6-160375026-C-T

Position:

• chr6-160375026-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.430-22953C>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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
SLC22A3	NM_021977.4	c.430-22953C>T		intron_variant		ENST00000275300.3
LOC124901453	XR_007059843.1	n.7395-4580G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC22A3	ENST00000275300.3	c.430-22953C>T		intron_variant		1	NM_021977.4	P1
	ENST00000663900.1	n.1100-4580G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.415

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.372

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.327

Alfa AF: 0.294 Hom.: 9780

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

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: rs1018234; hg19: chr6-160796058;