rs11950562

Variant names:

• chr5-132316836-A-C
• rs11950562
• NM_003059.3:c.652+3068A>C

Your query was ambiguous. Multiple possible variants found:

• chr5-132316836-A-C
• chr5-132316836-A-T

Variant summary

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

The NM_003059.3(SLC22A4):​c.652+3068A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 152,128 control chromosomes in the GnomAD database, including 11,097 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 0.36 (11097 hom., cov: 32)
• Consequence: SLC22A4 NM_003059.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 50 publications found

Genes affected

SLC22A4 (HGNC:10968): (solute carrier family 22 member 4) 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. The encoded protein is an organic cation transporter and plasma integral membrane protein containing eleven putative transmembrane domains as well as a nucleotide-binding site motif. Transport by this protein is at least partially ATP-dependent. [provided by RefSeq, Jul 2008]

MIR3936HG (HGNC:40538): (MIR3936 host gene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003059.3. 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
	SLC22A4	NM_003059.3	MANE Select	c.652+3068A>C		intron	N/A	NP_003050.2
	MIR3936HG	NR_110997.1		n.825-4583T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A4	ENST00000200652.4	TSL:1 MANE Select	c.652+3068A>C		intron	N/A	ENSP00000200652.3
	MIR3936HG	ENST00000621103.4	TSL:1	n.825-4583T>G		intron	N/A
	SLC22A4	ENST00000491257.1	TSL:4	n.456+3068A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55281 AN: 152010 Hom.: 11090 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.364 AC: 55312 AN: 152128 Hom.: 11097 Cov.: 32 AF XY: 0.350 AC XY: 26050 AN XY: 74400

African (AFR) AF: 0.267 AC: 11067 AN: 41508

American (AMR) AF: 0.361 AC: 5510 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1706 AN: 3470

East Asian (EAS) AF: 0.00270 AC: 14 AN: 5194

South Asian (SAS) AF: 0.127 AC: 614 AN: 4828

European-Finnish (FIN) AF: 0.333 AC: 3521 AN: 10574

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.461 AC: 31300 AN: 67960

Other (OTH) AF: 0.404 AC: 850 AN: 2104

Alfa AF: 0.420 Hom.: 28879

Bravo AF: 0.367

Asia WGS AF: 0.0820 AC: 284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.0
DANN	Benign	0.70
PhyloP100		0.25
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: rs11950562; hg19: chr5-131652529;