6-160261205-C-T

Variant names:

• chr6-160261205-C-T
• rs316024
• ENST00000366952.1:c.-1296-518G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000366952.1(SLC22A2):​c.-1296-518G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 152,032 control chromosomes in the GnomAD database, including 8,575 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 0.32 (8575 hom., cov: 32)
• Consequence: SLC22A2 ENST00000366952.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.747
• Publications: 17 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A2	ENST00000366952.1	c.-1296-518G>A		intron_variant	Intron 1 of 7	5		ENSP00000355919.1

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49112 AN: 151914 Hom.: 8560 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.323 AC: 49153 AN: 152032 Hom.: 8575 Cov.: 32 AF XY: 0.331 AC XY: 24640 AN XY: 74332

African (AFR) AF: 0.227 AC: 9415 AN: 41446

American (AMR) AF: 0.498 AC: 7602 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 980 AN: 3468

East Asian (EAS) AF: 0.453 AC: 2341 AN: 5170

South Asian (SAS) AF: 0.381 AC: 1829 AN: 4804

European-Finnish (FIN) AF: 0.377 AC: 3994 AN: 10582

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 22042 AN: 67976

Other (OTH) AF: 0.318 AC: 672 AN: 2110

Alfa AF: 0.331 Hom.: 15865

Bravo AF: 0.328

Asia WGS AF: 0.409 AC: 1423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.8
DANN	Benign	0.60
PhyloP100		0.75
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs316024; hg19: chr6-160682237;