rs11950562

chr5-132316836-A-Cchr5-132316836-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003059.3(SLC22A4):c.652+3068A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 152,128 control chromosomes in the GnomAD database, including 11,097 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 0.36 (11097 hom., cov: 32)
• Consequence: SLC22A4 NM_003059.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC22A4	NM_003059.3	c.652+3068A>C		intron_variant		ENST00000200652.4
MIR3936HG	NR_110997.1	n.825-4583T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC22A4	ENST00000200652.4	c.652+3068A>C		intron_variant		1	NM_003059.3	P1
MIR3936HG	ENST00000621103.4	n.825-4583T>G		intron_variant, non_coding_transcript_variant		1
SLC22A4	ENST00000491257.1	n.456+3068A>C		intron_variant, non_coding_transcript_variant		4
MIR3936HG	ENST00000669845.1	n.451-4583T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55281 AN: 152010 Hom.: 11090 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.364 AC: 55312 AN: 152128 Hom.: 11097 Cov.: 32 AF XY: 0.350 AC XY: 26050 AN XY: 74400

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.492

Gnomad4 EAS AF: 0.00270

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.461

Gnomad4 OTH AF: 0.404

Alfa AF: 0.394 Hom.: 6387

Bravo AF: 0.367

Asia WGS AF: 0.0820 AC: 284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.0
Dann	Benign	0.70

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

Publications

LitVar

Other links and lift over

dbSNP: rs11950562; hg19: chr5-131652529;