dbSNP rs938554: SLC2A9:c.815-3496G>C (chr4-9924068-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_020041.3(SLC2A9):c.815-3496G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 151,958 control chromosomes in the GnomAD database, including 40,028 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 0.72 ( 39998 hom., cov: 30)

Exomes 𝑓: 0.77 ( 30 hom. )

Consequence

SLC2A9
NM_020041.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.221

Publications

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

SLC2A9 links:

ENSG00000249219 (HGNC:40637):

ENSG00000249219 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=-1.01).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.958 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A9	NM_020041.3	MANE Select	c.815-3496G>C		intron	N/A	NP_064425.2
	SLC2A9	NM_001001290.2		c.728-3496G>C		intron	N/A	NP_001001290.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SLC2A9	ENST00000264784.8	TSL:1 MANE Select	c.815-3496G>C	intron	N/A	ENSP00000264784.3
SLC2A9	ENST00000309065.7	TSL:1	c.728-3496G>C	intron	N/A	ENSP00000311383.3
SLC2A9	ENST00000505104.5	TSL:1	n.849-3496G>C	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.718

AC:

108918

AN:

151736

Hom.:

39974

Cov.:

show subpopulations

Gnomad AFR

AF:

0.572

Gnomad AMI

AF:

0.836

Gnomad AMR

AF:

0.639

Gnomad ASJ

AF:

0.750

Gnomad EAS

AF:

0.981

Gnomad SAS

AF:

0.771

Gnomad FIN

AF:

0.818

Gnomad MID

AF:

0.736

Gnomad NFE

AF:

0.781

Gnomad OTH

AF:

0.732

GnomAD4 exome

AF:

0.775

AC:

AN:

102

Hom.:

Cov.:

AF XY:

0.762

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.813

AC:

AN:

Other (OTH)

AF:

0.750

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<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:

0.718

AC:

108991

AN:

151856

Hom.:

39998

Cov.:

AF XY:

0.720

AC XY:

53458

AN XY:

74204

show subpopulations

African (AFR)

AF:

0.573

AC:

23681

AN:

41352

American (AMR)

AF:

0.638

AC:

9742

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.750

AC:

2603

AN:

3470

East Asian (EAS)

AF:

0.981

AC:

5046

AN:

5144

South Asian (SAS)

AF:

0.770

AC:

3695

AN:

4796

European-Finnish (FIN)

AF:

0.818

AC:

8649

AN:

10568

Middle Eastern (MID)

AF:

0.735

AC:

216

AN:

294

European-Non Finnish (NFE)

AF:

0.781

AC:

53047

AN:

67948

Other (OTH)

AF:

0.735

AC:

1550

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1442

2884

4325

5767

7209

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

834

1668

2502

3336

4170

<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:

0.748

Hom.:

5357

Bravo

AF:

0.700

Asia WGS

AF:

0.847

AC:

2947

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.83

(source)

DANN

Benign

0.56

PhyloP100

-0.22

Mutation Taster

=100/0

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over