rs2306772

Variant names:

• chr5-132340288-C-T
• rs2306772
• NM_003059.3:c.1445-277C>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.1445-277C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0767 in 151,914 control chromosomes in the GnomAD database, including 569 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 0.077 (569 hom., cov: 31)
• Consequence: SLC22A4 NM_003059.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.510
• Publications: 17 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC22A4	NM_003059.3	c.1445-277C>T		intron_variant	Intron 8 of 9	ENST00000200652.4	NP_003050.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A4	ENST00000200652.4	c.1445-277C>T		intron_variant	Intron 8 of 9	1	NM_003059.3	ENSP00000200652.3
MIR3936HG	ENST00000621103.4	n.561-5362G>A		intron_variant	Intron 5 of 7	1
MIR3936HG	ENST00000616965.1	n.344-5362G>A		intron_variant	Intron 3 of 4	5
MIR3936HG	ENST00000669845.1	n.187-5362G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0767 AC: 11643 AN: 151792 Hom.: 570 Cov.: 31

Gnomad AFR AF: 0.0616

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.0491

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.0640

Gnomad FIN AF: 0.0756

Gnomad MID AF: 0.0605

Gnomad NFE AF: 0.0767

Gnomad OTH AF: 0.0760

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

GnomAD4 genome AF: 0.0767 AC: 11646 AN: 151914 Hom.: 569 Cov.: 31 AF XY: 0.0758 AC XY: 5629 AN XY: 74240

African (AFR) AF: 0.0617 AC: 2556 AN: 41430

American (AMR) AF: 0.0490 AC: 748 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 377 AN: 3468

East Asian (EAS) AF: 0.267 AC: 1374 AN: 5142

South Asian (SAS) AF: 0.0638 AC: 307 AN: 4810

European-Finnish (FIN) AF: 0.0756 AC: 796 AN: 10532

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0767 AC: 5210 AN: 67968

Other (OTH) AF: 0.0761 AC: 160 AN: 2102

Alfa AF: 0.0743 Hom.: 747

Bravo AF: 0.0746

Asia WGS AF: 0.124 AC: 430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.27
PhyloP100		0.51
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: rs2306772; hg19: chr5-131675981;