rs662301

chr6-160275887-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000419196.1(ENSG00000230234):n.224C>T 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 0.0497 in 152,302 control chromosomes in the GnomAD database, including 270 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 0.050 (270 hom., cov: 32)
  • Exomes 𝑓: 0.15 (0 hom.)
• Consequence: ENST00000419196.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.41

Genes affected

(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

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.23).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0748 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378088	XR_001744437.2	n.262C>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000419196.1	n.224C>T		non_coding_transcript_exon_variant	2/2	3
SLC22A2	ENST00000366952.1	c.-1297+1566G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0497 AC: 7566 AN: 152138 Hom.: 270 Cov.: 32

Gnomad AFR AF: 0.0125

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0368

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0116

Gnomad FIN AF: 0.0578

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0765

Gnomad OTH AF: 0.0482

GnomAD4 exome AF: 0.152 AC: 7 AN: 46 Hom.: 0 Cov.: 0 AF XY: 0.192 AC XY: 5 AN XY: 26

Gnomad4 FIN exome AF: 0.167

Gnomad4 NFE exome AF: 0.158

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0497 AC: 7567 AN: 152256 Hom.: 270 Cov.: 32 AF XY: 0.0466 AC XY: 3469 AN XY: 74444

Gnomad4 AFR AF: 0.0124

Gnomad4 AMR AF: 0.0368

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0120

Gnomad4 FIN AF: 0.0578

Gnomad4 NFE AF: 0.0765

Gnomad4 OTH AF: 0.0477

Alfa AF: 0.0686 Hom.: 242

Bravo AF: 0.0485

Asia WGS AF: 0.0100 AC: 37 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.23
Cadd	Benign	17
Dann	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs662301; hg19: chr6-160696919;