rs7637863

Positions:

chr3-171014637-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_000340.2(SLC2A2):c.203C>T(p.Pro68Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00476 in 1,613,978 control chromosomes in the GnomAD database, including 21 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 Likely benign (★★).

Frequency

Genomes: 𝑓 0.0033 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0049 ( 19 hom. )

Consequence

SLC2A2
NM_000340.2 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: 1.15

Variant links:

Genes affected

SLC2A2 (HGNC:11006): (solute carrier family 2 member 2) This gene encodes an integral plasma membrane glycoprotein of the liver, islet beta cells, intestine, and kidney epithelium. The encoded protein mediates facilitated bidirectional glucose transport. Because of its low affinity for glucose, it has been suggested as a glucose sensor. Mutations in this gene are associated with susceptibility to diseases, including Fanconi-Bickel syndrome and noninsulin-dependent diabetes mellitus (NIDDM). Alternative splicing results in multiple transcript variants of this gene. [provided by RefSeq, Jul 2013]

SLC2A2 links:

ENSG00000286856 (HGNC:):

ENSG00000286856 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0051350296).

BP6

Variant 3-171014637-G-A is Benign according to our data. Variant chr3-171014637-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 516406.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-171014637-G-A is described in Lovd as [Likely_benign]. Variant chr3-171014637-G-A is described in Lovd as [Benign].

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00334 (508/152164) while in subpopulation NFE AF= 0.00535 (364/68012). AF 95% confidence interval is 0.0049. There are 2 homozygotes in gnomad4. There are 225 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A2	NM_000340.2 linkuse as main transcript	c.203C>T	p.Pro68Leu	missense_variant	3/11	ENST00000314251.8	NP_000331.1	P11168-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A2	ENST00000314251.8 linkuse as main transcript	c.203C>T	p.Pro68Leu	missense_variant	3/11	1	NM_000340.2	ENSP00000323568.3		P11168-1

Frequencies

GnomAD3 genomes

AF:

0.00333

AC:

506

AN:

152046

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00121

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00288

Gnomad ASJ

AF:

0.000576

Gnomad EAS

AF:

0.00116

Gnomad SAS

AF:

0.000415

Gnomad FIN

AF:

0.00255

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00535

Gnomad OTH

AF:

0.00526

GnomAD3 exomes

AF:

0.00382

AC:

961

AN:

251468

Hom.:

AF XY:

0.00381

AC XY:

518

AN XY:

135904

show subpopulations

Gnomad AFR exome

AF:

0.00117

Gnomad AMR exome

AF:

0.00295

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000979

Gnomad SAS exome

AF:

0.000980

Gnomad FIN exome

AF:

0.00337

Gnomad NFE exome

AF:

0.00612

Gnomad OTH exome

AF:

0.00375

GnomAD4 exome

AF:

0.00490

AC:

7169

AN:

1461814

Hom.:

Cov.:

AF XY:

0.00475

AC XY:

3452

AN XY:

727216

show subpopulations

Gnomad4 AFR exome

AF:

0.000777

Gnomad4 AMR exome

AF:

0.00284

Gnomad4 ASJ exome

AF:

0.000153

Gnomad4 EAS exome

AF:

0.00154

Gnomad4 SAS exome

AF:

0.000985

Gnomad4 FIN exome

AF:

0.00344

Gnomad4 NFE exome

AF:

0.00581

Gnomad4 OTH exome

AF:

0.00354

GnomAD4 genome

AF:

0.00334

AC:

508

AN:

152164

Hom.:

Cov.:

AF XY:

0.00303

AC XY:

225

AN XY:

74378

show subpopulations

Gnomad4 AFR

AF:

0.00120

Gnomad4 AMR

AF:

0.00288

Gnomad4 ASJ

AF:

0.000576

Gnomad4 EAS

AF:

0.00116

Gnomad4 SAS

AF:

0.000831

Gnomad4 FIN

AF:

0.00255

Gnomad4 NFE

AF:

0.00535

Gnomad4 OTH

AF:

0.00520

Alfa

AF:

0.00440

Hom.:

Bravo

AF:

0.00346

TwinsUK

AF:

0.00620

AC:

ALSPAC

AF:

0.00675

AC:

ESP6500AA

AF:

0.000908

AC:

ESP6500EA

AF:

0.00488

AC:

ExAC

AF:

0.00423

AC:

514

Asia WGS

AF:

0.00231

AC:

AN:

3478

EpiCase

AF:

0.00425

EpiControl

AF:

0.00474

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:8

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Likely benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Aug 01, 2024	ENSG00000286856: BS2; SLC2A2: BP4, BS2 -

not specified

Benign:2

Benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 07, 2017	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Fanconi-Bickel syndrome

Benign:2

Likely benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 13, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 29, 2024	- -

Monogenic diabetes

Benign:1

Benign, criteria provided, single submitter

research

Personalized Diabetes Medicine Program, University of Maryland School of Medicine

Jan 18, 2019

ACMG criteria: BS1 (MAF 0.6% in EurNF in gnomAD), BS2 (4 homozygotes in ExAC, 50 cases and 41 controls in type2diabetesgenetics.org), BS3 (PMID 23986439 shows our variant has similar expression, localization and size compared to WT protein): benign (REVEL 0.289 + PP3/3 predictors + BP4/8 predictors: conflicting evidence, not using) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.087

BayesDel_addAF

Benign

-0.44

BayesDel_noAF

Benign

-0.40

CADD

Benign

DANN

Benign

0.72

DEOGEN2

Benign

0.36

Eigen

Benign

-1.0

Eigen_PC

Benign

-0.91

FATHMM_MKL

Benign

0.057

LIST_S2

Benign

0.59

M_CAP

Benign

0.039

MetaRNN

Benign

0.0051

MetaSVM

Benign

-0.86

MutationAssessor

Benign

0.81

PrimateAI

Benign

0.28

PROVEAN

Benign

-0.88

REVEL

Benign

0.29

Sift

Benign

0.039

Sift4G

Benign

0.070

Polyphen

0.0010

Vest4

0.11

MVP

0.69

MPC

0.16

ClinPred

0.0037

GERP RS

3.7

Varity_R

0.047

gMVP

0.47

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