rs2073839

Variant names:

• chr5-132314552-C-T
• rs2073839
• NM_003059.3:c.652+784C>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.652+784C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0719 in 152,238 control chromosomes in the GnomAD database, including 533 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 0.072 (533 hom., cov: 32)
• Consequence: SLC22A4 NM_003059.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333
• Publications: 6 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=-0.82).
• 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.652+784C>T		intron_variant	Intron 3 of 9	ENST00000200652.4	NP_003050.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A4	ENST00000200652.4	c.652+784C>T		intron_variant	Intron 3 of 9	1	NM_003059.3	ENSP00000200652.3
MIR3936HG	ENST00000621103.4	n.825-2299G>A		intron_variant	Intron 7 of 7	1
SLC22A4	ENST00000491257.1	n.456+784C>T		intron_variant	Intron 3 of 3	4
MIR3936HG	ENST00000669845.1	n.451-2299G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0720 AC: 10947 AN: 152120 Hom.: 536 Cov.: 32

Gnomad AFR AF: 0.0454

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.0478

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.0645

Gnomad FIN AF: 0.0751

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0765

Gnomad OTH AF: 0.0722

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

GnomAD4 genome AF: 0.0719 AC: 10946 AN: 152238 Hom.: 533 Cov.: 32 AF XY: 0.0712 AC XY: 5299 AN XY: 74408

African (AFR) AF: 0.0454 AC: 1889 AN: 41570

American (AMR) AF: 0.0477 AC: 730 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 363 AN: 3468

East Asian (EAS) AF: 0.269 AC: 1386 AN: 5162

South Asian (SAS) AF: 0.0644 AC: 310 AN: 4816

European-Finnish (FIN) AF: 0.0751 AC: 797 AN: 10606

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

European-Non Finnish (NFE) AF: 0.0765 AC: 5200 AN: 67998

Other (OTH) AF: 0.0724 AC: 153 AN: 2112

Alfa AF: 0.0729 Hom.: 715

Bravo AF: 0.0692

Asia WGS AF: 0.122 AC: 424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.0
DANN	Benign	0.45
PhyloP100		-0.33
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: rs2073839; hg19: chr5-131650245;