rs3127594

chr6-160217072-T-Achr6-160217072-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC22A2	NM_003058.4	c.*360A>T		3_prime_UTR_variant	11/11	ENST00000366953.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC22A2	ENST00000366953.8	c.*360A>T		3_prime_UTR_variant	11/11	1	NM_003058.4	P1
SLC22A2	ENST00000498556.1	n.677A>T		non_coding_transcript_exon_variant	3/3	5
SLC22A2	ENST00000486916.5	n.640+7633A>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR exome AF: 0.163

Gnomad4 AMR exome AF: 0.0661

Gnomad4 ASJ exome AF: 0.0524

Gnomad4 EAS exome AF: 0.0345

Gnomad4 SAS exome AF: 0.0990

Gnomad4 FIN exome AF: 0.122

Gnomad4 NFE exome AF: 0.120

Gnomad4 OTH exome AF: 0.0968

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

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.0848

Gnomad4 ASJ AF: 0.0510

Gnomad4 EAS AF: 0.0447

Gnomad4 SAS AF: 0.0843

Gnomad4 FIN AF: 0.0937

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.107

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.7
Dann	Benign	0.77

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: rs3127594; hg19: chr6-160638104;