Genetic Variant NM_001024939.4:c.1354G>A (chr22-23884703-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 NM_001024939.4(SLC2A11):c.1354G>A(p.Ala452Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0246 in 1,613,994 control chromosomes in the GnomAD database, including 589 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 0.032 ( 87 hom., cov: 32)

Exomes 𝑓: 0.024 ( 502 hom. )

Consequence

SLC2A11
NM_001024939.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.15

Publications

9 publications found

Variant links:

Genes affected

SLC2A11 (HGNC:14239): (solute carrier family 2 member 11) This gene belongs to a family of proteins that mediate the transport of sugars across the cell membrane. The encoded protein transports glucose and fructose. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]

SLC2A11 links:

ENSG00000251357 (HGNC:):

ENSG00000251357 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 (MetaRNN=0.0027993321).

BA1

GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.0598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A11	NM_001024939.4 link	c.1354G>A	p.Ala452Thr	missense_variant	Exon 12 of 12	ENST00000316185.9	NP_001020110.1	Q9BYW1-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A11	ENST00000316185.9 link	c.1354G>A	p.Ala452Thr	missense_variant	Exon 12 of 12	1	NM_001024939.4	ENSP00000326748.8		Q9BYW1-3
ENSG00000251357	ENST00000433835.3 link	c.431+7532G>A		intron_variant	Intron 4 of 5	5		ENSP00000400325.3		H7C1H1

Frequencies

GnomAD3 genomes

AF:

0.0323

AC:

4914

AN:

152064

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0459

Gnomad AMI

AF:

0.0285

Gnomad AMR

AF:

0.0332

Gnomad ASJ

AF:

0.0452

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00830

Gnomad FIN

AF:

0.0222

Gnomad MID

AF:

0.0823

Gnomad NFE

AF:

0.0287

Gnomad OTH

AF:

0.0346

GnomAD2 exomes

AF:

0.0247

AC:

6219

AN:

251342

AF XY:

0.0244

show subpopulations

Gnomad AFR exome

AF:

0.0466

Gnomad AMR exome

AF:

0.0240

Gnomad ASJ exome

AF:

0.0493

Gnomad EAS exome

AF:

0.0000544

Gnomad FIN exome

AF:

0.0242

Gnomad NFE exome

AF:

0.0280

Gnomad OTH exome

AF:

0.0328

GnomAD4 exome

AF:

0.0238

AC:

34741

AN:

1461812

Hom.:

502

Cov.:

AF XY:

0.0238

AC XY:

17280

AN XY:

727216

show subpopulations

African (AFR)

AF:

0.0456

AC:

1526

AN:

33476

American (AMR)

AF:

0.0248

AC:

1110

AN:

44718

Ashkenazi Jewish (ASJ)

AF:

0.0483

AC:

1262

AN:

26128

East Asian (EAS)

AF:

0.00

AC:

AN:

39700

South Asian (SAS)

AF:

0.00839

AC:

724

AN:

86252

European-Finnish (FIN)

AF:

0.0251

AC:

1342

AN:

53420

Middle Eastern (MID)

AF:

0.0652

AC:

376

AN:

5768

European-Non Finnish (NFE)

AF:

0.0240

AC:

26731

AN:

1111958

Other (OTH)

AF:

0.0277

AC:

1670

AN:

60392

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.485

Heterozygous variant carriers

1994

3987

5981

7974

9968

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

968

1936

2904

3872

4840

<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:

0.0323

AC:

4923

AN:

152182

Hom.:

Cov.:

AF XY:

0.0318

AC XY:

2363

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.0459

AC:

1905

AN:

41510

American (AMR)

AF:

0.0332

AC:

508

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.0452

AC:

157

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5178

South Asian (SAS)

AF:

0.00851

AC:

AN:

4818

European-Finnish (FIN)

AF:

0.0222

AC:

236

AN:

10612

Middle Eastern (MID)

AF:

0.0884

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0287

AC:

1952

AN:

68004

Other (OTH)

AF:

0.0343

AC:

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

242

484

725

967

1209

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

108

162

216

270

<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:

0.0291

Hom.:

295

Bravo

AF:

0.0335

TwinsUK

AF:

0.0186

AC:

ALSPAC

AF:

0.0231

AC:

ESP6500AA

AF:

0.0468

AC:

206

ESP6500EA

AF:

0.0287

AC:

247

ExAC

AF:

0.0248

AC:

3005

Asia WGS

AF:

0.00895

AC:

AN:

3478

EpiCase

AF:

0.0315

EpiControl

AF:

0.0321

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.43

BayesDel_noAF

Benign

-0.36

CADD

Benign

(source)

DANN

Uncertain

0.99

DEOGEN2

Benign

0.29

T;.;.

Eigen

Benign

-0.30

Eigen_PC

Benign

-0.36

FATHMM_MKL

Uncertain

0.89

LIST_S2

Benign

0.71

T;T;T

MetaRNN

Benign

0.0028

T;T;T

MetaSVM

Benign

-0.94

MutationAssessor

Benign

1.0

L;.;.

PhyloP100

4.1

PrimateAI

Uncertain

0.55

PROVEAN

Benign

-2.2

N;N;N

REVEL

Uncertain

0.32

Sift

Benign

0.087

T;T;T

Sift4G

Benign

0.083

T;T;T

Polyphen

0.24

B;.;D

Vest4

0.17

MPC

0.41

ClinPred

0.017

GERP RS

1.1

Varity_R

0.11

Mutation Taster

=94/6

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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