9-19639715-T-C

Position:

• chr9-19639715-T-C

Variant summary

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

The NM_020344.4(SLC24A2):​c.931-17416A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.745 in 152,196 control chromosomes in the GnomAD database, including 42,331 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 0.74 (42331 hom., cov: 34)
• Consequence: SLC24A2 NM_020344.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.150

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC24A2	NM_020344.4	c.931-17416A>G		intron_variant		ENST00000341998.7	NP_065077.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC24A2	ENST00000341998.7	c.931-17416A>G		intron_variant		1	NM_020344.4	ENSP00000344801.1
SLC24A2	ENST00000286344.4	c.931-17416A>G		intron_variant		1		ENSP00000286344.3

Frequencies

GnomAD3 genomes AF: 0.745 AC: 113264 AN: 152078 Hom.: 42271 Cov.: 34

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.787

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.863

Gnomad SAS AF: 0.772

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.738

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

GnomAD4 genome AF: 0.745 AC: 113381 AN: 152196 Hom.: 42331 Cov.: 34 AF XY: 0.747 AC XY: 55601 AN XY: 74404

Gnomad4 AFR AF: 0.753

Gnomad4 AMR AF: 0.787

Gnomad4 ASJ AF: 0.702

Gnomad4 EAS AF: 0.863

Gnomad4 SAS AF: 0.773

Gnomad4 FIN AF: 0.759

Gnomad4 NFE AF: 0.722

Gnomad4 OTH AF: 0.739

Alfa AF: 0.731 Hom.: 18507

Bravo AF: 0.749

Asia WGS AF: 0.833 AC: 2898 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.3
DANN	Benign	0.67

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs748530; hg19: chr9-19639713;