rs6018008

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_030777.4(SLC2A10):c.1552A>G(p.Thr518Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00544 in 1,613,926 control chromosomes in the GnomAD database, including 332 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. T518T) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.026 ( 156 hom., cov: 32)

Exomes 𝑓: 0.0033 ( 176 hom. )

Consequence

SLC2A10
NM_030777.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: -3.13

Publications

12 publications found

Variant links:

Genes affected

SLC2A10 (HGNC:13444): (solute carrier family 2 member 10) This gene encodes a member of the class III facilitative glucose transporter family. The encoded protein plays a role in regulation of glucose homeostasis. Mutations in this gene have been associated with arterial tortuosity syndrome.[provided by RefSeq, Dec 2009]

SLC2A10 Gene-Disease associations (from GenCC):

arterial tortuosity syndrome
Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: PanelApp Australia, G2P, Orphanet, Labcorp Genetics (formerly Invitae), ClinGen, Ambry Genetics, Genomics England PanelApp

SLC2A10 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0019231439).

BP6

Variant 20-46733760-A-G is Benign according to our data. Variant chr20-46733760-A-G is described in ClinVar as Benign. ClinVar VariationId is 139181.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0838 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030777.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A10	NM_030777.4	MANE Select	c.1552A>G	p.Thr518Ala	missense	Exon 5 of 5	NP_110404.1	O95528

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
SLC2A10	ENST00000359271.4	TSL:1 MANE Select	c.1552A>G	p.Thr518Ala	missense	Exon 5 of 5	ENSP00000352216.2	O95528
SLC2A10	ENST00000862794.1		c.1846A>G	p.Thr616Ala	missense	Exon 5 of 5	ENSP00000532853.1
SLC2A10	ENST00000862792.1		c.1684A>G	p.Thr562Ala	missense	Exon 6 of 6	ENSP00000532851.1

Frequencies

GnomAD3 genomes

AF:

0.0253

AC:

3849

AN:

152072

Hom.:

148

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0854

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0102

Gnomad ASJ

AF:

0.0164

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.00228

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.000676

Gnomad OTH

AF:

0.0158

GnomAD2 exomes

AF:

0.00760

AC:

1907

AN:

251048

AF XY:

0.00577

show subpopulations

Gnomad AFR exome

AF:

0.0873

Gnomad AMR exome

AF:

0.00532

Gnomad ASJ exome

AF:

0.0150

Gnomad EAS exome

AF:

0.000652

Gnomad FIN exome

AF:

0.000232

Gnomad NFE exome

AF:

0.000767

Gnomad OTH exome

AF:

0.00375

GnomAD4 exome

AF:

0.00335

AC:

4890

AN:

1461736

Hom.:

176

Cov.:

AF XY:

0.00302

AC XY:

2194

AN XY:

727168

show subpopulations

African (AFR)

AF:

0.0906

AC:

3031

AN:

33452

American (AMR)

AF:

0.00572

AC:

256

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.0144

AC:

377

AN:

26134

East Asian (EAS)

AF:

0.000327

AC:

AN:

39700

South Asian (SAS)

AF:

0.00119

AC:

103

AN:

86256

European-Finnish (FIN)

AF:

0.000169

AC:

AN:

53370

Middle Eastern (MID)

AF:

0.00798

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

0.000494

AC:

549

AN:

1111944

Other (OTH)

AF:

0.00838

AC:

506

AN:

60388

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.453

Heterozygous variant carriers

249

498

747

996

1245

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

108

216

324

432

540

<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:

0.0256

AC:

3890

AN:

152190

Hom.:

156

Cov.:

AF XY:

0.0250

AC XY:

1858

AN XY:

74412

show subpopulations

African (AFR)

AF:

0.0861

AC:

3574

AN:

41496

American (AMR)

AF:

0.0102

AC:

156

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0164

AC:

AN:

3472

East Asian (EAS)

AF:

0.00136

AC:

AN:

5162

South Asian (SAS)

AF:

0.00228

AC:

AN:

4830

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10610

Middle Eastern (MID)

AF:

0.0170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000676

AC:

AN:

68014

Other (OTH)

AF:

0.0161

AC:

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

174

347

521

694

868

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

114

152

190

<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:

0.00742

Hom.:

Bravo

AF:

0.0279

TwinsUK

AF:

0.00108

AC:

ALSPAC

AF:

0.000259

AC:

ESP6500AA

AF:

0.0803

AC:

354

ESP6500EA

AF:

0.000814

AC:

ExAC

AF:

0.00881

AC:

1069

Asia WGS

AF:

0.0190

AC:

AN:

3478

EpiCase

AF:

0.000872

EpiControl

AF:

0.00101

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (3)

Arterial tortuosity syndrome (2)

Familial thoracic aortic aneurysm and aortic dissection (2)

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.057

BayesDel_addAF

Benign

-0.63

BayesDel_noAF

Benign

-0.61

CADD

Benign

0.0070

(source)

DANN

Benign

0.22

DEOGEN2

Benign

0.10

Eigen

Benign

-1.9

Eigen_PC

Benign

-1.9

FATHMM_MKL

Benign

0.00065

LIST_S2

Benign

0.040

MetaRNN

Benign

0.0019

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-0.34

PhyloP100

-3.1

PrimateAI

Benign

0.23

PROVEAN

Benign

-0.76

REVEL

Benign

0.18

Sift

Benign

0.63

Sift4G

Benign

0.57

Polyphen

0.0

Vest4

0.022

MVP

0.40

MPC

0.064

ClinPred

0.00030

GERP RS

-7.8

Varity_R

0.023

gMVP

0.55

Mutation Taster

=97/3

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over