6-160216207-T-C

Variant names:

• chr6-160216207-T-C
• rs596881
• ENST00000486916.5:n.640+8498A>G

Variant summary

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

The ENST00000486916.5(SLC22A2):​n.640+8498A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.845 in 151,972 control chromosomes in the GnomAD database, including 55,088 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 0.84 (55088 hom., cov: 31)
• Consequence: SLC22A2 ENST00000486916.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940
• Publications: 16 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.898 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	ENST00000486916.5	n.640+8498A>G		intron_variant	Intron 5 of 5	3

Frequencies

GnomAD3 genomes AF: 0.845 AC: 128313 AN: 151852 Hom.: 55049 Cov.: 31

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.896

Gnomad AMR AF: 0.910

Gnomad ASJ AF: 0.891

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.930

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.902

Gnomad OTH AF: 0.853

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

GnomAD4 genome AF: 0.845 AC: 128404 AN: 151972 Hom.: 55088 Cov.: 31 AF XY: 0.849 AC XY: 63118 AN XY: 74324

African (AFR) AF: 0.693 AC: 28650 AN: 41316

American (AMR) AF: 0.910 AC: 13899 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.891 AC: 3092 AN: 3472

East Asian (EAS) AF: 0.878 AC: 4527 AN: 5158

South Asian (SAS) AF: 0.866 AC: 4176 AN: 4822

European-Finnish (FIN) AF: 0.930 AC: 9859 AN: 10596

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.902 AC: 61335 AN: 68024

Other (OTH) AF: 0.856 AC: 1808 AN: 2112

Alfa AF: 0.882 Hom.: 189613

Bravo AF: 0.837

Asia WGS AF: 0.875 AC: 3042 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.8
DANN	Benign	0.21
PhyloP100		-0.094

Splicing

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

Other links and lift over

dbSNP: rs596881; hg19: chr6-160637239;