chr6-160247009-C-T

Variant names:

• chr6-160247009-C-T
• rs316021
• NM_003058.4:c.957+175G>A

Variant summary

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

The NM_003058.4(SLC22A2):​c.957+175G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.702 in 152,102 control chromosomes in the GnomAD database, including 39,128 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 0.70 (39128 hom., cov: 32)
• Consequence: SLC22A2 NM_003058.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.142
• Publications: 8 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC22A2	NM_003058.4	c.957+175G>A		intron_variant	Intron 5 of 10	ENST00000366953.8	NP_003049.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A2	ENST00000366953.8	c.957+175G>A		intron_variant	Intron 5 of 10	1	NM_003058.4	ENSP00000355920.3
SLC22A2	ENST00000366952.1	c.894+175G>A		intron_variant	Intron 7 of 7	5		ENSP00000355919.1
SLC22A2	ENST00000491092.1	n.854+175G>A		intron_variant	Intron 4 of 9	5

Frequencies

GnomAD3 genomes AF: 0.702 AC: 106732 AN: 151984 Hom.: 39100 Cov.: 32

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.839

Gnomad AMR AF: 0.815

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.763

Gnomad SAS AF: 0.791

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.729

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

GnomAD4 genome AF: 0.702 AC: 106797 AN: 152102 Hom.: 39128 Cov.: 32 AF XY: 0.710 AC XY: 52838 AN XY: 74372

African (AFR) AF: 0.474 AC: 19656 AN: 41440

American (AMR) AF: 0.816 AC: 12476 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.789 AC: 2739 AN: 3472

East Asian (EAS) AF: 0.764 AC: 3945 AN: 5162

South Asian (SAS) AF: 0.793 AC: 3824 AN: 4822

European-Finnish (FIN) AF: 0.847 AC: 8979 AN: 10598

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.774 AC: 52664 AN: 67998

Other (OTH) AF: 0.732 AC: 1547 AN: 2112

Alfa AF: 0.761 Hom.: 87773

Bravo AF: 0.690

Asia WGS AF: 0.792 AC: 2755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.3
DANN	Benign	0.56
PhyloP100		0.14
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs316021; hg19: chr6-160668041;