rs3127594

Variant names:

• chr6-160217072-T-A
• rs3127594
• NM_003058.4:c.*360A>T

Your query was ambiguous. Multiple possible variants found:

• chr6-160217072-T-A
• chr6-160217072-T-C

Variant summary

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

The NM_003058.4(SLC22A2):​c.*360A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 174,332 control chromosomes in the GnomAD database, including 1,401 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 0.12 (1262 hom., cov: 33)
  • Exomes 𝑓: 0.11 (139 hom.)
• Consequence: SLC22A2 NM_003058.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09
• Publications: 15 publications found

Genes affected

SLC22A2 (HGNC:10966): (solute carrier family 22 member 2) Polyspecific organic cation transporters in the liver, kidney, intestine, and other organs are critical for elimination of many endogenous small organic cations as well as a wide array of drugs and environmental toxins. This gene is one of three similar cation transporter genes located in a cluster on chromosome 6. The encoded protein contains twelve putative transmembrane domains and is a plasma integral membrane protein. It is found primarily in the kidney, where it may mediate the first step in cation reabsorption. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003058.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A2	NM_003058.4	MANE Select	c.*360A>T		3_prime_UTR	Exon 11 of 11	NP_003049.2	O15244-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A2	ENST00000366953.8	TSL:1 MANE Select	c.*360A>T		3_prime_UTR	Exon 11 of 11	ENSP00000355920.3	O15244-1
	SLC22A2	ENST00000498556.1	TSL:5	n.677A>T		non_coding_transcript_exon	Exon 3 of 3
	SLC22A2	ENST00000486916.5	TSL:3	n.640+7633A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18369 AN: 152038 Hom.: 1262 Cov.: 33

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.0851

Gnomad ASJ AF: 0.0510

Gnomad EAS AF: 0.0448

Gnomad SAS AF: 0.0836

Gnomad FIN AF: 0.0937

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.108

GnomAD4 exome AF: 0.109 AC: 2415 AN: 22176 Hom.: 139 Cov.: 0 AF XY: 0.108 AC XY: 1211 AN XY: 11264

African (AFR) AF: 0.163 AC: 165 AN: 1014

American (AMR) AF: 0.0661 AC: 46 AN: 696

Ashkenazi Jewish (ASJ) AF: 0.0524 AC: 53 AN: 1012

East Asian (EAS) AF: 0.0345 AC: 54 AN: 1564

South Asian (SAS) AF: 0.0990 AC: 19 AN: 192

European-Finnish (FIN) AF: 0.122 AC: 98 AN: 800

Middle Eastern (MID) AF: 0.0814 AC: 7 AN: 86

European-Non Finnish (NFE) AF: 0.120 AC: 1817 AN: 15200

Other (OTH) AF: 0.0968 AC: 156 AN: 1612

GnomAD4 genome AF: 0.121 AC: 18380 AN: 152156 Hom.: 1262 Cov.: 33 AF XY: 0.118 AC XY: 8745 AN XY: 74394

African (AFR) AF: 0.163 AC: 6761 AN: 41464

American (AMR) AF: 0.0848 AC: 1296 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0510 AC: 177 AN: 3472

East Asian (EAS) AF: 0.0447 AC: 232 AN: 5190

South Asian (SAS) AF: 0.0843 AC: 407 AN: 4828

European-Finnish (FIN) AF: 0.0937 AC: 993 AN: 10600

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8199 AN: 67996

Other (OTH) AF: 0.107 AC: 226 AN: 2110

Alfa AF: 0.112 Hom.: 599

Bravo AF: 0.120

Asia WGS AF: 0.0730 AC: 252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.7
DANN	Benign	0.77
PhyloP100		1.1
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: rs3127594; hg19: chr6-160638104;