NM_015482.2:c.655-17229A>C

Variant names:

• chr6-3433084-T-G
• rs17309827
• NM_015482.2:c.655-17229A>C

Variant summary

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

The NM_015482.2(SLC22A23):​c.655-17229A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 152,130 control chromosomes in the GnomAD database, including 8,164 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 0.30 (8164 hom., cov: 33)
• Consequence: SLC22A23 NM_015482.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.257

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 (EAS) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC22A23	NM_015482.2	c.655-17229A>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.655-17229A>C		intron_variant	Intron 1 of 9	5	NM_015482.2	ENSP00000385028.3

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46200 AN: 152012 Hom.: 8164 Cov.: 33

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.304 AC: 46208 AN: 152130 Hom.: 8164 Cov.: 33 AF XY: 0.309 AC XY: 22981 AN XY: 74384

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.476

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.318

Alfa AF: 0.359 Hom.: 18538

Bravo AF: 0.293

Asia WGS AF: 0.333 AC: 1153 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	3.6
DANN	Benign	0.83

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: rs17309827; hg19: chr6-3433318;