6-160277707-C-A

Variant names:

• chr6-160277707-C-A
• rs9457880
• XR_001744437.2:n.2082C>A

Variant summary

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

The XR_001744437.2(LOC105378088):​n.2082C>A 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 0.0432 in 152,192 control chromosomes in the GnomAD database, including 265 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 0.043 (265 hom., cov: 32)
  • Exomes 𝑓: 0.063 (0 hom.)
• Consequence: LOC105378088 XR_001744437.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.961

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378088	XR_001744437.2	n.2082C>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A2	ENST00000366952.1	c.-1551G>T		upstream_gene_variant		5		ENSP00000355919.1

Frequencies

GnomAD3 genomes AF: 0.0433 AC: 6576 AN: 152042 Hom.: 265 Cov.: 32

Gnomad AFR AF: 0.0123

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0204

Gnomad ASJ AF: 0.0352

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.0772

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0441

Gnomad OTH AF: 0.0445

GnomAD4 exome AF: 0.0625 AC: 2 AN: 32 Hom.: 0 AF XY: 0.0769 AC XY: 2 AN XY: 26

Gnomad4 AFR exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0769

GnomAD4 genome AF: 0.0432 AC: 6574 AN: 152160 Hom.: 265 Cov.: 32 AF XY: 0.0477 AC XY: 3547 AN XY: 74368

Gnomad4 AFR AF: 0.0123

Gnomad4 AMR AF: 0.0204

Gnomad4 ASJ AF: 0.0352

Gnomad4 EAS AF: 0.183

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.0772

Gnomad4 NFE AF: 0.0441

Gnomad4 OTH AF: 0.0440

Alfa AF: 0.0429 Hom.: 47

Bravo AF: 0.0355

Asia WGS AF: 0.188 AC: 652 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.094
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9457880; hg19: chr6-160698739;