rs11568506

Variant names:

• chr5-132335767-G-A
• rs11568506
• NM_003059.3:c.1262-51G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-132335767-G-A
• chr5-132335767-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_003059.3(SLC22A4):​c.1262-51G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0196 in 1,439,874 control chromosomes in the GnomAD database, including 354 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 0.014 (27 hom., cov: 32)
  • Exomes 𝑓: 0.020 (327 hom.)
• Consequence: SLC22A4 NM_003059.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104

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=-0.78).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0145 (2204/152314) while in subpopulation NFE AF = 0.0216 (1472/68024). AF 95% confidence interval is 0.0207. There are 27 homozygotes in GnomAd4. There are 1043 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position FAILED quality control check.
• BS2: High Homozygotes in GnomAd4 at 27 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC22A4	NM_003059.3	c.1262-51G>A		intron_variant	Intron 7 of 9	ENST00000200652.4	NP_003050.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A4	ENST00000200652.4	c.1262-51G>A		intron_variant	Intron 7 of 9	1	NM_003059.3	ENSP00000200652.3
MIR3936HG	ENST00000621103.4	n.561-841C>T		intron_variant	Intron 5 of 7	1
MIR3936HG	ENST00000616965.1	n.344-841C>T		intron_variant	Intron 3 of 4	5
MIR3936HG	ENST00000669845.1	n.187-841C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0145 AC: 2204 AN: 152196 Hom.: 27 Cov.: 32

Gnomad AFR AF: 0.00364

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0158

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00311

Gnomad FIN AF: 0.0242

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0216

Gnomad OTH AF: 0.0100

GnomAD2 exomes AF: 0.0171 AC: 4285 AN: 250286 AF XY: 0.0167

Gnomad AFR exome AF: 0.00334

Gnomad AMR exome AF: 0.0258

Gnomad ASJ exome AF: 0.00854

Gnomad EAS exome AF: 0.000109

Gnomad FIN exome AF: 0.0229

Gnomad NFE exome AF: 0.0222

Gnomad OTH exome AF: 0.0216

GnomAD4 exome AF: 0.0202 AC: 25961 AN: 1287560 Hom.: 327 Cov.: 19 AF XY: 0.0195 AC XY: 12674 AN XY: 650212

Gnomad4 AFR exome AF: 0.00294 AC: 88 AN: 29972

Gnomad4 AMR exome AF: 0.0254 AC: 1129 AN: 44476

Gnomad4 ASJ exome AF: 0.00782 AC: 196 AN: 25074

Gnomad4 EAS exome AF: 0.0000515 AC: 2 AN: 38866

Gnomad4 SAS exome AF: 0.00358 AC: 295 AN: 82498

Gnomad4 FIN exome AF: 0.0230 AC: 1212 AN: 52798

Gnomad4 NFE exome AF: 0.0231 AC: 22049 AN: 954116

Gnomad4 Remaining exome AF: 0.0177 AC: 968 AN: 54628

GnomAD4 genome AF: 0.0145 AC: 2204 AN: 152314 Hom.: 27 Cov.: 32 AF XY: 0.0140 AC XY: 1043 AN XY: 74470

Gnomad4 AFR AF: 0.00366 AC: 0.00365666 AN: 0.00365666

Gnomad4 AMR AF: 0.0157 AC: 0.0156801 AN: 0.0156801

Gnomad4 ASJ AF: 0.0101 AC: 0.0100806 AN: 0.0100806

Gnomad4 EAS AF: 0.00 AC: 0 AN: 0

Gnomad4 SAS AF: 0.00311 AC: 0.00310816 AN: 0.00310816

Gnomad4 FIN AF: 0.0242 AC: 0.0242224 AN: 0.0242224

Gnomad4 NFE AF: 0.0216 AC: 0.0216394 AN: 0.0216394

Gnomad4 OTH AF: 0.00992 AC: 0.00992439 AN: 0.00992439

Alfa AF: 0.0189 Hom.: 23

Bravo AF: 0.0142

Asia WGS AF: 0.00144 AC: 5 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	10
DANN	Benign	0.74
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

Publications

LitVar

Other links and lift over

dbSNP: rs11568506; hg19: chr5-131671460;