chr9-19881866-C-G

Position:

• chr9-19881866-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_017014592.2(SLC24A2):​c.-293+9265G>C 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: SLC24A2 XM_017014592.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.342

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]

ENSG00000286685 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC24A2	XM_017014592.2	c.-293+9265G>C		intron_variant			XP_016870081.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000286685	ENST00000656603.1	n.101-10853C>G		intron_variant

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

Gnomad4 AFR AF: 0.524

Gnomad4 AMR AF: 0.635

Gnomad4 ASJ AF: 0.663

Gnomad4 EAS AF: 0.539

Gnomad4 SAS AF: 0.765

Gnomad4 FIN AF: 0.759

Gnomad4 NFE AF: 0.746

Gnomad4 OTH AF: 0.677

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1857437; hg19: chr9-19881864;