rs394352

chr6-160387363-C-T

Variant summary

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

The NM_021977.4(SLC22A3):c.430-10616C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,126 control chromosomes in the GnomAD database, including 5,086 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 0.25 (5086 hom., cov: 32)
• Consequence: SLC22A3 NM_021977.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.465

Genes affected

SLC22A3 (HGNC:10967): (solute carrier family 22 member 3) 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. This gene is one of three similar cation transporter genes located in a cluster on chromosome 6. The encoded protein contains twelve putative transmembrane domains and is a plasma integral membrane protein. [provided by RefSeq, Jul 2008]

LOC124901453 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC22A3	NM_021977.4	c.430-10616C>T		intron_variant		ENST00000275300.3
LOC124901453	XR_007059843.1	n.4791G>A		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC22A3	ENST00000275300.3	c.430-10616C>T		intron_variant		1	NM_021977.4	P1

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37974 AN: 152008 Hom.: 5083 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.250 AC: 37993 AN: 152126 Hom.: 5086 Cov.: 32 AF XY: 0.253 AC XY: 18786 AN XY: 74352

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.353

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.269

Alfa AF: 0.276 Hom.: 6592

Bravo AF: 0.239

Asia WGS AF: 0.358 AC: 1242 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	2.2
Dann	Benign	0.43
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs394352; hg19: chr6-160808395;