Variant 22-23857517-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000398356.6(SLC2A11):c.28C>T(p.Arg10Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0355 in 1,612,776 control chromosomes in the GnomAD database, including 3,608 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/16 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 0.095 ( 1629 hom., cov: 31)

Exomes 𝑓: 0.029 ( 1979 hom. )

Consequence

SLC2A11
ENST00000398356.6 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.114

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:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.005146295).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.266 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	Protein
SLC2A11	NM_001282864.2 linkuse as main transcript	c.28C>T	p.Arg10Trp	missense_variant	1/11	NP_001269793.1
SLC2A11	NM_030807.5 linkuse as main transcript	c.28C>T	p.Arg10Trp	missense_variant	2/13	NP_110434.3
SLC2A11	NM_001024938.4 linkuse as main transcript	c.21+526C>T		intron_variant		NP_001020109.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000609825.2 linkuse as main transcript	n.159G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.0949

AC:

14366

AN:

151364

Hom.:

1623

Cov.:

show subpopulations

Gnomad AFR

AF:

0.270

Gnomad AMI

AF:

0.0307

Gnomad AMR

AF:

0.0582

Gnomad ASJ

AF:

0.0649

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00664

Gnomad FIN

AF:

0.00908

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.0273

Gnomad OTH

AF:

0.0960

GnomAD3 exomes

AF:

0.0415

AC:

10287

AN:

248108

Hom.:

711

AF XY:

0.0362

AC XY:

4874

AN XY:

134752

show subpopulations

Gnomad AFR exome

AF:

0.278

Gnomad AMR exome

AF:

0.0363

Gnomad ASJ exome

AF:

0.0662

Gnomad EAS exome

AF:

0.0000553

Gnomad SAS exome

AF:

0.00685

Gnomad FIN exome

AF:

0.0113

Gnomad NFE exome

AF:

0.0289

Gnomad OTH exome

AF:

0.0470

GnomAD4 exome

AF:

0.0293

AC:

42847

AN:

1461300

Hom.:

1979

Cov.:

AF XY:

0.0281

AC XY:

20458

AN XY:

726970

show subpopulations

Gnomad4 AFR exome

AF:

0.288

Gnomad4 AMR exome

AF:

0.0390

Gnomad4 ASJ exome

AF:

0.0645

Gnomad4 EAS exome

AF:

0.0000756

Gnomad4 SAS exome

AF:

0.00738

Gnomad4 FIN exome

AF:

0.0139

Gnomad4 NFE exome

AF:

0.0228

Gnomad4 OTH exome

AF:

0.0441

GnomAD4 genome

AF:

0.0951

AC:

14403

AN:

151476

Hom.:

1629

Cov.:

AF XY:

0.0910

AC XY:

6741

AN XY:

74040

show subpopulations

Gnomad4 AFR

AF:

0.270

Gnomad4 AMR

AF:

0.0582

Gnomad4 ASJ

AF:

0.0649

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00664

Gnomad4 FIN

AF:

0.00908

Gnomad4 NFE

AF:

0.0273

Gnomad4 OTH

AF:

0.0950

Alfa

AF:

0.0402

Hom.:

669

Bravo

AF:

0.108

TwinsUK

AF:

0.0181

AC:

ALSPAC

AF:

0.0226

AC:

ESP6500AA

AF:

0.273

AC:

1204

ESP6500EA

AF:

0.0310

AC:

267

ExAC

AF:

0.0466

AC:

5657

Asia WGS

AF:

0.0200

AC:

AN:

3478

EpiCase

AF:

0.0302

EpiControl

AF:

0.0297

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.45

BayesDel_noAF

Benign

-0.28

CADD

Benign

6.6

DANN

Uncertain

0.99

DEOGEN2

Benign

0.029

.;T

Eigen

Benign

-0.49

Eigen_PC

Benign

-0.70

FATHMM_MKL

Benign

0.026

LIST_S2

Benign

0.72

T;T

MetaRNN

Benign

0.0051

T;T

MetaSVM

Benign

-1.1

MutationTaster

Benign

1.0

P;P;P;P

PROVEAN

Benign

-1.6

N;.

REVEL

Uncertain

0.34

Sift

Uncertain

0.0060

D;.

Sift4G

Uncertain

0.016

D;D

Vest4

0.19

MPC

0.34

ClinPred

0.059

GERP RS

0.75

gMVP

0.37

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over