6-160276730-A-G

Variant summary

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

The XR_001744437.2(LOC105378088):n.1105A>G 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 0.691 in 152,134 control chromosomes in the GnomAD database, including 36,639 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 0.69 (36639 hom., cov: 32)
• Consequence: LOC105378088 XR_001744437.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.214

Genes affected

LOC105378088 (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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378088	XR_001744437.2	n.1105A>G		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC22A2	ENST00000366952.1	c.-1297+723T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.691 AC: 104993 AN: 152016 Hom.: 36608 Cov.: 32

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.916

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.693

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

GnomAD4 genome AF: 0.691 AC: 105072 AN: 152134 Hom.: 36639 Cov.: 32 AF XY: 0.692 AC XY: 51470 AN XY: 74354

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.673

Gnomad4 ASJ AF: 0.616

Gnomad4 EAS AF: 0.916

Gnomad4 SAS AF: 0.721

Gnomad4 FIN AF: 0.665

Gnomad4 NFE AF: 0.658

Gnomad4 OTH AF: 0.697

Alfa AF: 0.661 Hom.: 37090

Bravo AF: 0.691

Asia WGS AF: 0.827 AC: 2876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.7
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs533452; hg19: chr6-160697762;