6-160255184-C-T

Position:

• chr6-160255184-C-T

Variant summary

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

The NM_003058.4(SLC22A2):​c.518+1430G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,216 control chromosomes in the GnomAD database, including 1,014 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 0.11 (1014 hom., cov: 33)
• Consequence: SLC22A2 NM_003058.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.37

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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.126 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC22A2	NM_003058.4	c.518+1430G>A		intron_variant		ENST00000366953.8	NP_003049.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC22A2	ENST00000366953.8	c.518+1430G>A		intron_variant		1	NM_003058.4	ENSP00000355920	P1
SLC22A2	ENST00000366952.1	c.455+1430G>A		intron_variant		5		ENSP00000355919
SLC22A2	ENST00000491092.1	n.415+3160G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16913 AN: 152098 Hom.: 1013 Cov.: 33

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0800

Gnomad ASJ AF: 0.0585

Gnomad EAS AF: 0.0920

Gnomad SAS AF: 0.0715

Gnomad FIN AF: 0.0953

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.0990

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

GnomAD4 genome AF: 0.111 AC: 16919 AN: 152216 Hom.: 1014 Cov.: 33 AF XY: 0.107 AC XY: 7969 AN XY: 74408

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.0797

Gnomad4 ASJ AF: 0.0585

Gnomad4 EAS AF: 0.0920

Gnomad4 SAS AF: 0.0720

Gnomad4 FIN AF: 0.0953

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.0980

Alfa AF: 0.124 Hom.: 306

Bravo AF: 0.109

Asia WGS AF: 0.0740 AC: 255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.8
DANN	Benign	0.60

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3798156; hg19: chr6-160676216;