dbSNP rs1810126: SLC22A3:c.*63C>T (chr6-160451119-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.42

Publications

47 publications found

Variant links:

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]

SLC22A3 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC22A3	NM_021977.4 link	c.*63C>T		3_prime_UTR_variant	Exon 11 of 11	ENST00000275300.3	NP_068812.1	O75751

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A3	ENST00000275300.3 link	c.*63C>T		3_prime_UTR_variant	Exon 11 of 11	1	NM_021977.4	ENSP00000275300.2		O75751

Frequencies

GnomAD3 genomes

AF:

0.299

AC:

45410

AN:

151948

Hom.:

7929

Cov.:

show subpopulations

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.:

AF XY:

0.365

AC XY:

241864

AN XY:

663224

show subpopulations

African (AFR)

AF:

0.108

AC:

3263

AN:

30238

American (AMR)

AF:

0.506

AC:

19761

AN:

39052

Ashkenazi Jewish (ASJ)

AF:

0.221

AC:

5502

AN:

24944

East Asian (EAS)

AF:

0.473

AC:

17119

AN:

36206

South Asian (SAS)

AF:

0.277

AC:

21712

AN:

78326

European-Finnish (FIN)

AF:

0.306

AC:

15262

AN:

49880

Middle Eastern (MID)

AF:

0.210

AC:

1169

AN:

5572

European-Non Finnish (NFE)

AF:

0.383

AC:

388879

AN:

1014728

Other (OTH)

AF:

0.343

AC:

19109

AN:

55744

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

15412

30824

46236

61648

77060

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

12072

24144

36216

48288

60360

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.299

AC:

45436

AN:

152066

Hom.:

7943

Cov.:

AF XY:

0.296

AC XY:

22018

AN XY:

74318

show subpopulations

African (AFR)

AF:

0.125

AC:

5167

AN:

41486

American (AMR)

AF:

0.434

AC:

6636

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.219

AC:

759

AN:

3466

East Asian (EAS)

AF:

0.463

AC:

2395

AN:

5176

South Asian (SAS)

AF:

0.276

AC:

1329

AN:

4812

European-Finnish (FIN)

AF:

0.296

AC:

3128

AN:

10552

Middle Eastern (MID)

AF:

0.187

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.367

AC:

24947

AN:

67982

Other (OTH)

AF:

0.305

AC:

643

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1532

3064

4595

6127

7659

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

458

916

1374

1832

2290

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.347

Hom.:

37226

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

(source)

DANN

Benign

0.68

PhyloP100

1.4

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over