Variant rs2292334 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_021977.4(SLC22A3):c.1233G>A(p.Ala411Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 1,613,838 control chromosomes in the GnomAD database, including 111,736 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.30 ( 8067 hom., cov: 32)

Exomes 𝑓: 0.37 ( 103669 hom. )

Consequence

SLC22A3
NM_021977.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -5.61

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.7).

BP6

Variant 6-160437156-G-A is Benign according to our data. Variant chr6-160437156-G-A is described in ClinVar as [Benign]. Clinvar id is 1264425.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-5.61 with no splicing effect.

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	Protein	UniProt
SLC22A3	NM_021977.4 linkuse as main transcript	c.1233G>A	p.Ala411Ala	synonymous_variant	7/11	ENST00000275300.3	NP_068812.1	O75751

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC22A3	ENST00000275300.3 linkuse as main transcript	c.1233G>A	p.Ala411Ala	synonymous_variant	7/11	1	NM_021977.4	ENSP00000275300.2		O75751

Frequencies

GnomAD3 genomes

AF:

0.303

AC:

46100

AN:

151964

Hom.:

8055

Cov.:

show subpopulations

Gnomad AFR

AF:

0.138

Gnomad AMI

AF:

0.418

Gnomad AMR

AF:

0.436

Gnomad ASJ

AF:

0.217

Gnomad EAS

AF:

0.462

Gnomad SAS

AF:

0.278

Gnomad FIN

AF:

0.297

Gnomad MID

AF:

0.272

Gnomad NFE

AF:

0.368

Gnomad OTH

AF:

0.314

GnomAD3 exomes

AF:

0.357

AC:

89650

AN:

251244

Hom.:

17471

AF XY:

0.349

AC XY:

47365

AN XY:

135762

show subpopulations

Gnomad AFR exome

AF:

0.128

Gnomad AMR exome

AF:

0.520

Gnomad ASJ exome

AF:

0.223

Gnomad EAS exome

AF:

0.445

Gnomad SAS exome

AF:

0.274

Gnomad FIN exome

AF:

0.308

Gnomad NFE exome

AF:

0.370

Gnomad OTH exome

AF:

0.341

GnomAD4 exome

AF:

0.370

AC:

541035

AN:

1461756

Hom.:

103669

Cov.:

AF XY:

0.366

AC XY:

266104

AN XY:

727204

show subpopulations

Gnomad4 AFR exome

AF:

0.126

Gnomad4 AMR exome

AF:

0.509

Gnomad4 ASJ exome

AF:

0.222

Gnomad4 EAS exome

AF:

0.469

Gnomad4 SAS exome

AF:

0.277

Gnomad4 FIN exome

AF:

0.307

Gnomad4 NFE exome

AF:

0.384

Gnomad4 OTH exome

AF:

0.346

GnomAD4 genome

AF:

0.303

AC:

46128

AN:

152082

Hom.:

8067

Cov.:

AF XY:

0.301

AC XY:

22386

AN XY:

74338

show subpopulations

Gnomad4 AFR

AF:

0.137

Gnomad4 AMR

AF:

0.437

Gnomad4 ASJ

AF:

0.217

Gnomad4 EAS

AF:

0.462

Gnomad4 SAS

AF:

0.278

Gnomad4 FIN

AF:

0.297

Gnomad4 NFE

AF:

0.368

Gnomad4 OTH

AF:

0.317

Alfa

AF:

0.351

Hom.:

23713

Bravo

AF:

0.309

Asia WGS

AF:

0.383

AC:

1330

AN:

3478

EpiCase

AF:

0.349

EpiControl

AF:

0.345

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 09, 2020

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

0.28

DANN

Benign

0.69

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over