Variant 5-132313493-A-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_003059.3(SLC22A4):c.498-121A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.663 in 875,446 control chromosomes in the GnomAD database, including 195,674 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.69 ( 36432 hom., cov: 33)

Exomes 𝑓: 0.66 ( 159242 hom. )

Consequence

SLC22A4
NM_003059.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0980

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 5-132313493-A-G is Benign according to our data. Variant chr5-132313493-A-G is described in ClinVar as [Benign]. Clinvar id is 1220625.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC22A4	NM_003059.3 linkuse as main transcript	c.498-121A>G		intron_variant		ENST00000200652.4
MIR3936HG	NR_110997.1 linkuse as main transcript	n.825-1240T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris
SLC22A4	ENST00000200652.4 linkuse as main transcript	c.498-121A>G	intron_variant	1	NM_003059.3	P1
MIR3936HG	ENST00000621103.4 linkuse as main transcript	n.825-1240T>C	intron_variant, non_coding_transcript_variant	1
SLC22A4	ENST00000491257.1 linkuse as main transcript	n.302-121A>G	intron_variant, non_coding_transcript_variant	4
MIR3936HG	ENST00000669845.1 linkuse as main transcript	n.451-1240T>C	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.688

AC:

104597

AN:

151974

Hom.:

36401

Cov.:

show subpopulations

Gnomad AFR

AF:

0.763

Gnomad AMI

AF:

0.870

Gnomad AMR

AF:

0.702

Gnomad ASJ

AF:

0.699

Gnomad EAS

AF:

0.621

Gnomad SAS

AF:

0.438

Gnomad FIN

AF:

0.561

Gnomad MID

AF:

0.580

Gnomad NFE

AF:

0.680

Gnomad OTH

AF:

0.693

GnomAD4 exome

AF:

0.658

AC:

475814

AN:

723354

Hom.:

159242

AF XY:

0.646

AC XY:

250412

AN XY:

387366

show subpopulations

Gnomad4 AFR exome

AF:

0.760

Gnomad4 AMR exome

AF:

0.713

Gnomad4 ASJ exome

AF:

0.714

Gnomad4 EAS exome

AF:

0.636

Gnomad4 SAS exome

AF:

0.439

Gnomad4 FIN exome

AF:

0.567

Gnomad4 NFE exome

AF:

0.692

Gnomad4 OTH exome

AF:

0.666

GnomAD4 genome

AF:

0.688

AC:

104682

AN:

152092

Hom.:

36432

Cov.:

AF XY:

0.677

AC XY:

50335

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.763

Gnomad4 AMR

AF:

0.702

Gnomad4 ASJ

AF:

0.699

Gnomad4 EAS

AF:

0.620

Gnomad4 SAS

AF:

0.437

Gnomad4 FIN

AF:

0.561

Gnomad4 NFE

AF:

0.680

Gnomad4 OTH

AF:

0.693

Alfa

AF:

0.681

Hom.:

28865

Bravo

AF:

0.709

Asia WGS

AF:

0.524

AC:

1825

AN:

3478

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

May 14, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.5

DANN

Benign

0.74

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