rs1086567

chr6-160185309-G-A

Variant summary

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

The ENST00000486916.5(SLC22A2):n.641-13872C>T 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 0.542 in 151,868 control chromosomes in the GnomAD database, including 22,955 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 0.54 (22955 hom., cov: 32)
• Consequence: SLC22A2 ENST00000486916.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.619 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.641-13872C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.542 AC: 82255 AN: 151750 Hom.: 22941 Cov.: 32

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.542 AC: 82298 AN: 151868 Hom.: 22955 Cov.: 32 AF XY: 0.539 AC XY: 39989 AN XY: 74218

Gnomad4 AFR AF: 0.416

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.637

Gnomad4 EAS AF: 0.526

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.596

Gnomad4 NFE AF: 0.624

Gnomad4 OTH AF: 0.549

Alfa AF: 0.588 Hom.: 3273

Bravo AF: 0.530

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.2
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1086567; hg19: chr6-160606341;