rs576075

chr6-160264504-C-T

Variant summary

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

The ENST00000366952.1(SLC22A2):c.-1296-3817G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 151,986 control chromosomes in the GnomAD database, including 5,003 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 0.25 (5003 hom., cov: 32)
• Consequence: SLC22A2 ENST00000366952.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.42

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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC22A2	ENST00000366952.1	c.-1296-3817G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37789 AN: 151872 Hom.: 5002 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.0896

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.270

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.249 AC: 37802 AN: 151986 Hom.: 5003 Cov.: 32 AF XY: 0.244 AC XY: 18092 AN XY: 74276

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.354

Gnomad4 EAS AF: 0.0896

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.253

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.270

Alfa AF: 0.276 Hom.: 2918

Bravo AF: 0.245

Asia WGS AF: 0.113 AC: 397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	5.2
Dann	Benign	0.25

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs576075; hg19: chr6-160685536;