rs316006

Variant names:

• chr6-160225333-T-A
• rs316006
• NM_003058.4:c.1502-529A>T

Your query was ambiguous. Multiple possible variants found:

• chr6-160225333-T-A
• chr6-160225333-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.1502-529A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.703 in 152,134 control chromosomes in the GnomAD database, including 39,345 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 0.70 (39345 hom., cov: 33)
• Consequence: SLC22A2 NM_003058.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520
• Publications: 7 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=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.805 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A2	NM_003058.4	MANE Select	c.1502-529A>T		intron	N/A	NP_003049.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A2	ENST00000366953.8	TSL:1 MANE Select	c.1502-529A>T		intron	N/A	ENSP00000355920.3
	SLC22A2	ENST00000486916.5	TSL:3	n.541-529A>T		intron	N/A
	SLC22A2	ENST00000491092.1	TSL:5	n.1399-529A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.704 AC: 106952 AN: 152016 Hom.: 39323 Cov.: 33

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.839

Gnomad AMR AF: 0.816

Gnomad ASJ AF: 0.794

Gnomad EAS AF: 0.799

Gnomad SAS AF: 0.794

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.776

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.703 AC: 107015 AN: 152134 Hom.: 39345 Cov.: 33 AF XY: 0.711 AC XY: 52879 AN XY: 74378

African (AFR) AF: 0.472 AC: 19591 AN: 41476

American (AMR) AF: 0.817 AC: 12482 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.794 AC: 2754 AN: 3470

East Asian (EAS) AF: 0.799 AC: 4146 AN: 5186

South Asian (SAS) AF: 0.794 AC: 3823 AN: 4814

European-Finnish (FIN) AF: 0.847 AC: 8972 AN: 10598

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.776 AC: 52740 AN: 67984

Other (OTH) AF: 0.731 AC: 1545 AN: 2114

Alfa AF: 0.669 Hom.: 2187

Bravo AF: 0.692

Asia WGS AF: 0.797 AC: 2773 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.2
DANN	Benign	0.81
PhyloP100		0.052
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs316006; hg19: chr6-160646365;