Genetic Variant SLC2A4:p.Asn130Asn (chr17-7283804-T-C) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001042.3(SLC2A4):c.390T>C(p.Asn130Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.637 in 1,613,772 control chromosomes in the GnomAD database, including 329,905 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 0.70 ( 37714 hom., cov: 32)

Exomes 𝑓: 0.63 ( 292191 hom. )

Consequence

SLC2A4
NM_001042.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.48

Publications

48 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:

ENSG00000263342 (HGNC:):

ENSG00000263342 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.06).

BP7

Synonymous conserved (PhyloP=-3.48 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.846 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A4	NM_001042.3 link	c.390T>C	p.Asn130Asn	synonymous_variant	Exon 4 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.390T>C	p.Asn130Asn	synonymous_variant	Exon 4 of 11	1	NM_001042.3	ENSP00000320935.8		P14672-1

Frequencies

GnomAD3 genomes

AF:

0.696

AC:

105825

AN:

151940

Hom.:

37644

Cov.:

show subpopulations

Gnomad AFR

AF:

0.853

Gnomad AMI

AF:

0.584

Gnomad AMR

AF:

0.664

Gnomad ASJ

AF:

0.634

Gnomad EAS

AF:

0.648

Gnomad SAS

AF:

0.652

Gnomad FIN

AF:

0.640

Gnomad MID

AF:

0.788

Gnomad NFE

AF:

0.628

Gnomad OTH

AF:

0.708

GnomAD2 exomes

AF:

0.647

AC:

162129

AN:

250728

AF XY:

0.646

show subpopulations

Gnomad AFR exome

AF:

0.858

Gnomad AMR exome

AF:

0.595

Gnomad ASJ exome

AF:

0.636

Gnomad EAS exome

AF:

0.643

Gnomad FIN exome

AF:

0.627

Gnomad NFE exome

AF:

0.634

Gnomad OTH exome

AF:

0.648

GnomAD4 exome

AF:

0.630

AC:

921529

AN:

1461714

Hom.:

292191

Cov.:

AF XY:

0.631

AC XY:

459101

AN XY:

727158

show subpopulations

African (AFR)

AF:

0.863

AC:

28880

AN:

33480

American (AMR)

AF:

0.605

AC:

27063

AN:

44716

Ashkenazi Jewish (ASJ)

AF:

0.644

AC:

16842

AN:

26136

East Asian (EAS)

AF:

0.639

AC:

25358

AN:

39698

South Asian (SAS)

AF:

0.653

AC:

56333

AN:

86256

European-Finnish (FIN)

AF:

0.624

AC:

33258

AN:

53330

Middle Eastern (MID)

AF:

0.738

AC:

4255

AN:

5768

European-Non Finnish (NFE)

AF:

0.621

AC:

690551

AN:

1111940

Other (OTH)

AF:

0.646

AC:

38989

AN:

60390

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

22464

44928

67392

89856

112320

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

18560

37120

55680

74240

92800

<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:

0.697

AC:

105960

AN:

152058

Hom.:

37714

Cov.:

AF XY:

0.696

AC XY:

51772

AN XY:

74336

show subpopulations

African (AFR)

AF:

0.854

AC:

35451

AN:

41522

American (AMR)

AF:

0.664

AC:

10152

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.634

AC:

2200

AN:

3470

East Asian (EAS)

AF:

0.647

AC:

3333

AN:

5148

South Asian (SAS)

AF:

0.653

AC:

3152

AN:

4824

European-Finnish (FIN)

AF:

0.640

AC:

6772

AN:

10576

Middle Eastern (MID)

AF:

0.789

AC:

232

AN:

294

European-Non Finnish (NFE)

AF:

0.628

AC:

42638

AN:

67924

Other (OTH)

AF:

0.712

AC:

1500

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1636

3272

4908

6544

8180

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

814

1628

2442

3256

4070

<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:

0.644

Hom.:

55591

Bravo

AF:

0.704

Asia WGS

AF:

0.687

AC:

2391

AN:

3478

EpiCase

AF:

0.648

EpiControl

AF:

0.649

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.027

(source)

DANN

Benign

0.45

PhyloP100

-3.5

Mutation Taster

=99/1

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