Genetic Variant SLC2A9:c.-175-954G>A (chr4-10041218-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+13615G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 152,074 control chromosomes in the GnomAD database, including 15,585 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 0.43 ( 15585 hom., cov: 33)

Consequence

SLC2A9
ENST00000513129.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.967

Publications

6 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:

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new If you want to explore the variant's impact on the transcript ENST00000513129.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.93).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.569 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC2A9	ENST00000506583.5	TSL:5	c.-175-954G>A	intron	N/A	ENSP00000422209.1	Q9NRM0-2
SLC2A9	ENST00000513129.1	TSL:3	c.-41+13615G>A	intron	N/A	ENSP00000426800.1	D6REK5
SLC2A9-AS1	ENST00000733256.1		n.319-14641C>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.429

AC:

65204

AN:

151958

Hom.:

15581

Cov.:

show subpopulations

Gnomad AFR

AF:

0.206

Gnomad AMI

AF:

0.693

Gnomad AMR

AF:

0.402

Gnomad ASJ

AF:

0.498

Gnomad EAS

AF:

0.424

Gnomad SAS

AF:

0.587

Gnomad FIN

AF:

0.523

Gnomad MID

AF:

0.430

Gnomad NFE

AF:

0.538

Gnomad OTH

AF:

0.447

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.429

AC:

65216

AN:

152074

Hom.:

15585

Cov.:

AF XY:

0.430

AC XY:

31960

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.206

AC:

8544

AN:

41492

American (AMR)

AF:

0.401

AC:

6137

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.498

AC:

1729

AN:

3470

East Asian (EAS)

AF:

0.425

AC:

2188

AN:

5152

South Asian (SAS)

AF:

0.587

AC:

2835

AN:

4826

European-Finnish (FIN)

AF:

0.523

AC:

5531

AN:

10572

Middle Eastern (MID)

AF:

0.425

AC:

124

AN:

292

European-Non Finnish (NFE)

AF:

0.538

AC:

36555

AN:

67964

Other (OTH)

AF:

0.447

AC:

942

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1814

3629

5443

7258

9072

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

614

1228

1842

2456

3070

<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:

0.438

Hom.:

3276

Bravo

AF:

0.409

Asia WGS

AF:

0.509

AC:

1768

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.32

(source)

DANN

Benign

0.51

PhyloP100

-0.97

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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