Genetic Variant SLC2A4:n.-192C>A (chr17-7281743-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 ENST00000572485.5(SLC2A4):n.-192C>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 0.545 in 644,948 control chromosomes in the GnomAD database, including 99,019 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 ( 19809 hom., cov: 33)

Exomes 𝑓: 0.56 ( 79210 hom. )

Consequence

SLC2A4
ENST00000572485.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.349

Publications

45 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=-0.54).

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.-192C>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.-192C>A		5_prime_UTR_variant	Exon 1 of 11	1	NM_001042.3	ENSP00000320935.8		P14672-1

Frequencies

GnomAD3 genomes

AF:

0.493

AC:

74856

AN:

151970

Hom.:

19791

Cov.:

show subpopulations

Gnomad AFR

AF:

0.291

Gnomad AMI

AF:

0.549

Gnomad AMR

AF:

0.526

Gnomad ASJ

AF:

0.591

Gnomad EAS

AF:

0.376

Gnomad SAS

AF:

0.560

Gnomad FIN

AF:

0.622

Gnomad MID

AF:

0.620

Gnomad NFE

AF:

0.584

Gnomad OTH

AF:

0.540

GnomAD4 exome

AF:

0.561

AC:

276289

AN:

492860

Hom.:

79210

Cov.:

AF XY:

0.564

AC XY:

147213

AN XY:

260912

show subpopulations

African (AFR)

AF:

0.284

AC:

3821

AN:

13446

American (AMR)

AF:

0.490

AC:

12108

AN:

24728

Ashkenazi Jewish (ASJ)

AF:

0.600

AC:

9307

AN:

15518

East Asian (EAS)

AF:

0.363

AC:

11308

AN:

31130

South Asian (SAS)

AF:

0.575

AC:

29835

AN:

51892

European-Finnish (FIN)

AF:

0.610

AC:

23801

AN:

39004

Middle Eastern (MID)

AF:

0.613

AC:

1298

AN:

2118

European-Non Finnish (NFE)

AF:

0.590

AC:

169898

AN:

287776

Other (OTH)

AF:

0.547

AC:

14913

AN:

27248

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

6125

12250

18375

24500

30625

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

900

1800

2700

3600

4500

<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:

0.493

AC:

74913

AN:

152088

Hom.:

19809

Cov.:

AF XY:

0.497

AC XY:

36953

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.290

AC:

12053

AN:

41500

American (AMR)

AF:

0.526

AC:

8046

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.591

AC:

2046

AN:

3464

East Asian (EAS)

AF:

0.376

AC:

1931

AN:

5140

South Asian (SAS)

AF:

0.562

AC:

2711

AN:

4824

European-Finnish (FIN)

AF:

0.622

AC:

6593

AN:

10596

Middle Eastern (MID)

AF:

0.622

AC:

183

AN:

294

European-Non Finnish (NFE)

AF:

0.584

AC:

39695

AN:

67952

Other (OTH)

AF:

0.546

AC:

1155

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1873

3746

5618

7491

9364

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:

0.558

Hom.:

62475

Bravo

AF:

0.473

Asia WGS

AF:

0.481

AC:

1672

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

(source)

DANN

Benign

0.69

PhyloP100

0.35

PromoterAI

-0.0015

Neutral

(source)

Mutation Taster

=299/1

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