6-160216530-A-G

Position:

• chr6-160216530-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000486916.5(SLC22A2):​n.640+8175T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.723 in 151,878 control chromosomes in the GnomAD database, including 41,145 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 0.72 (41145 hom., cov: 32)
• Consequence: SLC22A2 ENST00000486916.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.494

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC22A2	ENST00000486916.5	n.640+8175T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.723 AC: 109783 AN: 151762 Hom.: 41114 Cov.: 32

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.825

Gnomad ASJ AF: 0.840

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.723 AC: 109859 AN: 151878 Hom.: 41145 Cov.: 32 AF XY: 0.731 AC XY: 54238 AN XY: 74228

Gnomad4 AFR AF: 0.528

Gnomad4 AMR AF: 0.825

Gnomad4 ASJ AF: 0.840

Gnomad4 EAS AF: 0.833

Gnomad4 SAS AF: 0.782

Gnomad4 FIN AF: 0.836

Gnomad4 NFE AF: 0.781

Gnomad4 OTH AF: 0.748

Alfa AF: 0.762 Hom.: 10547

Bravo AF: 0.716

Asia WGS AF: 0.799 AC: 2739 AN: 3426

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.3
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs595374; hg19: chr6-160637562;