9-19512413-C-T

Variant summary

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

The NM_020344.4(SLC24A2):c.*3740G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 152,074 control chromosomes in the GnomAD database, including 8,880 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 0.32 (8879 hom., cov: 32)
  • Exomes 𝑓: 0.29 (1 hom.)
• Consequence: SLC24A2 NM_020344.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73

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]

LOC105375988 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.563 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC24A2	NM_020344.4	c.*3740G>A		3_prime_UTR_variant	11/11	ENST00000341998.7
LOC105375988	XR_007061431.1	n.692+24851C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC24A2	ENST00000341998.7	c.*3740G>A		3_prime_UTR_variant	11/11	1	NM_020344.4	P3
SLC24A2	ENST00000286344.4	c.*3740G>A		3_prime_UTR_variant	10/10	1		A1

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48666 AN: 151932 Hom.: 8846 Cov.: 32

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.0419

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.208

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.271

GnomAD4 exome AF: 0.292 AC: 7 AN: 24 Hom.: 1 Cov.: 0 AF XY: 0.375 AC XY: 6 AN XY: 16

Gnomad4 NFE exome AF: 0.250

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.321 AC: 48755 AN: 152050 Hom.: 8879 Cov.: 32 AF XY: 0.329 AC XY: 24413 AN XY: 74300

Gnomad4 AFR AF: 0.431

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.580

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.280

Alfa AF: 0.278 Hom.: 1642

Bravo AF: 0.333

Asia WGS AF: 0.517 AC: 1796 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.1
Dann	Benign	0.72

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: rs7872265; hg19: chr9-19512411;