NM_015482.2:c.1210+3501C>A

Variant names:

• chr6-3294590-G-T
• rs9378357
• NM_015482.2:c.1210+3501C>A

Variant summary

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

The NM_015482.2(SLC22A23):​c.1210+3501C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,152 control chromosomes in the GnomAD database, including 4,773 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 (4773 hom., cov: 33)
• Consequence: SLC22A23 NM_015482.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89

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]

PSMG4 (HGNC:21108): (proteasome assembly chaperone 4) Predicted to be involved in proteasome assembly. Predicted to be part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC22A23	NM_015482.2	c.1210+3501C>A		intron_variant	Intron 5 of 9	ENST00000406686.8	NP_056297.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A23	ENST00000406686.8	c.1210+3501C>A		intron_variant	Intron 5 of 9	5	NM_015482.2	ENSP00000385028.3

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29669 AN: 152032 Hom.: 4758 Cov.: 33

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.0474

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.0744

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.195 AC: 29719 AN: 152152 Hom.: 4773 Cov.: 33 AF XY: 0.195 AC XY: 14489 AN XY: 74386

Gnomad4 AFR AF: 0.429

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.330

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.0474

Gnomad4 NFE AF: 0.0744

Gnomad4 OTH AF: 0.194

Alfa AF: 0.104 Hom.: 1199

Bravo AF: 0.212

Asia WGS AF: 0.310 AC: 1075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.13
DANN	Benign	0.65

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: rs9378357; hg19: chr6-3294824;