chr5-132339715-G-A

Variant names:

• chr5-132339715-G-A
• rs272873
• NM_003059.3:c.1445-850G>A

Variant summary

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

The NM_003059.3(SLC22A4):​c.1445-850G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0733 in 152,076 control chromosomes in the GnomAD database, including 690 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 0.073 (690 hom., cov: 32)
• Consequence: SLC22A4 NM_003059.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.340
• Publications: 7 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.228 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.1445-850G>A		intron	N/A	NP_003050.2
	MIR3936HG	NR_110997.1		n.561-4789C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A4	ENST00000200652.4	TSL:1 MANE Select	c.1445-850G>A		intron	N/A	ENSP00000200652.3
	MIR3936HG	ENST00000621103.4	TSL:1	n.561-4789C>T		intron	N/A
	MIR3936HG	ENST00000616965.1	TSL:5	n.344-4789C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0734 AC: 11150 AN: 151958 Hom.: 690 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.0381

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.0781

Gnomad FIN AF: 0.0498

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0284

Gnomad OTH AF: 0.0696

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

GnomAD4 genome AF: 0.0733 AC: 11152 AN: 152076 Hom.: 690 Cov.: 32 AF XY: 0.0770 AC XY: 5724 AN XY: 74354

African (AFR) AF: 0.108 AC: 4462 AN: 41466

American (AMR) AF: 0.154 AC: 2349 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0381 AC: 132 AN: 3466

East Asian (EAS) AF: 0.239 AC: 1233 AN: 5156

South Asian (SAS) AF: 0.0769 AC: 371 AN: 4826

European-Finnish (FIN) AF: 0.0498 AC: 527 AN: 10584

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0284 AC: 1930 AN: 68002

Other (OTH) AF: 0.0679 AC: 143 AN: 2106

Alfa AF: 0.0458 Hom.: 1485

Bravo AF: 0.0875

Asia WGS AF: 0.138 AC: 480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.81
DANN	Benign	0.55
PhyloP100		0.34
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: rs272873; hg19: chr5-131675408;