Genetic Variant SLC22A3:c.-29G>A (chr6-160348391-G-A) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_021977.4(SLC22A3):c.-29G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 1,429,486 control chromosomes in the GnomAD database, including 159,083 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.49 ( 18343 hom., cov: 34)

Exomes 𝑓: 0.47 ( 140740 hom. )

Consequence

SLC22A3
NM_021977.4 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.716

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

BP6

Variant 6-160348391-G-A is Benign according to our data. Variant chr6-160348391-G-A is described in ClinVar as [Benign]. Clinvar id is 1241019.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC22A3	NM_021977.4 link	c.-29G>A		5_prime_UTR_variant	Exon 1 of 11	ENST00000275300.3	NP_068812.1	O75751

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC22A3	ENST00000275300 link	c.-29G>A		5_prime_UTR_variant	Exon 1 of 11	1	NM_021977.4	ENSP00000275300.2		O75751

Frequencies

GnomAD3 genomes

AF:

0.489

AC:

74007

AN:

151460

Hom.:

18309

Cov.:

show subpopulations

Gnomad AFR

AF:

0.556

Gnomad AMI

AF:

0.396

Gnomad AMR

AF:

0.422

Gnomad ASJ

AF:

0.550

Gnomad EAS

AF:

0.303

Gnomad SAS

AF:

0.359

Gnomad FIN

AF:

0.495

Gnomad MID

AF:

0.484

Gnomad NFE

AF:

0.483

Gnomad OTH

AF:

0.481

GnomAD3 exomes

AF:

0.468

AC:

43965

AN:

93916

Hom.:

10421

AF XY:

0.472

AC XY:

25237

AN XY:

53460

show subpopulations

Gnomad AFR exome

AF:

0.574

Gnomad AMR exome

AF:

0.394

Gnomad ASJ exome

AF:

0.559

Gnomad EAS exome

AF:

0.338

Gnomad SAS exome

AF:

0.384

Gnomad FIN exome

AF:

0.516

Gnomad NFE exome

AF:

0.495

Gnomad OTH exome

AF:

0.505

GnomAD4 exome

AF:

0.467

AC:

596530

AN:

1277916

Hom.:

140740

Cov.:

AF XY:

0.466

AC XY:

291202

AN XY:

625548

show subpopulations

Gnomad4 AFR exome

AF:

0.562

Gnomad4 AMR exome

AF:

0.400

Gnomad4 ASJ exome

AF:

0.547

Gnomad4 EAS exome

AF:

0.299

Gnomad4 SAS exome

AF:

0.370

Gnomad4 FIN exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.474

Gnomad4 OTH exome

AF:

0.463

GnomAD4 genome

AF:

0.489

AC:

74093

AN:

151570

Hom.:

18343

Cov.:

AF XY:

0.487

AC XY:

36062

AN XY:

74078

show subpopulations

Gnomad4 AFR

AF:

0.557

Gnomad4 AMR

AF:

0.421

Gnomad4 ASJ

AF:

0.550

Gnomad4 EAS

AF:

0.303

Gnomad4 SAS

AF:

0.361

Gnomad4 FIN

AF:

0.495

Gnomad4 NFE

AF:

0.483

Gnomad4 OTH

AF:

0.480

Alfa

AF:

0.435

Hom.:

4551

Bravo

AF:

0.490

Asia WGS

AF:

0.356

AC:

1209

AN:

3394

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Nov 14, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 22231567) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

DANN

Benign

0.95

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.3

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