rs2076828

Variant names:

• chr6-160451754-C-G
• rs2076828
• NM_021977.4:c.*698C>G

Variant summary

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

The NM_021977.4(SLC22A3):​c.*698C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 152,028 control chromosomes in the GnomAD database, including 14,784 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 0.43 (14783 hom., cov: 32)
  • Exomes 𝑓: 0.33 (1 hom.)
• Consequence: SLC22A3 NM_021977.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 26 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021977.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A3	NM_021977.4	MANE Select	c.*698C>G		3_prime_UTR	Exon 11 of 11	NP_068812.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC22A3	ENST00000275300.3	TSL:1 MANE Select	c.*698C>G		3_prime_UTR	Exon 11 of 11	ENSP00000275300.2
	SLC22A3	ENST00000855214.1		c.*698C>G		3_prime_UTR	Exon 12 of 12	ENSP00000525273.1
	SLC22A3	ENST00000855213.1		c.*698C>G		3_prime_UTR	Exon 7 of 7	ENSP00000525272.1

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66050 AN: 151886 Hom.: 14768 Cov.: 32

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.458

GnomAD4 exome AF: 0.333 AC: 8 AN: 24 Hom.: 1 Cov.: 0 AF XY: 0.333 AC XY: 4 AN XY: 12

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.364 AC: 8 AN: 22

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.435 AC: 66092 AN: 152004 Hom.: 14783 Cov.: 32 AF XY: 0.442 AC XY: 32849 AN XY: 74268

African (AFR) AF: 0.430 AC: 17830 AN: 41460

American (AMR) AF: 0.323 AC: 4931 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1988 AN: 3468

East Asian (EAS) AF: 0.535 AC: 2763 AN: 5160

South Asian (SAS) AF: 0.610 AC: 2936 AN: 4812

European-Finnish (FIN) AF: 0.521 AC: 5495 AN: 10542

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.422 AC: 28682 AN: 67964

Other (OTH) AF: 0.457 AC: 965 AN: 2110

Alfa AF: 0.432 Hom.: 8291

Bravo AF: 0.417

Asia WGS AF: 0.533 AC: 1852 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.46
DANN	Benign	0.60
PhyloP100		-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: rs2076828; hg19: chr6-160872786;