rs653753

chr6-160205969-C-Gchr6-160205969-C-T

Variant summary

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

The ENST00000486916.5(SLC22A2):n.640+18736G>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.872 in 152,144 control chromosomes in the GnomAD database, including 57,964 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 0.87 (57964 hom., cov: 31)
• Consequence: SLC22A2 ENST00000486916.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990

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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 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	ENST00000486916.5	n.640+18736G>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.872 AC: 132604 AN: 152026 Hom.: 57916 Cov.: 31

Gnomad AFR AF: 0.856

Gnomad AMI AF: 0.854

Gnomad AMR AF: 0.911

Gnomad ASJ AF: 0.864

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.834

Gnomad FIN AF: 0.921

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.863

Gnomad OTH AF: 0.874

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

GnomAD4 genome AF: 0.872 AC: 132707 AN: 152144 Hom.: 57964 Cov.: 31 AF XY: 0.875 AC XY: 65060 AN XY: 74366

Gnomad4 AFR AF: 0.856

Gnomad4 AMR AF: 0.911

Gnomad4 ASJ AF: 0.864

Gnomad4 EAS AF: 0.960

Gnomad4 SAS AF: 0.834

Gnomad4 FIN AF: 0.921

Gnomad4 NFE AF: 0.863

Gnomad4 OTH AF: 0.876

Alfa AF: 0.876 Hom.: 6816

Bravo AF: 0.872

Asia WGS AF: 0.895 AC: 3112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	4.7
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs653753; hg19: chr6-160627001;