Variant rs3761659 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.653-93G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0791 in 1,146,206 control chromosomes in the GnomAD database, including 4,789 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.077 ( 571 hom., cov: 32)

Exomes 𝑓: 0.079 ( 4218 hom. )

Consequence

SLC22A4
NM_003059.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0250

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=-0.84).

BP6

Variant 5-132322091-G-C is Benign according to our data. Variant chr5-132322091-G-C is described in ClinVar as [Benign]. Clinvar id is 1280672.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.653-93G>C		intron_variant		ENST00000200652.4
MIR3936HG	NR_110997.1 linkuse as main transcript	n.825-9838C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris
SLC22A4	ENST00000200652.4 linkuse as main transcript	c.653-93G>C	intron_variant	1	NM_003059.3	P1
MIR3936HG	ENST00000621103.4 linkuse as main transcript	n.825-9838C>G	intron_variant, non_coding_transcript_variant	1
MIR3936HG	ENST00000669845.1 linkuse as main transcript	n.451-9838C>G	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.0768

AC:

11668

AN:

151998

Hom.:

574

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0616

Gnomad AMI

AF:

0.109

Gnomad AMR

AF:

0.0494

Gnomad ASJ

AF:

0.108

Gnomad EAS

AF:

0.269

Gnomad SAS

AF:

0.0647

Gnomad FIN

AF:

0.0752

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0766

Gnomad OTH

AF:

0.0761

GnomAD4 exome

AF:

0.0795

AC:

79023

AN:

994090

Hom.:

4218

AF XY:

0.0786

AC XY:

40433

AN XY:

514522

show subpopulations

Gnomad4 AFR exome

AF:

0.0592

Gnomad4 AMR exome

AF:

0.0340

Gnomad4 ASJ exome

AF:

0.110

Gnomad4 EAS exome

AF:

0.292

Gnomad4 SAS exome

AF:

0.0522

Gnomad4 FIN exome

AF:

0.0755

Gnomad4 NFE exome

AF:

0.0743

Gnomad4 OTH exome

AF:

0.0809

GnomAD4 genome

AF:

0.0767

AC:

11668

AN:

152116

Hom.:

571

Cov.:

AF XY:

0.0758

AC XY:

5634

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.0616

Gnomad4 AMR

AF:

0.0493

Gnomad4 ASJ

AF:

0.108

Gnomad4 EAS

AF:

0.268

Gnomad4 SAS

AF:

0.0646

Gnomad4 FIN

AF:

0.0752

Gnomad4 NFE

AF:

0.0766

Gnomad4 OTH

AF:

0.0762

Alfa

AF:

0.0785

Hom.:

Bravo

AF:

0.0746

Asia WGS

AF:

0.123

AC:

429

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

-0.84

CADD

Benign

2.4

DANN

Benign

0.48

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