dbSNP rs5418: SLC2A4:n.-162G>A (chr17-7281773-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000572485.5(SLC2A4):n.-162G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.547 in 733,514 control chromosomes in the GnomAD database, including 113,231 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 0.49 ( 19820 hom., cov: 33)

Exomes 𝑓: 0.56 ( 93411 hom. )

Consequence

SLC2A4
ENST00000572485.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.281

Publications

47 publications found

Variant links:

Genes affected

SLC2A4 (HGNC:11009): (solute carrier family 2 member 4) This gene is a member of the solute carrier family 2 (facilitated glucose transporter) family and encodes a protein that functions as an insulin-regulated facilitative glucose transporter. In the absence of insulin, this integral membrane protein is sequestered within the cells of muscle and adipose tissue. Within minutes of insulin stimulation, the protein moves to the cell surface and begins to transport glucose across the cell membrane. Mutations in this gene have been associated with noninsulin-dependent diabetes mellitus (NIDDM). [provided by RefSeq, Jul 2008]

SLC2A4 links:

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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=-0.79).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A4	NM_001042.3 link	c.-162G>A		5_prime_UTR_variant	Exon 1 of 11	ENST00000317370.13	NP_001033.1	P14672-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A4	ENST00000317370.13 link	c.-162G>A		5_prime_UTR_variant	Exon 1 of 11	1	NM_001042.3	ENSP00000320935.8		P14672-1

Frequencies

GnomAD3 genomes

AF:

0.492

AC:

74867

AN:

152018

Hom.:

19801

Cov.:

show subpopulations

Gnomad AFR

AF:

0.290

Gnomad AMI

AF:

0.550

Gnomad AMR

AF:

0.526

Gnomad ASJ

AF:

0.591

Gnomad EAS

AF:

0.371

Gnomad SAS

AF:

0.560

Gnomad FIN

AF:

0.622

Gnomad MID

AF:

0.620

Gnomad NFE

AF:

0.584

Gnomad OTH

AF:

0.543

GnomAD4 exome

AF:

0.561

AC:

325970

AN:

581378

Hom.:

93411

Cov.:

AF XY:

0.565

AC XY:

174114

AN XY:

308176

show subpopulations

African (AFR)

AF:

0.283

AC:

4443

AN:

15672

American (AMR)

AF:

0.483

AC:

15480

AN:

32032

Ashkenazi Jewish (ASJ)

AF:

0.600

AC:

11331

AN:

18880

East Asian (EAS)

AF:

0.359

AC:

11386

AN:

31688

South Asian (SAS)

AF:

0.577

AC:

35141

AN:

60896

European-Finnish (FIN)

AF:

0.611

AC:

27770

AN:

45482

Middle Eastern (MID)

AF:

0.611

AC:

1504

AN:

2462

European-Non Finnish (NFE)

AF:

0.588

AC:

202289

AN:

343882

Other (OTH)

AF:

0.547

AC:

16626

AN:

30384

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

7261

14522

21784

29045

36306

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1710

3420

5130

6840

8550

<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:

0.492

AC:

74924

AN:

152136

Hom.:

19820

Cov.:

AF XY:

0.497

AC XY:

36941

AN XY:

74400

show subpopulations

African (AFR)

AF:

0.290

AC:

12052

AN:

41508

American (AMR)

AF:

0.526

AC:

8054

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.591

AC:

2050

AN:

3468

East Asian (EAS)

AF:

0.370

AC:

1912

AN:

5162

South Asian (SAS)

AF:

0.562

AC:

2709

AN:

4818

European-Finnish (FIN)

AF:

0.622

AC:

6596

AN:

10606

Middle Eastern (MID)

AF:

0.622

AC:

183

AN:

294

European-Non Finnish (NFE)

AF:

0.584

AC:

39712

AN:

67964

Other (OTH)

AF:

0.548

AC:

1158

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1842

3684

5525

7367

9209

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

672

1344

2016

2688

3360

<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:

0.549

Hom.:

41291

Bravo

AF:

0.473

Asia WGS

AF:

0.479

AC:

1666

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

6.0

(source)

DANN

Benign

0.74

PhyloP100

-0.28

PromoterAI

0.069

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=298/2

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