AC XY: 33465 AN XY: 74266

African (AFR) AF: 0.300 AC: 12430 AN: 41412

American (AMR) AF: 0.370 AC: 5648 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2012 AN: 3468

East Asian (EAS) AF: 0.138 AC: 716 AN: 5174

South Asian (SAS) AF: 0.303 AC: 1460 AN: 4814

European-Finnish (FIN) AF: 0.543 AC: 5731 AN: 10552

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.587 AC: 39885 AN: 67944

Other (OTH) AF: 0.461 AC: 974 AN: 2114

Alfa AF: 0.523 Hom.: 16137

Bravo AF: 0.440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.64
DANN	Benign	0.58
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs321225; hg19: chr9-20220838;