rs3127572

chr6-160261186-A-G

Variant summary

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

The ENST00000366952.1(SLC22A2):c.-1296-499T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,176 control chromosomes in the GnomAD database, including 1,836 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 0.14 (1836 hom., cov: 32)
• Consequence: SLC22A2 ENST00000366952.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.619

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.225 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.-1296-499T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21897 AN: 152058 Hom.: 1835 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.0538

Gnomad AMR AF: 0.0903

Gnomad ASJ AF: 0.0524

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.0758

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.144 AC: 21920 AN: 152176 Hom.: 1836 Cov.: 32 AF XY: 0.139 AC XY: 10350 AN XY: 74410

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.0900

Gnomad4 ASJ AF: 0.0524

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.0763

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.130

Alfa AF: 0.123 Hom.: 1916

Bravo AF: 0.145

Asia WGS AF: 0.0970 AC: 337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.0
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3127572; hg19: chr6-160682218;