Variant rs273909 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_003059.3(SLC22A4):c.952-96A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 847,052 control chromosomes in the GnomAD database, including 6,637 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.096 ( 956 hom., cov: 32)

Exomes 𝑓: 0.12 ( 5681 hom. )

Consequence

SLC22A4
NM_003059.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.50

Variant links:

Genes affected

SLC22A4 (HGNC:10968): (solute carrier family 22 member 4) 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. The encoded protein is an organic cation transporter and plasma integral membrane protein containing eleven putative transmembrane domains as well as a nucleotide-binding site motif. Transport by this protein is at least partially ATP-dependent. [provided by RefSeq, Jul 2008]

SLC22A4 links:

MIR3936HG (HGNC:40538): (MIR3936 host gene)

MIR3936HG links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 5-132331660-A-G is Benign according to our data. Variant chr5-132331660-A-G is described in ClinVar as [Benign]. Clinvar id is 1248012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC22A4	NM_003059.3 link	c.952-96A>G		intron_variant		ENST00000200652.4	NP_003050.2	Q9H015

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
SLC22A4	ENST00000200652.4 link	c.952-96A>G	intron_variant	1	NM_003059.3	ENSP00000200652.3	Q9H015
MIR3936HG	ENST00000621103.4 link	n.824+529T>C	intron_variant	1
MIR3936HG	ENST00000669845.1 link	n.450+529T>C	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.0957

AC:

14555

AN:

152126

Hom.:

956

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0262

Gnomad AMI

AF:

0.0681

Gnomad AMR

AF:

0.110

Gnomad ASJ

AF:

0.0573

Gnomad EAS

AF:

0.0335

Gnomad SAS

AF:

0.188

Gnomad FIN

AF:

0.218

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.117

Gnomad OTH

AF:

0.0842

GnomAD4 exome

AF:

0.117

AC:

81408

AN:

694808

Hom.:

5681

AF XY:

0.121

AC XY:

45118

AN XY:

374156

show subpopulations

Gnomad4 AFR exome

AF:

0.0267

Gnomad4 AMR exome

AF:

0.0954

Gnomad4 ASJ exome

AF:

0.0598

Gnomad4 EAS exome

AF:

0.0229

Gnomad4 SAS exome

AF:

0.186

Gnomad4 FIN exome

AF:

0.207

Gnomad4 NFE exome

AF:

0.113

Gnomad4 OTH exome

AF:

0.107

GnomAD4 genome

AF:

0.0956

AC:

14550

AN:

152244

Hom.:

956

Cov.:

AF XY:

0.101

AC XY:

7538

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.0261

Gnomad4 AMR

AF:

0.110

Gnomad4 ASJ

AF:

0.0573

Gnomad4 EAS

AF:

0.0336

Gnomad4 SAS

AF:

0.188

Gnomad4 FIN

AF:

0.218

Gnomad4 NFE

AF:

0.117

Gnomad4 OTH

AF:

0.0833

Alfa

AF:

0.109

Hom.:

1535

Bravo

AF:

0.0800

Asia WGS

AF:

0.120

AC:

418

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 15, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 19, 2024	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

8.4

DANN

Benign

0.73

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