Variant rs3733589 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_020041.3(SLC2A9):c.504C>T(p.Ile168=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.056 in 1,613,914 control chromosomes in the GnomAD database, including 6,141 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.075 ( 766 hom., cov: 33)

Exomes 𝑓: 0.054 ( 5375 hom. )

Consequence

SLC2A9
NM_020041.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.175

Variant links:

Genes affected

SLC2A9 (HGNC:13446): (solute carrier family 2 member 9) This gene encodes a member of the SLC2A facilitative glucose transporter family. Members of this family play a significant role in maintaining glucose homeostasis. The encoded protein may play a role in the development and survival of chondrocytes in cartilage matrices. Two transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

SLC2A9 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BP6

Variant 4-9985700-G-A is Benign according to our data. Variant chr4-9985700-G-A is described in ClinVar as [Benign]. Clinvar id is 350236.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.175 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A9	NM_020041.3 linkuse as main transcript	c.504C>T	p.Ile168=	synonymous_variant	4/12	ENST00000264784.8	NP_064425.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000264784.8 linkuse as main transcript	c.504C>T	p.Ile168=	synonymous_variant	4/12	1	NM_020041.3	ENSP00000264784	A2	Q9NRM0-1

Frequencies

GnomAD3 genomes

AF:

0.0745

AC:

11335

AN:

152152

Hom.:

763

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0980

Gnomad AMI

AF:

0.0219

Gnomad AMR

AF:

0.0930

Gnomad ASJ

AF:

0.0542

Gnomad EAS

AF:

0.391

Gnomad SAS

AF:

0.113

Gnomad FIN

AF:

0.0604

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.0334

Gnomad OTH

AF:

0.0646

GnomAD3 exomes

AF:

0.0887

AC:

22257

AN:

251016

Hom.:

2062

AF XY:

0.0852

AC XY:

11563

AN XY:

135652

show subpopulations

Gnomad AFR exome

AF:

0.0998

Gnomad AMR exome

AF:

0.114

Gnomad ASJ exome

AF:

0.0586

Gnomad EAS exome

AF:

0.395

Gnomad SAS exome

AF:

0.102

Gnomad FIN exome

AF:

0.0575

Gnomad NFE exome

AF:

0.0355

Gnomad OTH exome

AF:

0.0712

GnomAD4 exome

AF:

0.0540

AC:

78973

AN:

1461644

Hom.:

5375

Cov.:

AF XY:

0.0550

AC XY:

40008

AN XY:

727132

show subpopulations

Gnomad4 AFR exome

AF:

0.0985

Gnomad4 AMR exome

AF:

0.115

Gnomad4 ASJ exome

AF:

0.0588

Gnomad4 EAS exome

AF:

0.410

Gnomad4 SAS exome

AF:

0.104

Gnomad4 FIN exome

AF:

0.0577

Gnomad4 NFE exome

AF:

0.0324

Gnomad4 OTH exome

AF:

0.0680

GnomAD4 genome

AF:

0.0746

AC:

11364

AN:

152270

Hom.:

766

Cov.:

AF XY:

0.0794

AC XY:

5915

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.0983

Gnomad4 AMR

AF:

0.0929

Gnomad4 ASJ

AF:

0.0542

Gnomad4 EAS

AF:

0.390

Gnomad4 SAS

AF:

0.114

Gnomad4 FIN

AF:

0.0604

Gnomad4 NFE

AF:

0.0334

Gnomad4 OTH

AF:

0.0682

Alfa

AF:

0.0456

Hom.:

391

Bravo

AF:

0.0798

Asia WGS

AF:

0.203

AC:

706

AN:

3476

EpiCase

AF:

0.0347

EpiControl

AF:

0.0372

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Feb 18, 2020	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 30, 2024	- -

Hypouricemia, renal, 2

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

3.2

DANN

Benign

0.67

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