rs539958

chr6-160351810-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.429+2962C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 151,966 control chromosomes in the GnomAD database, including 19,423 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 0.50 (19423 hom., cov: 32)
• Consequence: SLC22A3 NM_021977.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.706

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC22A3	NM_021977.4	c.429+2962C>T		intron_variant		ENST00000275300.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC22A3	ENST00000275300.3	c.429+2962C>T		intron_variant		1	NM_021977.4	P1

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76106 AN: 151846 Hom.: 19387 Cov.: 32

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.501 AC: 76196 AN: 151966 Hom.: 19423 Cov.: 32 AF XY: 0.498 AC XY: 37013 AN XY: 74252

Gnomad4 AFR AF: 0.590

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.552

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.497

Gnomad4 NFE AF: 0.489

Gnomad4 OTH AF: 0.492

Alfa AF: 0.487 Hom.: 5091

Bravo AF: 0.505

Asia WGS AF: 0.362 AC: 1261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.98
Dann	Benign	0.66

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: rs539958; hg19: chr6-160772842;