5-132329685-A-G

Variant names:

• chr5-132329685-A-G
• rs272889
• NM_003059.3:c.952-2071A>G

Variant summary

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

The NM_003059.3(SLC22A4):​c.952-2071A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.629 in 152,000 control chromosomes in the GnomAD database, including 30,875 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 0.63 (30875 hom., cov: 30)
• Consequence: SLC22A4 NM_003059.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.571
• Publications: 57 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC22A4	NM_003059.3	c.952-2071A>G		intron_variant	Intron 5 of 9	ENST00000200652.4	NP_003050.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A4	ENST00000200652.4	c.952-2071A>G		intron_variant	Intron 5 of 9	1	NM_003059.3	ENSP00000200652.3
MIR3936HG	ENST00000621103.4	n.824+2504T>C		intron_variant	Intron 7 of 7	1
MIR3936HG	ENST00000669845.1	n.450+2504T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.629 AC: 95485 AN: 151880 Hom.: 30842 Cov.: 30

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.629 AC: 95573 AN: 152000 Hom.: 30875 Cov.: 30 AF XY: 0.618 AC XY: 45888 AN XY: 74288

African (AFR) AF: 0.744 AC: 30858 AN: 41484

American (AMR) AF: 0.659 AC: 10073 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 2049 AN: 3472

East Asian (EAS) AF: 0.351 AC: 1810 AN: 5164

South Asian (SAS) AF: 0.374 AC: 1804 AN: 4820

European-Finnish (FIN) AF: 0.495 AC: 5215 AN: 10534

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.612 AC: 41581 AN: 67938

Other (OTH) AF: 0.632 AC: 1331 AN: 2106

Alfa AF: 0.621 Hom.: 134443

Bravo AF: 0.653

Asia WGS AF: 0.402 AC: 1401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.070
DANN	Benign	0.61
PhyloP100		-0.57
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: rs272889; hg19: chr5-131665378;