chr6-160254732-T-C

Variant names:

• chr6-160254732-T-C
• rs316009
• NM_003058.4:c.518+1882A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003058.4(SLC22A2):​c.518+1882A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.912 in 152,230 control chromosomes in the GnomAD database, including 63,374 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 0.91 (63374 hom., cov: 32)
• Consequence: SLC22A2 NM_003058.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 25 publications found

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]

ENSG00000294112 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.94 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC22A2	NM_003058.4	c.518+1882A>G		intron_variant	Intron 2 of 10	ENST00000366953.8	NP_003049.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A2	ENST00000366953.8	c.518+1882A>G		intron_variant	Intron 2 of 10	1	NM_003058.4	ENSP00000355920.3
ENSG00000294112	ENST00000721154.1	n.153T>C		non_coding_transcript_exon_variant	Exon 2 of 3
SLC22A2	ENST00000366952.1	c.455+1882A>G		intron_variant	Intron 4 of 7	5		ENSP00000355919.1
SLC22A2	ENST00000491092.1	n.415+3612A>G		intron_variant	Intron 1 of 9	5

Frequencies

GnomAD3 genomes AF: 0.912 AC: 138688 AN: 152112 Hom.: 63300 Cov.: 32

Gnomad AFR AF: 0.917

Gnomad AMI AF: 0.898

Gnomad AMR AF: 0.929

Gnomad ASJ AF: 0.860

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.877

Gnomad FIN AF: 0.941

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.902

Gnomad OTH AF: 0.912

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

GnomAD4 genome AF: 0.912 AC: 138821 AN: 152230 Hom.: 63374 Cov.: 32 AF XY: 0.914 AC XY: 68020 AN XY: 74434

African (AFR) AF: 0.917 AC: 38076 AN: 41532

American (AMR) AF: 0.929 AC: 14223 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.860 AC: 2980 AN: 3466

East Asian (EAS) AF: 0.963 AC: 4980 AN: 5174

South Asian (SAS) AF: 0.879 AC: 4231 AN: 4816

European-Finnish (FIN) AF: 0.941 AC: 9983 AN: 10612

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.902 AC: 61347 AN: 68006

Other (OTH) AF: 0.913 AC: 1931 AN: 2114

Alfa AF: 0.902 Hom.: 106377

Bravo AF: 0.912

Asia WGS AF: 0.926 AC: 3222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.011
DANN	Benign	0.31
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs316009; hg19: chr6-160675764;