rs9391988

Positions:

• chr6-3307629-G-A

Variant summary

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

The NM_015482.2(SLC22A23):​c.1083-9411C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 152,110 control chromosomes in the GnomAD database, including 5,157 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 0.24 (5157 hom., cov: 33)
• Consequence: SLC22A23 NM_015482.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC22A23	NM_015482.2	c.1083-9411C>T		intron_variant		ENST00000406686.8	NP_056297.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC22A23	ENST00000406686.8	c.1083-9411C>T		intron_variant		5	NM_015482.2	ENSP00000385028	P2

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35798 AN: 151994 Hom.: 5154 Cov.: 33

Gnomad AFR AF: 0.0626

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.235 AC: 35798 AN: 152110 Hom.: 5157 Cov.: 33 AF XY: 0.240 AC XY: 17856 AN XY: 74346

Gnomad4 AFR AF: 0.0624

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.243

Alfa AF: 0.254 Hom.: 856

Bravo AF: 0.219

Asia WGS AF: 0.271 AC: 945 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.6
DANN	Benign	0.63

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: rs9391988; hg19: chr6-3307863;