Variant 5-132313529-G-A 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.498-85G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0786 in 1,244,976 control chromosomes in the GnomAD database, including 5,114 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.073 ( 540 hom., cov: 33)

Exomes 𝑓: 0.079 ( 4574 hom. )

Consequence

SLC22A4
NM_003059.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.128

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=-0.8).

BP6

Variant 5-132313529-G-A is Benign according to our data. Variant chr5-132313529-G-A is described in ClinVar as [Benign]. Clinvar id is 1280356.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.257 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.498-85G>A		intron_variant		ENST00000200652.4
MIR3936HG	NR_110997.1 linkuse as main transcript	n.825-1276C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris
SLC22A4	ENST00000200652.4 linkuse as main transcript	c.498-85G>A	intron_variant	1	NM_003059.3	P1
MIR3936HG	ENST00000621103.4 linkuse as main transcript	n.825-1276C>T	intron_variant, non_coding_transcript_variant	1
SLC22A4	ENST00000491257.1 linkuse as main transcript	n.302-85G>A	intron_variant, non_coding_transcript_variant	4
MIR3936HG	ENST00000669845.1 linkuse as main transcript	n.451-1276C>T	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.0728

AC:

11080

AN:

152166

Hom.:

543

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0483

Gnomad AMI

AF:

0.109

Gnomad AMR

AF:

0.0479

Gnomad ASJ

AF:

0.105

Gnomad EAS

AF:

0.269

Gnomad SAS

AF:

0.0650

Gnomad FIN

AF:

0.0752

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0765

Gnomad OTH

AF:

0.0731

GnomAD4 exome

AF:

0.0794

AC:

86719

AN:

1092692

Hom.:

4574

AF XY:

0.0787

AC XY:

44149

AN XY:

560848

show subpopulations

Gnomad4 AFR exome

AF:

0.0453

Gnomad4 AMR exome

AF:

0.0330

Gnomad4 ASJ exome

AF:

0.108

Gnomad4 EAS exome

AF:

0.293

Gnomad4 SAS exome

AF:

0.0523

Gnomad4 FIN exome

AF:

0.0758

Gnomad4 NFE exome

AF:

0.0749

Gnomad4 OTH exome

AF:

0.0800

GnomAD4 genome

AF:

0.0728

AC:

11079

AN:

152284

Hom.:

540

Cov.:

AF XY:

0.0720

AC XY:

5362

AN XY:

74448

show subpopulations

Gnomad4 AFR

AF:

0.0483

Gnomad4 AMR

AF:

0.0478

Gnomad4 ASJ

AF:

0.105

Gnomad4 EAS

AF:

0.268

Gnomad4 SAS

AF:

0.0648

Gnomad4 FIN

AF:

0.0752

Gnomad4 NFE

AF:

0.0765

Gnomad4 OTH

AF:

0.0733

Alfa

AF:

0.0744

Hom.:

543

Bravo

AF:

0.0699

Asia WGS

AF:

0.122

AC:

426

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 16, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

5.3

DANN

Benign

0.56

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