6-160375026-C-T

Variant names:

• chr6-160375026-C-T
• rs1018234
• NM_021977.4:c.430-22953C>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.430-22953C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,956 control chromosomes in the GnomAD database, including 8,276 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 0.32 (8276 hom., cov: 32)
• Consequence: SLC22A3 NM_021977.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0820
• Publications: 13 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC22A3	NM_021977.4	c.430-22953C>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.430-22953C>T		intron_variant	Intron 1 of 10	1	NM_021977.4	ENSP00000275300.2
ENSG00000287656	ENST00000663900.1	n.1100-4580G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49169 AN: 151838 Hom.: 8267 Cov.: 32

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.324 AC: 49214 AN: 151956 Hom.: 8276 Cov.: 32 AF XY: 0.324 AC XY: 24060 AN XY: 74284

African (AFR) AF: 0.415 AC: 17186 AN: 41444

American (AMR) AF: 0.229 AC: 3503 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1326 AN: 3470

East Asian (EAS) AF: 0.372 AC: 1921 AN: 5166

South Asian (SAS) AF: 0.373 AC: 1791 AN: 4800

European-Finnish (FIN) AF: 0.292 AC: 3085 AN: 10552

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.286 AC: 19434 AN: 67944

Other (OTH) AF: 0.327 AC: 688 AN: 2106

Alfa AF: 0.296 Hom.: 13700

Bravo AF: 0.324

Asia WGS AF: 0.375 AC: 1302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.43
PhyloP100		-0.082
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: rs1018234; hg19: chr6-160796058;