6-3271554-C-G

Position:

• chr6-3271554-C-G

Variant summary

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

The NM_015482.2(SLC22A23):​c.*1501G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 152,350 control chromosomes in the GnomAD database, including 38,812 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 0.65 (38754 hom., cov: 32)
  • Exomes 𝑓: 0.79 (58 hom.)
• Consequence: SLC22A23 NM_015482.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.68

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC22A23	NM_015482.2	c.*1501G>C		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.*1501G>C		3_prime_UTR_variant	10/10	5	NM_015482.2	ENSP00000385028.3
SLC22A23	ENST00000436008	c.*1501G>C		3_prime_UTR_variant	11/11	5		ENSP00000410245.2
PSMG4	ENST00000454610.2	c.135+12358C>G		intron_variant		2		ENSP00000415768.2
PSMG4	ENST00000451246.2	c.175-10682C>G		intron_variant		3		ENSP00000407702.2

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99441 AN: 152048 Hom.: 38747 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.818

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.923

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.858

Gnomad OTH AF: 0.670

GnomAD4 exome AF: 0.786 AC: 143 AN: 182 Hom.: 58 Cov.: 0 AF XY: 0.741 AC XY: 80 AN XY: 108

Gnomad4 AFR exome AF: 0.500

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 0.793

Gnomad4 FIN exome AF: 0.900

Gnomad4 NFE exome AF: 0.667

Gnomad4 OTH exome AF: 0.875

GnomAD4 genome AF: 0.654 AC: 99458 AN: 152168 Hom.: 38754 Cov.: 32 AF XY: 0.658 AC XY: 48972 AN XY: 74410

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.747

Gnomad4 ASJ AF: 0.818

Gnomad4 EAS AF: 0.593

Gnomad4 SAS AF: 0.638

Gnomad4 FIN AF: 0.923

Gnomad4 NFE AF: 0.858

Gnomad4 OTH AF: 0.669

Alfa AF: 0.661 Hom.: 2636

Bravo AF: 0.621

Asia WGS AF: 0.604 AC: 2101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.026
DANN	Benign	0.49

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: rs3211066; hg19: chr6-3271788;