rs614564

Positions:

• chr6-160271687-A-G

Variant summary

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

The ENST00000366952.1(SLC22A2):​c.-1297+5766T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 152,136 control chromosomes in the GnomAD database, including 8,880 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 0.34 (8880 hom., cov: 33)
• Consequence: SLC22A2 ENST00000366952.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC22A2	ENST00000366952.1	c.-1297+5766T>C		intron_variant		5		ENSP00000355919

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51740 AN: 152018 Hom.: 8877 Cov.: 33

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.340 AC: 51779 AN: 152136 Hom.: 8880 Cov.: 33 AF XY: 0.338 AC XY: 25178 AN XY: 74382

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.328

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.369

Alfa AF: 0.349 Hom.: 9785

Bravo AF: 0.337

Asia WGS AF: 0.333 AC: 1162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.099
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs614564; hg19: chr6-160692719;