5-132333468-G-T

Variant names:

• chr5-132333468-G-T
• rs272882
• NM_003059.3:c.1047-1250G>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.1047-1250G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.706 in 152,046 control chromosomes in the GnomAD database, including 38,402 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 0.71 (38402 hom., cov: 31)
• Consequence: SLC22A4 NM_003059.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 15 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=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC22A4	NM_003059.3	c.1047-1250G>T		intron_variant	Intron 6 of 9	ENST00000200652.4	NP_003050.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A4	ENST00000200652.4	c.1047-1250G>T		intron_variant	Intron 6 of 9	1	NM_003059.3	ENSP00000200652.3
MIR3936HG	ENST00000621103.4	n.703-1158C>A		intron_variant	Intron 6 of 7	1
MIR3936HG	ENST00000616965.1	n.486-1158C>A		intron_variant	Intron 4 of 4	5
MIR3936HG	ENST00000669845.1	n.329-1158C>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.706 AC: 107186 AN: 151928 Hom.: 38369 Cov.: 31

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.869

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.709

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

GnomAD4 genome AF: 0.706 AC: 107274 AN: 152046 Hom.: 38402 Cov.: 31 AF XY: 0.694 AC XY: 51556 AN XY: 74320

African (AFR) AF: 0.806 AC: 33428 AN: 41494

American (AMR) AF: 0.709 AC: 10822 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2426 AN: 3472

East Asian (EAS) AF: 0.619 AC: 3194 AN: 5160

South Asian (SAS) AF: 0.439 AC: 2117 AN: 4824

European-Finnish (FIN) AF: 0.571 AC: 6013 AN: 10538

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.689 AC: 46813 AN: 67972

Other (OTH) AF: 0.708 AC: 1493 AN: 2108

Alfa AF: 0.695 Hom.: 14161

Bravo AF: 0.728

Asia WGS AF: 0.526 AC: 1830 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.22
DANN	Benign	0.34
PhyloP100		-1.8
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: rs272882; hg19: chr5-131669161;