dbSNP rs10516197: SLC2A9:c.-175-212G>A (chr4-10040476-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000513129.1(SLC2A9):c.-41+14357G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,262 control chromosomes in the GnomAD database, including 1,353 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.10 ( 1353 hom., cov: 33)

Exomes 𝑓: 0.056 ( 0 hom. )

Consequence

SLC2A9
ENST00000513129.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.147

Publications

4 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:

SLC2A9-AS1 (HGNC:59109):

SLC2A9-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000513129.1. 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_001001290.2		c.-387G>A		upstream_gene	N/A	NP_001001290.1	Q9NRM0-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC2A9	ENST00000506583.5	TSL:5	c.-175-212G>A	intron	N/A	ENSP00000422209.1	Q9NRM0-2
SLC2A9	ENST00000513129.1	TSL:3	c.-41+14357G>A	intron	N/A	ENSP00000426800.1	D6REK5
SLC2A9-AS1	ENST00000733256.1		n.319-15383C>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.100

AC:

15206

AN:

152090

Hom.:

1346

Cov.:

show subpopulations

Gnomad AFR

AF:

0.131

Gnomad AMI

AF:

0.0406

Gnomad AMR

AF:

0.183

Gnomad ASJ

AF:

0.0697

Gnomad EAS

AF:

0.460

Gnomad SAS

AF:

0.161

Gnomad FIN

AF:

0.0726

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.0375

Gnomad OTH

AF:

0.0942

GnomAD4 exome

AF:

0.0556

AC:

AN:

Hom.:

AF XY:

0.0750

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0652

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.558

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.100

AC:

15235

AN:

152208

Hom.:

1353

Cov.:

AF XY:

0.106

AC XY:

7861

AN XY:

74414

show subpopulations

African (AFR)

AF:

0.131

AC:

5438

AN:

41548

American (AMR)

AF:

0.183

AC:

2791

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.0697

AC:

242

AN:

3472

East Asian (EAS)

AF:

0.459

AC:

2378

AN:

5178

South Asian (SAS)

AF:

0.162

AC:

777

AN:

4810

European-Finnish (FIN)

AF:

0.0726

AC:

769

AN:

10592

Middle Eastern (MID)

AF:

0.156

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0375

AC:

2549

AN:

68012

Other (OTH)

AF:

0.0984

AC:

208

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

648

1296

1944

2592

3240

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

166

332

498

664

830

<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:

0.0828

Hom.:

244

Bravo

AF:

0.111

Asia WGS

AF:

0.270

AC:

935

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.0

(source)

DANN

Benign

0.58

PhyloP100

-0.15

PromoterAI

0.0050

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over