Variant rs60699980 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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. 11/19 in silico tools predict 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

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons	MANE	UniProt
SLC2A11	NM_001024939.4 linkuse as main transcript	c.1354G>A	p.Ala452Thr	missense_variant	12/12	ENST00000316185.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A11	ENST00000316185.9 linkuse as main transcript	c.1354G>A	p.Ala452Thr	missense_variant	12/12	1	NM_001024939.4		Q9BYW1-3

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

GnomAD3 exomes

AF:

0.0247

AC:

6219

AN:

251342

Hom.:

AF XY:

0.0244

AC XY:

3311

AN XY:

135830

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 SAS exome

AF:

0.00748

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

Gnomad4 AFR exome

AF:

0.0456

Gnomad4 AMR exome

AF:

0.0248

Gnomad4 ASJ exome

AF:

0.0483

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00839

Gnomad4 FIN exome

AF:

0.0251

Gnomad4 NFE exome

AF:

0.0240

Gnomad4 OTH exome

AF:

0.0277

GnomAD4 genome

AF:

0.0323

AC:

4923

AN:

152182

Hom.:

Cov.:

AF XY:

0.0318

AC XY:

2363

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.0459

Gnomad4 AMR

AF:

0.0332

Gnomad4 ASJ

AF:

0.0452

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00851

Gnomad4 FIN

AF:

0.0222

Gnomad4 NFE

AF:

0.0287

Gnomad4 OTH

AF:

0.0343

Alfa

AF:

0.0296

Hom.:

130

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

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;.;.

MutationTaster

Benign

0.58

D;D;D

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

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

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over