6-160192675-T-C

Variant summary

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

The ENST00000486916.5(SLC22A2):n.641-21238A>G 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 0.708 in 151,838 control chromosomes in the GnomAD database, including 38,064 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 0.71 (38064 hom., cov: 31)
• Consequence: SLC22A2 ENST00000486916.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.195

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 = 0.808 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.641-21238A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.708 AC: 107425 AN: 151722 Hom.: 38033 Cov.: 31

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.809

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.828

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.708 AC: 107509 AN: 151838 Hom.: 38064 Cov.: 31 AF XY: 0.708 AC XY: 52518 AN XY: 74218

Gnomad4 AFR AF: 0.711

Gnomad4 AMR AF: 0.732

Gnomad4 ASJ AF: 0.758

Gnomad4 EAS AF: 0.829

Gnomad4 SAS AF: 0.670

Gnomad4 FIN AF: 0.673

Gnomad4 NFE AF: 0.696

Gnomad4 OTH AF: 0.715

Alfa AF: 0.695 Hom.: 20020

Bravo AF: 0.713

Asia WGS AF: 0.747 AC: 2589 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.7
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs791190; hg19: chr6-160613707;