6-3270344-C-T

Position:

• chr6-3270344-C-T

Variant summary

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

The NM_015482.2(SLC22A23):​c.*2711G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0902 in 152,482 control chromosomes in the GnomAD database, including 726 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 0.090 (726 hom., cov: 33)
  • Exomes 𝑓: 0.075 (0 hom.)
• Consequence: SLC22A23 NM_015482.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

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]

SLC22A23 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC22A23	NM_015482.2	c.*2711G>A		3_prime_UTR_variant	10/10	ENST00000406686.8	NP_056297.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC22A23	ENST00000406686	c.*2711G>A		3_prime_UTR_variant	10/10	5	NM_015482.2	ENSP00000385028.3

Frequencies

GnomAD3 genomes AF: 0.0902 AC: 13727 AN: 152138 Hom.: 726 Cov.: 33

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.0407

Gnomad AMR AF: 0.0925

Gnomad ASJ AF: 0.0761

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0400

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.0734

Gnomad OTH AF: 0.108

GnomAD4 exome AF: 0.0752 AC: 17 AN: 226 Hom.: 0 Cov.: 0 AF XY: 0.0811 AC XY: 12 AN XY: 148

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.0786

Gnomad4 SAS exome AF: 0.500

Gnomad4 NFE exome AF: 0.0556

Gnomad4 OTH exome AF: 0.167

GnomAD4 genome AF: 0.0903 AC: 13743 AN: 152256 Hom.: 726 Cov.: 33 AF XY: 0.0890 AC XY: 6627 AN XY: 74454

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.0928

Gnomad4 ASJ AF: 0.0761

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.0400

Gnomad4 NFE AF: 0.0733

Gnomad4 OTH AF: 0.107

Alfa AF: 0.0732 Hom.: 565

Bravo AF: 0.0964

Asia WGS AF: 0.0840 AC: 294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.091
DANN	Benign	0.62

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: rs1127473; hg19: chr6-3270578;