chr6-160248686-T-C

Variant names:

• chr6-160248686-T-C
• rs3912161
• NM_003058.4:c.842+530A>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.842+530A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0596 in 152,268 control chromosomes in the GnomAD database, including 393 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 0.060 (393 hom., cov: 33)
• Consequence: SLC22A2 NM_003058.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.320
• Publications: 9 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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC22A2	NM_003058.4	c.842+530A>G		intron_variant	Intron 4 of 10	ENST00000366953.8	NP_003049.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A2	ENST00000366953.8	c.842+530A>G		intron_variant	Intron 4 of 10	1	NM_003058.4	ENSP00000355920.3
SLC22A2	ENST00000366952.1	c.779+530A>G		intron_variant	Intron 6 of 7	5		ENSP00000355919.1
SLC22A2	ENST00000491092.1	n.739+530A>G		intron_variant	Intron 3 of 9	5

Frequencies

GnomAD3 genomes AF: 0.0596 AC: 9063 AN: 152150 Hom.: 391 Cov.: 33

Gnomad AFR AF: 0.0137

Gnomad AMI AF: 0.0681

Gnomad AMR AF: 0.0952

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.0890

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0620

Gnomad OTH AF: 0.0775

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

GnomAD4 genome AF: 0.0596 AC: 9073 AN: 152268 Hom.: 393 Cov.: 33 AF XY: 0.0640 AC XY: 4764 AN XY: 74442

African (AFR) AF: 0.0136 AC: 567 AN: 41562

American (AMR) AF: 0.0957 AC: 1463 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 359 AN: 3470

East Asian (EAS) AF: 0.102 AC: 531 AN: 5182

South Asian (SAS) AF: 0.153 AC: 738 AN: 4820

European-Finnish (FIN) AF: 0.0890 AC: 943 AN: 10598

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0619 AC: 4213 AN: 68026

Other (OTH) AF: 0.0786 AC: 166 AN: 2112

Alfa AF: 0.0655 Hom.: 744

Bravo AF: 0.0552

Asia WGS AF: 0.140 AC: 487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.64
DANN	Benign	0.77
PhyloP100		-0.32
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: rs3912161; hg19: chr6-160669718;