rs316006

Positions:

• chr6-160225333-T-A
• chr6-160225333-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.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

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 (AMR) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC22A2	NM_003058.4	c.1502-529A>T		intron_variant		ENST00000366953.8	NP_003049.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC22A2	ENST00000366953.8	c.1502-529A>T		intron_variant		1	NM_003058.4	ENSP00000355920	P1
SLC22A2	ENST00000486916.5	n.541-529A>T		intron_variant, non_coding_transcript_variant		3
SLC22A2	ENST00000491092.1	n.1399-529A>T		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.472

Gnomad4 AMR AF: 0.817

Gnomad4 ASJ AF: 0.794

Gnomad4 EAS AF: 0.799

Gnomad4 SAS AF: 0.794

Gnomad4 FIN AF: 0.847

Gnomad4 NFE AF: 0.776

Gnomad4 OTH AF: 0.731

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.2
DANN	Benign	0.81

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

Publications

LitVar

Other links and lift over

dbSNP: rs316006; hg19: chr6-160646365;