rs1810126

chr6-160451119-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.*63C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 1,486,756 control chromosomes in the GnomAD database, including 102,141 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 0.30 (7943 hom., cov: 32)
  • Exomes 𝑓: 0.37 (94198 hom.)
• Consequence: SLC22A3 NM_021977.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.42

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=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC22A3	NM_021977.4	c.*63C>T		3_prime_UTR_variant	11/11	ENST00000275300.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC22A3	ENST00000275300.3	c.*63C>T		3_prime_UTR_variant	11/11	1	NM_021977.4	P1

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45410 AN: 151948 Hom.: 7929 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.304

GnomAD4 exome AF: 0.368 AC: 491776 AN: 1334690 Hom.: 94198 Cov.: 20 AF XY: 0.365 AC XY: 241864 AN XY: 663224

Gnomad4 AFR exome AF: 0.108

Gnomad4 AMR exome AF: 0.506

Gnomad4 ASJ exome AF: 0.221

Gnomad4 EAS exome AF: 0.473

Gnomad4 SAS exome AF: 0.277

Gnomad4 FIN exome AF: 0.306

Gnomad4 NFE exome AF: 0.383

Gnomad4 OTH exome AF: 0.343

GnomAD4 genome AF: 0.299 AC: 45436 AN: 152066 Hom.: 7943 Cov.: 32 AF XY: 0.296 AC XY: 22018 AN XY: 74318

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.434

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.463

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.305

Alfa AF: 0.355 Hom.: 19135

Bravo AF: 0.303

Asia WGS AF: 0.381 AC: 1322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
Cadd	Benign	8.0
Dann	Benign	0.68

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: rs1810126; hg19: chr6-160872151; COSMIC: COSV51712123; COSMIC: COSV51712123;