NM_020041.3:c.844G>A

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.844G>A(p.Val282Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 1,613,968 control chromosomes in the GnomAD database, including 46,504 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.28 ( 6967 hom., cov: 33)

Exomes 𝑓: 0.22 ( 39537 hom. )

Consequence

SLC2A9
NM_020041.3 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.76

Publications

145 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 Gene-Disease associations (from GenCC):

hypouricemia, renal, 2
Inheritance: AR, AD, SD Classification: STRONG, MODERATE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, PanelApp Australia
hereditary renal hypouricemia
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

SLC2A9 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=0.027513742).

BP6

Variant 4-9920543-C-T is Benign according to our data. Variant chr4-9920543-C-T is described in ClinVar as Benign. ClinVar VariationId is 350215.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020041.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A9	NM_020041.3	MANE Select	c.844G>A	p.Val282Ile	missense	Exon 7 of 12	NP_064425.2
	SLC2A9	NM_001001290.2		c.757G>A	p.Val253Ile	missense	Exon 8 of 13	NP_001001290.1	Q9NRM0-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
SLC2A9	ENST00000264784.8	TSL:1 MANE Select	c.844G>A	p.Val282Ile	missense	Exon 7 of 12	ENSP00000264784.3	Q9NRM0-1
SLC2A9	ENST00000309065.7	TSL:1	c.757G>A	p.Val253Ile	missense	Exon 8 of 13	ENSP00000311383.3	Q9NRM0-2
SLC2A9	ENST00000505104.5	TSL:1	n.878G>A		non_coding_transcript_exon	Exon 8 of 12

Frequencies

GnomAD3 genomes

AF:

0.282

AC:

42936

AN:

152072

Hom.:

6956

Cov.:

show subpopulations

Gnomad AFR

AF:

0.428

Gnomad AMI

AF:

0.164

Gnomad AMR

AF:

0.361

Gnomad ASJ

AF:

0.250

Gnomad EAS

AF:

0.0187

Gnomad SAS

AF:

0.229

Gnomad FIN

AF:

0.182

Gnomad MID

AF:

0.263

Gnomad NFE

AF:

0.219

Gnomad OTH

AF:

0.267

GnomAD2 exomes

AF:

0.243

AC:

61149

AN:

251162

AF XY:

0.236

show subpopulations

Gnomad AFR exome

AF:

0.439

Gnomad AMR exome

AF:

0.398

Gnomad ASJ exome

AF:

0.238

Gnomad EAS exome

AF:

0.0158

Gnomad FIN exome

AF:

0.183

Gnomad NFE exome

AF:

0.218

Gnomad OTH exome

AF:

0.234

GnomAD4 exome

AF:

0.224

AC:

327053

AN:

1461778

Hom.:

39537

Cov.:

AF XY:

0.223

AC XY:

162344

AN XY:

727190

show subpopulations

African (AFR)

AF:

0.435

AC:

14557

AN:

33480

American (AMR)

AF:

0.392

AC:

17521

AN:

44714

Ashkenazi Jewish (ASJ)

AF:

0.233

AC:

6102

AN:

26136

East Asian (EAS)

AF:

0.0117

AC:

463

AN:

39700

South Asian (SAS)

AF:

0.242

AC:

20845

AN:

86252

European-Finnish (FIN)

AF:

0.180

AC:

9589

AN:

53358

Middle Eastern (MID)

AF:

0.260

AC:

1502

AN:

5768

European-Non Finnish (NFE)

AF:

0.218

AC:

242694

AN:

1111974

Other (OTH)

AF:

0.228

AC:

13780

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

14574

29147

43721

58294

72868

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8468

16936

25404

33872

42340

<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:

0.282

AC:

42983

AN:

152190

Hom.:

6967

Cov.:

AF XY:

0.279

AC XY:

20794

AN XY:

74404

show subpopulations

African (AFR)

AF:

0.428

AC:

17749

AN:

41494

American (AMR)

AF:

0.361

AC:

5523

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

867

AN:

3472

East Asian (EAS)

AF:

0.0189

AC:

AN:

5180

South Asian (SAS)

AF:

0.229

AC:

1106

AN:

4826

European-Finnish (FIN)

AF:

0.182

AC:

1927

AN:

10604

Middle Eastern (MID)

AF:

0.265

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.220

AC:

14926

AN:

68000

Other (OTH)

AF:

0.265

AC:

559

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1516

3032

4548

6064

7580

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

414

828

1242

1656

2070

<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:

0.241

Hom.:

9477

Bravo

AF:

0.300

TwinsUK

AF:

0.227

AC:

841

ALSPAC

AF:

0.209

AC:

805

ESP6500AA

AF:

0.414

AC:

1826

ESP6500EA

AF:

0.221

AC:

1898

ExAC

AF:

0.239

AC:

28971

Asia WGS

AF:

0.153

AC:

532

AN:

3478

EpiCase

AF:

0.227

EpiControl

AF:

0.229

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (3)

Hypouricemia, renal, 2 (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.17

BayesDel_addAF

Benign

-0.64

BayesDel_noAF

Benign

-0.55

CADD

Benign

4.5

(source)

DANN

Benign

0.95

DEOGEN2

Benign

0.10

Eigen

Benign

-0.58

Eigen_PC

Benign

-0.64

FATHMM_MKL

Uncertain

0.88

LIST_S2

Benign

0.72

MetaRNN

Benign

0.028

MetaSVM

Benign

-0.98

MutationAssessor

Uncertain

2.1

PhyloP100

1.8

PrimateAI

Benign

0.30

PROVEAN

Benign

-0.47

REVEL

Benign

0.23

Sift

Benign

0.16

Sift4G

Benign

0.25

Polyphen

0.61

Vest4

0.078

MPC

0.18

ClinPred

0.0080

GERP RS

1.6

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.052

gMVP

0.40

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over