dbSNP rs7976243: SLC2A3:c.108+323G>T (chr12-7933487-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_006931.3(SLC2A3):c.108+323G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 456,834 control chromosomes in the GnomAD database, including 22,329 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 0.29 ( 6753 hom., cov: 32)

Exomes 𝑓: 0.31 ( 15576 hom. )

Consequence

SLC2A3
NM_006931.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0730

Publications

10 publications found

Variant links:

Genes affected

SLC2A3 (HGNC:11007): (solute carrier family 2 member 3) Enables dehydroascorbic acid transmembrane transporter activity; glucose binding activity; and glucose transmembrane transporter activity. Involved in glucose import across plasma membrane and transport across blood-brain barrier. Is integral component of plasma membrane. Biomarker of Alzheimer's disease; acanthosis nigricans; diabetes mellitus; and type 2 diabetes mellitus. [provided by Alliance of Genome Resources, Apr 2022]

SLC2A3 Gene-Disease associations (from GenCC):

Huntington disease
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

SLC2A3 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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A3	NM_006931.3 link	c.108+323G>T		intron_variant	Intron 2 of 9	ENST00000075120.12	NP_008862.1	P11169

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A3	ENST00000075120.12 link	c.108+323G>T		intron_variant	Intron 2 of 9	1	NM_006931.3	ENSP00000075120.7		P11169

Frequencies

GnomAD3 genomes

AF:

0.295

AC:

44744

AN:

151764

Hom.:

6753

Cov.:

show subpopulations

Gnomad AFR

AF:

0.284

Gnomad AMI

AF:

0.257

Gnomad AMR

AF:

0.291

Gnomad ASJ

AF:

0.344

Gnomad EAS

AF:

0.527

Gnomad SAS

AF:

0.410

Gnomad FIN

AF:

0.278

Gnomad MID

AF:

0.301

Gnomad NFE

AF:

0.277

Gnomad OTH

AF:

0.303

GnomAD4 exome

AF:

0.312

AC:

95214

AN:

304950

Hom.:

15576

Cov.:

AF XY:

0.318

AC XY:

51012

AN XY:

160324

show subpopulations

African (AFR)

AF:

0.283

AC:

2808

AN:

9930

American (AMR)

AF:

0.282

AC:

3262

AN:

11560

Ashkenazi Jewish (ASJ)

AF:

0.341

AC:

3276

AN:

9608

East Asian (EAS)

AF:

0.520

AC:

10733

AN:

20638

South Asian (SAS)

AF:

0.405

AC:

12393

AN:

30632

European-Finnish (FIN)

AF:

0.298

AC:

5068

AN:

16996

Middle Eastern (MID)

AF:

0.325

AC:

432

AN:

1328

European-Non Finnish (NFE)

AF:

0.278

AC:

51746

AN:

186236

Other (OTH)

AF:

0.305

AC:

5496

AN:

18022

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

2949

5897

8846

11794

14743

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

416

832

1248

1664

2080

<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:

0.295

AC:

44789

AN:

151884

Hom.:

6753

Cov.:

AF XY:

0.299

AC XY:

22211

AN XY:

74208

show subpopulations

African (AFR)

AF:

0.284

AC:

11759

AN:

41436

American (AMR)

AF:

0.291

AC:

4442

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.344

AC:

1192

AN:

3466

East Asian (EAS)

AF:

0.527

AC:

2713

AN:

5148

South Asian (SAS)

AF:

0.409

AC:

1971

AN:

4816

European-Finnish (FIN)

AF:

0.278

AC:

2931

AN:

10542

Middle Eastern (MID)

AF:

0.315

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.277

AC:

18812

AN:

67904

Other (OTH)

AF:

0.304

AC:

643

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1552

3105

4657

6210

7762

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

468

936

1404

1872

2340

<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:

0.280

Hom.:

25307

Bravo

AF:

0.292

Asia WGS

AF:

0.439

AC:

1527

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.73

(source)

DANN

Benign

0.53

PhyloP100

-0.073

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over