rs744375

chr6-3349674-A-G

Variant summary

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

The NM_015482.2(SLC22A23):c.914-25672T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 152,056 control chromosomes in the GnomAD database, including 13,372 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 0.39 (13372 hom., cov: 33)
• Consequence: SLC22A23 NM_015482.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.638

Genes affected

SLC22A23 (HGNC:21106): (solute carrier family 22 member 23) SLC22A23 belongs to a large family of transmembrane proteins that function as uniporters, symporters, and antiporters to transport organic ions across cell membranes (Jacobsson et al., 2007 [PubMed 17714910]).[supplied by OMIM, Mar 2008]

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 (AFR) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC22A23	NM_015482.2	c.914-25672T>C		intron_variant		ENST00000406686.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC22A23	ENST00000406686.8	c.914-25672T>C		intron_variant		5	NM_015482.2	P2

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59719 AN: 151938 Hom.: 13366 Cov.: 33

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.393 AC: 59775 AN: 152056 Hom.: 13372 Cov.: 33 AF XY: 0.390 AC XY: 28991 AN XY: 74340

Gnomad4 AFR AF: 0.614

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.526

Gnomad4 SAS AF: 0.406

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.386

Alfa AF: 0.320 Hom.: 15863

Bravo AF: 0.412

Asia WGS AF: 0.472 AC: 1640 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	12
Dann	Benign	0.70

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: rs744375; hg19: chr6-3349908;