rs17136561

Variant names:

• chr6-3439463-T-G
• rs17136561
• NM_015482.2:c.654+16443A>C

Variant summary

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

The NM_015482.2(SLC22A23):​c.654+16443A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 332,700 control chromosomes in the GnomAD database, including 6,626 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 0.20 (3463 hom., cov: 32)
  • Exomes 𝑓: 0.18 (3163 hom.)
• Consequence: SLC22A23 NM_015482.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.211
• Publications: 2 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC22A23	NM_015482.2	c.654+16443A>C		intron_variant	Intron 1 of 9	ENST00000406686.8	NP_056297.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A23	ENST00000406686.8	c.654+16443A>C		intron_variant	Intron 1 of 9	5	NM_015482.2	ENSP00000385028.3

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31104 AN: 151904 Hom.: 3458 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.0883

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.187

GnomAD4 exome AF: 0.178 AC: 32072 AN: 180678 Hom.: 3163 Cov.: 0 AF XY: 0.170 AC XY: 17335 AN XY: 102134

African (AFR) AF: 0.285 AC: 1394 AN: 4896

American (AMR) AF: 0.117 AC: 1045 AN: 8944

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 715 AN: 4174

East Asian (EAS) AF: 0.0977 AC: 666 AN: 6820

South Asian (SAS) AF: 0.100 AC: 3608 AN: 36040

European-Finnish (FIN) AF: 0.248 AC: 2073 AN: 8352

Middle Eastern (MID) AF: 0.127 AC: 86 AN: 678

European-Non Finnish (NFE) AF: 0.204 AC: 20888 AN: 102170

Other (OTH) AF: 0.186 AC: 1597 AN: 8604

GnomAD4 genome AF: 0.205 AC: 31135 AN: 152022 Hom.: 3463 Cov.: 32 AF XY: 0.203 AC XY: 15108 AN XY: 74306

African (AFR) AF: 0.272 AC: 11279 AN: 41452

American (AMR) AF: 0.133 AC: 2040 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 569 AN: 3470

East Asian (EAS) AF: 0.110 AC: 567 AN: 5168

South Asian (SAS) AF: 0.0874 AC: 421 AN: 4818

European-Finnish (FIN) AF: 0.245 AC: 2581 AN: 10548

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13164 AN: 67972

Other (OTH) AF: 0.185 AC: 390 AN: 2108

Alfa AF: 0.207 Hom.: 407

Bravo AF: 0.198

Asia WGS AF: 0.105 AC: 364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	12
DANN	Benign	0.79
PhyloP100		-0.21
PromoterAI		0.016	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17136561; hg19: chr6-3439697;