9-19881866-C-G

Variant names:

• chr9-19881866-C-G
• rs1857437
• ENST00000656603.1:n.101-10853C>G

Variant summary

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

The ENST00000656603.1(ENSG00000286685):​n.101-10853C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.667 in 151,964 control chromosomes in the GnomAD database, including 34,606 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 0.67 (34606 hom., cov: 32)
• Consequence: ENSG00000286685 ENST00000656603.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.342
• Publications: 5 publications found

Genes affected

ENSG00000286685 (HGNC:):

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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656603.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286685	ENST00000656603.1		n.101-10853C>G		intron	N/A
	ENSG00000286685	ENST00000751385.1		n.181-10853C>G		intron	N/A
	ENSG00000286685	ENST00000751386.1		n.183-10853C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.667 AC: 101228 AN: 151846 Hom.: 34575 Cov.: 32

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.894

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.667 AC: 101295 AN: 151964 Hom.: 34606 Cov.: 32 AF XY: 0.667 AC XY: 49543 AN XY: 74266

African (AFR) AF: 0.524 AC: 21698 AN: 41418

American (AMR) AF: 0.635 AC: 9700 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2293 AN: 3460

East Asian (EAS) AF: 0.539 AC: 2781 AN: 5160

South Asian (SAS) AF: 0.765 AC: 3684 AN: 4818

European-Finnish (FIN) AF: 0.759 AC: 8025 AN: 10572

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.746 AC: 50689 AN: 67954

Other (OTH) AF: 0.677 AC: 1432 AN: 2114

Alfa AF: 0.640 Hom.: 2242

Bravo AF: 0.651

Asia WGS AF: 0.643 AC: 2233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.7
DANN	Benign	0.52
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs1857437; hg19: chr9-19881864;