6-160275286-G-T

Variant names:

• chr6-160275286-G-T
• rs478112
• ENST00000366952.1:c.-1297+2167C>A

Variant summary

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

The ENST00000366952.1(SLC22A2):​c.-1297+2167C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 151,926 control chromosomes in the GnomAD database, including 16,945 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 0.47 (16945 hom., cov: 32)
• Consequence: SLC22A2 ENST00000366952.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365
• Publications: 1 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]

ENSG00000230234 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000366952.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A2	ENST00000366952.1	TSL:5	c.-1297+2167C>A		intron	N/A	ENSP00000355919.1
	ENSG00000230234	ENST00000419196.1	TSL:3	n.98-475G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71021 AN: 151808 Hom.: 16932 Cov.: 32

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.468 AC: 71073 AN: 151926 Hom.: 16945 Cov.: 32 AF XY: 0.462 AC XY: 34301 AN XY: 74244

African (AFR) AF: 0.527 AC: 21840 AN: 41406

American (AMR) AF: 0.331 AC: 5062 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1637 AN: 3468

East Asian (EAS) AF: 0.464 AC: 2393 AN: 5156

South Asian (SAS) AF: 0.378 AC: 1818 AN: 4814

European-Finnish (FIN) AF: 0.433 AC: 4560 AN: 10526

Middle Eastern (MID) AF: 0.507 AC: 148 AN: 292

European-Non Finnish (NFE) AF: 0.475 AC: 32316 AN: 67966

Other (OTH) AF: 0.483 AC: 1021 AN: 2114

Alfa AF: 0.459 Hom.: 2682

Bravo AF: 0.462

Asia WGS AF: 0.420 AC: 1461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.6
DANN	Benign	0.80
PhyloP100		-0.36
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: rs478112; hg19: chr6-160696318;