6-160231826-T-C

Variant names:

• chr6-160231826-T-C
• rs315978
• NM_003058.4:c.1502-7022A>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.1502-7022A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.877 in 151,784 control chromosomes in the GnomAD database, including 58,682 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 0.88 (58682 hom., cov: 31)
• Consequence: SLC22A2 NM_003058.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.138
• Publications: 5 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.944 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003058.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A2	NM_003058.4	MANE Select	c.1502-7022A>G		intron	N/A	NP_003049.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A2	ENST00000366953.8	TSL:1 MANE Select	c.1502-7022A>G		intron	N/A	ENSP00000355920.3
	SLC22A2	ENST00000486916.5	TSL:3	n.541-7022A>G		intron	N/A
	SLC22A2	ENST00000491092.1	TSL:5	n.1399-7022A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.877 AC: 132949 AN: 151666 Hom.: 58619 Cov.: 31

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.893

Gnomad AMR AF: 0.915

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.966

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.940

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.897

Gnomad OTH AF: 0.884

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

GnomAD4 genome AF: 0.877 AC: 133072 AN: 151784 Hom.: 58682 Cov.: 31 AF XY: 0.880 AC XY: 65303 AN XY: 74240

African (AFR) AF: 0.805 AC: 33102 AN: 41122

American (AMR) AF: 0.915 AC: 13993 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.846 AC: 2938 AN: 3472

East Asian (EAS) AF: 0.966 AC: 4990 AN: 5164

South Asian (SAS) AF: 0.866 AC: 4165 AN: 4810

European-Finnish (FIN) AF: 0.940 AC: 9961 AN: 10592

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.897 AC: 61009 AN: 68014

Other (OTH) AF: 0.887 AC: 1869 AN: 2108

Alfa AF: 0.888 Hom.: 74646

Bravo AF: 0.873

Asia WGS AF: 0.915 AC: 3180 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.27
DANN	Benign	0.42
PhyloP100		0.14
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: rs315978; hg19: chr6-160652858;