chr9-20145990-T-C

Variant names:

• chr9-20145990-T-C
• rs2039461
• XM_017014592.2:c.-528-141603A>G

Variant summary

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

The XM_017014592.2(SLC24A2):​c.-528-141603A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 151,902 control chromosomes in the GnomAD database, including 18,399 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 0.44 (18399 hom., cov: 31)
• Consequence: SLC24A2 XM_017014592.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.565
• Publications: 3 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67588 AN: 151786 Hom.: 18403 Cov.: 31

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.0824

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.445 AC: 67572 AN: 151902 Hom.: 18399 Cov.: 31 AF XY: 0.436 AC XY: 32349 AN XY: 74236

African (AFR) AF: 0.172 AC: 7117 AN: 41472

American (AMR) AF: 0.360 AC: 5498 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1913 AN: 3468

East Asian (EAS) AF: 0.0826 AC: 427 AN: 5168

South Asian (SAS) AF: 0.452 AC: 2175 AN: 4810

European-Finnish (FIN) AF: 0.555 AC: 5825 AN: 10498

Middle Eastern (MID) AF: 0.459 AC: 134 AN: 292

European-Non Finnish (NFE) AF: 0.630 AC: 42788 AN: 67926

Other (OTH) AF: 0.460 AC: 971 AN: 2110

Alfa AF: 0.563 Hom.: 73510

Bravo AF: 0.416

Asia WGS AF: 0.266 AC: 922 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.2
DANN	Benign	0.86
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs2039461; hg19: chr9-20145988;