chr6-160205969-C-G

Variant names:

• chr6-160205969-C-G
• rs653753
• ENST00000801769.1:n.766C>G

Variant summary

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

The ENST00000801769.1(ENSG00000304281):​n.766C>G variant causes a non coding transcript exon 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: ENSG00000304281 ENST00000801769.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990
• Publications: 4 publications found

Genes affected

ENSG00000304281 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000801769.1. 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
	ENSG00000304281	ENST00000801769.1		n.766C>G		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000304281	ENST00000801770.1		n.469C>G		non_coding_transcript_exon	Exon 2 of 2
	SLC22A2	ENST00000486916.5	TSL:3	n.640+18736G>C		intron	N/A

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

African (AFR) AF: 0.856 AC: 35506 AN: 41488

American (AMR) AF: 0.911 AC: 13921 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.864 AC: 3000 AN: 3472

East Asian (EAS) AF: 0.960 AC: 4973 AN: 5178

South Asian (SAS) AF: 0.834 AC: 4011 AN: 4808

European-Finnish (FIN) AF: 0.921 AC: 9759 AN: 10596

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.863 AC: 58660 AN: 68002

Other (OTH) AF: 0.876 AC: 1851 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.7
DANN	Benign	0.86
PhyloP100		-0.099

Splicing

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

Other links and lift over

dbSNP: rs653753; hg19: chr6-160627001;