6-3269871-C-T

Variant names:

• chr6-3269871-C-T
• rs3813486
• NM_015482.2:c.*3184G>A

Variant summary

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

The NM_015482.2(SLC22A23):​c.*3184G>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 0.855 in 152,870 control chromosomes in the GnomAD database, including 56,103 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 0.86 (55877 hom., cov: 34)
  • Exomes 𝑓: 0.87 (226 hom.)
• Consequence: SLC22A23 NM_015482.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600
• Publications: 3 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]

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.862 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC22A23	NM_015482.2	c.*3184G>A		3_prime_UTR_variant	Exon 10 of 10	ENST00000406686.8	NP_056297.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A23	ENST00000406686.8	c.*3184G>A		3_prime_UTR_variant	Exon 10 of 10	5	NM_015482.2	ENSP00000385028.3

Frequencies

GnomAD3 genomes AF: 0.855 AC: 130154 AN: 152164 Hom.: 55835 Cov.: 34

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.895

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.864

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.911

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.868

Gnomad OTH AF: 0.826

GnomAD4 exome AF: 0.874 AC: 514 AN: 588 Hom.: 226 Cov.: 0 AF XY: 0.861 AC XY: 298 AN XY: 346

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.809 AC: 110 AN: 136

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.892 AC: 387 AN: 434

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.875 AC: 7 AN: 8

Other (OTH) AF: 1.00 AC: 10 AN: 10

GnomAD4 genome AF: 0.855 AC: 130253 AN: 152282 Hom.: 55877 Cov.: 34 AF XY: 0.854 AC XY: 63610 AN XY: 74454

African (AFR) AF: 0.862 AC: 35807 AN: 41536

American (AMR) AF: 0.832 AC: 12731 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.864 AC: 2997 AN: 3470

East Asian (EAS) AF: 0.681 AC: 3524 AN: 5178

South Asian (SAS) AF: 0.768 AC: 3713 AN: 4834

European-Finnish (FIN) AF: 0.911 AC: 9655 AN: 10604

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.868 AC: 59048 AN: 68034

Other (OTH) AF: 0.826 AC: 1747 AN: 2116

Alfa AF: 0.862 Hom.: 10058

Bravo AF: 0.847

Asia WGS AF: 0.751 AC: 2608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.73
DANN	Benign	0.76
PhyloP100		0.060
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: rs3813486; hg19: chr6-3270105;