rs2276961

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_020041.3(SLC2A9):c.73G>A(p.Gly25Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 1,613,966 control chromosomes in the GnomAD database, including 227,232 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in ClinVar.

Frequency

Genomes: 𝑓 0.44 ( 16328 hom., cov: 34)

Exomes 𝑓: 0.53 ( 210904 hom. )

Consequence

SLC2A9
NM_020041.3 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -0.194

Publications

50 publications found

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:

SLC2A9-AS1 (HGNC:40636): (SLC2A9 antisense RNA 1)

SLC2A9-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.5187014E-5).

BP6

Variant 4-10021357-C-T is Benign according to our data. Variant chr4-10021357-C-T is described in ClinVar as Benign. ClinVar VariationId is 347006.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A9	NM_020041.3 link	c.73G>A	p.Gly25Arg	missense_variant	Exon 1 of 12	ENST00000264784.8	NP_064425.2	Q9NRM0-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000264784.8 link	c.73G>A	p.Gly25Arg	missense_variant	Exon 1 of 12	1	NM_020041.3	ENSP00000264784.3		Q9NRM0-1

Frequencies

GnomAD3 genomes

AF:

0.440

AC:

66971

AN:

152052

Hom.:

16319

Cov.:

show subpopulations

Gnomad AFR

AF:

0.211

Gnomad AMI

AF:

0.713

Gnomad AMR

AF:

0.489

Gnomad ASJ

AF:

0.499

Gnomad EAS

AF:

0.426

Gnomad SAS

AF:

0.585

Gnomad FIN

AF:

0.525

Gnomad MID

AF:

0.455

Gnomad NFE

AF:

0.540

Gnomad OTH

AF:

0.457

GnomAD2 exomes

AF:

0.515

AC:

129356

AN:

251402

AF XY:

0.524

show subpopulations

Gnomad AFR exome

AF:

0.202

Gnomad AMR exome

AF:

0.537

Gnomad ASJ exome

AF:

0.517

Gnomad EAS exome

AF:

0.424

Gnomad FIN exome

AF:

0.531

Gnomad NFE exome

AF:

0.540

Gnomad OTH exome

AF:

0.518

GnomAD4 exome

AF:

0.534

AC:

780055

AN:

1461796

Hom.:

210904

Cov.:

AF XY:

0.536

AC XY:

389939

AN XY:

727202

show subpopulations

African (AFR)

AF:

0.196

AC:

6576

AN:

33480

American (AMR)

AF:

0.530

AC:

23695

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.517

AC:

13516

AN:

26136

East Asian (EAS)

AF:

0.448

AC:

17793

AN:

39700

South Asian (SAS)

AF:

0.597

AC:

51454

AN:

86254

European-Finnish (FIN)

AF:

0.534

AC:

28535

AN:

53420

Middle Eastern (MID)

AF:

0.466

AC:

2674

AN:

5740

European-Non Finnish (NFE)

AF:

0.544

AC:

605128

AN:

1111954

Other (OTH)

AF:

0.508

AC:

30684

AN:

60388

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

23239

46478

69718

92957

116196

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

17044

34088

51132

68176

85220

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.440

AC:

66989

AN:

152170

Hom.:

16328

Cov.:

AF XY:

0.442

AC XY:

32910

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.210

AC:

8738

AN:

41520

American (AMR)

AF:

0.489

AC:

7481

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.499

AC:

1729

AN:

3468

East Asian (EAS)

AF:

0.426

AC:

2204

AN:

5174

South Asian (SAS)

AF:

0.586

AC:

2828

AN:

4830

European-Finnish (FIN)

AF:

0.525

AC:

5560

AN:

10590

Middle Eastern (MID)

AF:

0.449

AC:

131

AN:

292

European-Non Finnish (NFE)

AF:

0.540

AC:

36702

AN:

67980

Other (OTH)

AF:

0.457

AC:

966

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1883

3765

5648

7530

9413

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

620

1240

1860

2480

3100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.513

Hom.:

24604

Bravo

AF:

0.426

TwinsUK

AF:

0.546

AC:

2024

ALSPAC

AF:

0.551

AC:

2124

ESP6500AA

AF:

0.216

AC:

952

ESP6500EA

AF:

0.537

AC:

4618

ExAC

AF:

0.510

AC:

61941

Asia WGS

AF:

0.509

AC:

1767

AN:

3478

EpiCase

AF:

0.542

EpiControl

AF:

0.528

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Nov 12, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant is associated with the following publications: (PMID: 30315176) -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Hypouricemia, renal, 2

Benign:2

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

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. -

Jul 15, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.096

BayesDel_addAF

Benign

-0.61

BayesDel_noAF

Benign

-0.50

CADD

Benign

5.0

(source)

DANN

Benign

0.92

DEOGEN2

Benign

0.039

Eigen

Benign

-1.3

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.066

LIST_S2

Benign

0.38

MetaRNN

Benign

0.000015

MetaSVM

Benign

-0.98

MutationAssessor

Benign

0.0

PhyloP100

-0.19

PrimateAI

Benign

0.29

PROVEAN

Benign

-0.020

REVEL

Benign

0.075

Sift

Pathogenic

0.0

Sift4G

Pathogenic

0.0

Polyphen

0.013

Vest4

0.056

MutPred

0.20

Loss of glycosylation at P29 (P = 0.0224);

MPC

0.13

ClinPred

0.015

GERP RS

-0.40

PromoterAI

-0.082

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.18

gMVP

0.25

Mutation Taster

=93/7

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over