rs1510229

Variant names:

• chr6-160384637-C-T
• rs1510229
• NM_021977.4:c.430-13342C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_021977.4(SLC22A3):​c.430-13342C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 151,956 control chromosomes in the GnomAD database, including 5,122 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 (5122 hom., cov: 31)
• Consequence: SLC22A3 NM_021977.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 8 publications found

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]

ENSG00000287656 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC22A3	NM_021977.4	c.430-13342C>T		intron_variant	Intron 1 of 10	ENST00000275300.3	NP_068812.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A3	ENST00000275300.3	c.430-13342C>T		intron_variant	Intron 1 of 10	1	NM_021977.4	ENSP00000275300.2
ENSG00000287656	ENST00000663900.1	n.1008+214G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38171 AN: 151838 Hom.: 5119 Cov.: 31

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.251 AC: 38189 AN: 151956 Hom.: 5122 Cov.: 31 AF XY: 0.254 AC XY: 18875 AN XY: 74248

African (AFR) AF: 0.170 AC: 7067 AN: 41472

American (AMR) AF: 0.197 AC: 3013 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1222 AN: 3464

East Asian (EAS) AF: 0.370 AC: 1899 AN: 5132

South Asian (SAS) AF: 0.371 AC: 1771 AN: 4776

European-Finnish (FIN) AF: 0.293 AC: 3095 AN: 10580

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.284 AC: 19287 AN: 67922

Other (OTH) AF: 0.270 AC: 571 AN: 2114

Alfa AF: 0.274 Hom.: 9350

Bravo AF: 0.241

Asia WGS AF: 0.359 AC: 1246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.32
PhyloP100		-1.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		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: rs1510229; hg19: chr6-160805669;