rs3805673

Variant names:

• chr5-132323410-G-A
• rs3805673
• NM_003059.3:c.824+1055G>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.824+1055G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0735 in 152,266 control chromosomes in the GnomAD database, including 548 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 (548 hom., cov: 32)
• Consequence: SLC22A4 NM_003059.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 4 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC22A4	NM_003059.3	c.824+1055G>A		intron_variant	Intron 4 of 9	ENST00000200652.4	NP_003050.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A4	ENST00000200652.4	c.824+1055G>A		intron_variant	Intron 4 of 9	1	NM_003059.3	ENSP00000200652.3
MIR3936HG	ENST00000621103.4	n.824+8779C>T		intron_variant	Intron 7 of 7	1
SLC22A4	ENST00000425923.1	n.173-1051G>A		intron_variant	Intron 1 of 2	3
MIR3936HG	ENST00000669845.1	n.450+8779C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0736 AC: 11191 AN: 152148 Hom.: 551 Cov.: 32

Gnomad AFR AF: 0.0504

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.0482

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.0646

Gnomad FIN AF: 0.0752

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0766

Gnomad OTH AF: 0.0737

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

GnomAD4 genome AF: 0.0735 AC: 11190 AN: 152266 Hom.: 548 Cov.: 32 AF XY: 0.0728 AC XY: 5419 AN XY: 74450

African (AFR) AF: 0.0504 AC: 2093 AN: 41546

American (AMR) AF: 0.0481 AC: 736 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 376 AN: 3466

East Asian (EAS) AF: 0.269 AC: 1392 AN: 5176

South Asian (SAS) AF: 0.0645 AC: 311 AN: 4822

European-Finnish (FIN) AF: 0.0752 AC: 798 AN: 10608

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

European-Non Finnish (NFE) AF: 0.0766 AC: 5210 AN: 68030

Other (OTH) AF: 0.0739 AC: 156 AN: 2112

Alfa AF: 0.0737 Hom.: 675

Bravo AF: 0.0706

Asia WGS AF: 0.122 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.1
DANN	Benign	0.64
PhyloP100		-1.1
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: rs3805673; hg19: chr5-131659103;