Variant chr17-7285140-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001042.3(SLC2A4):c.1073C>T(p.Ala358Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00564 in 1,604,184 control chromosomes in the GnomAD database, including 39 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.0051 ( 6 hom., cov: 32)

Exomes 𝑓: 0.0057 ( 33 hom. )

Consequence

SLC2A4
NM_001042.3 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.489

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.01050356).

BP6

Variant 17-7285140-C-T is Benign according to our data. Variant chr17-7285140-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2647324.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 6 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A4	NM_001042.3 linkuse as main transcript	c.1073C>T	p.Ala358Val	missense_variant	9/11	ENST00000317370.13	NP_001033.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A4	ENST00000317370.13 linkuse as main transcript	c.1073C>T	p.Ala358Val	missense_variant	9/11	1	NM_001042.3	ENSP00000320935	P1	P14672-1

Frequencies

GnomAD3 genomes

AF:

0.00513

AC:

781

AN:

152214

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000916

Gnomad AMI

AF:

0.0417

Gnomad AMR

AF:

0.00301

Gnomad ASJ

AF:

0.0107

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00228

Gnomad FIN

AF:

0.0129

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00682

Gnomad OTH

AF:

0.00287

GnomAD3 exomes

AF:

0.00597

AC:

1381

AN:

231164

Hom.:

AF XY:

0.00613

AC XY:

765

AN XY:

124834

show subpopulations

Gnomad AFR exome

AF:

0.000742

Gnomad AMR exome

AF:

0.00306

Gnomad ASJ exome

AF:

0.0118

Gnomad EAS exome

AF:

0.0000580

Gnomad SAS exome

AF:

0.00292

Gnomad FIN exome

AF:

0.0140

Gnomad NFE exome

AF:

0.00736

Gnomad OTH exome

AF:

0.00871

GnomAD4 exome

AF:

0.00569

AC:

8261

AN:

1451852

Hom.:

Cov.:

AF XY:

0.00572

AC XY:

4125

AN XY:

721546

show subpopulations

Gnomad4 AFR exome

AF:

0.000688

Gnomad4 AMR exome

AF:

0.00302

Gnomad4 ASJ exome

AF:

0.0110

Gnomad4 EAS exome

AF:

0.0000254

Gnomad4 SAS exome

AF:

0.00286

Gnomad4 FIN exome

AF:

0.0127

Gnomad4 NFE exome

AF:

0.00591

Gnomad4 OTH exome

AF:

0.00558

GnomAD4 genome

AF:

0.00513

AC:

782

AN:

152332

Hom.:

Cov.:

AF XY:

0.00505

AC XY:

376

AN XY:

74496

show subpopulations

Gnomad4 AFR

AF:

0.000914

Gnomad4 AMR

AF:

0.00301

Gnomad4 ASJ

AF:

0.0107

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00248

Gnomad4 FIN

AF:

0.0129

Gnomad4 NFE

AF:

0.00682

Gnomad4 OTH

AF:

0.00284

Alfa

AF:

0.00651

Hom.:

Bravo

AF:

0.00404

TwinsUK

AF:

0.00270

AC:

ALSPAC

AF:

0.00467

AC:

ESP6500AA

AF:

0.00113

AC:

ESP6500EA

AF:

0.00709

AC:

ExAC

AF:

0.00574

AC:

696

Asia WGS

AF:

0.000577

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jul 01, 2024

SLC2A4: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.16

BayesDel_addAF

Benign

-0.31

BayesDel_noAF

Benign

-0.21

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Uncertain

0.44

T;T;.

Eigen

Benign

-0.17

Eigen_PC

Benign

-0.038

FATHMM_MKL

Benign

0.26

LIST_S2

Uncertain

0.89

D;D;D

MetaRNN

Benign

0.011

T;T;T

MetaSVM

Benign

-0.43

MutationTaster

Benign

0.93

D;D;D

PrimateAI

Uncertain

0.62

PROVEAN

Uncertain

-2.4

N;.;N

REVEL

Benign

0.16

Sift

Benign

0.097

T;.;T

Sift4G

Benign

0.54

T;T;T

Polyphen

0.17

B;.;B

Vest4

0.65

MVP

0.79

MPC

0.28

ClinPred

0.029

GERP RS

5.9

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.21

gMVP

0.49

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over