chr9-19897266-T-C

Variant names:

• chr9-19897266-T-C
• rs4977348
• XM_017014592.2:c.-390-6038A>G

Variant summary

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

The ENST00000751386.1(ENSG00000286685):​n.690T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 152,108 control chromosomes in the GnomAD database, including 8,188 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 0.31 (8188 hom., cov: 32)
• Consequence: ENSG00000286685 ENST00000751386.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281
• Publications: 4 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]

ENSG00000286685 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751386.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286685	ENST00000751386.1		n.690T>C		non_coding_transcript_exon	Exon 5 of 5
	ENSG00000286685	ENST00000751387.1		n.1046T>C		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000286685	ENST00000751388.1		n.800T>C		non_coding_transcript_exon	Exon 6 of 6

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47366 AN: 151988 Hom.: 8184 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.0912

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.312 AC: 47389 AN: 152108 Hom.: 8188 Cov.: 32 AF XY: 0.309 AC XY: 22962 AN XY: 74362

African (AFR) AF: 0.182 AC: 7571 AN: 41538

American (AMR) AF: 0.344 AC: 5249 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 941 AN: 3466

East Asian (EAS) AF: 0.0918 AC: 476 AN: 5184

South Asian (SAS) AF: 0.245 AC: 1180 AN: 4814

European-Finnish (FIN) AF: 0.393 AC: 4146 AN: 10546

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.395 AC: 26818 AN: 67978

Other (OTH) AF: 0.293 AC: 616 AN: 2104

Alfa AF: 0.372 Hom.: 17525

Bravo AF: 0.303

Asia WGS AF: 0.193 AC: 673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.43
DANN	Benign	0.60
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs4977348; hg19: chr9-19897264;