Variant chr3-171007094-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000340.2(SLC2A2):c.612+54A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 954,848 control chromosomes in the GnomAD database, including 53,782 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.41 ( 15482 hom., cov: 31)

Exomes 𝑓: 0.30 ( 38300 hom. )

Consequence

SLC2A2
NM_000340.2 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -2.90

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:

SLC2A2 (HGNC:):

SLC2A2 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 (BayesDel_noAF=-1.0).

BP6

Variant 3-171007094-T-C is Benign according to our data. Variant chr3-171007094-T-C is described in ClinVar as [Benign]. Clinvar id is 1292088.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A2	NM_000340.2 linkuse as main transcript	c.612+54A>G		intron_variant		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.612+54A>G		intron_variant		1	NM_000340.2	ENSP00000323568.3		P11168-1

Frequencies

GnomAD3 genomes

AF:

0.409

AC:

62026

AN:

151588

Hom.:

15451

Cov.:

show subpopulations

Gnomad AFR

AF:

0.712

Gnomad AMI

AF:

0.244

Gnomad AMR

AF:

0.352

Gnomad ASJ

AF:

0.330

Gnomad EAS

AF:

0.228

Gnomad SAS

AF:

0.274

Gnomad FIN

AF:

0.245

Gnomad MID

AF:

0.323

Gnomad NFE

AF:

0.294

Gnomad OTH

AF:

0.390

GnomAD4 exome

AF:

0.299

AC:

240233

AN:

803142

Hom.:

38300

AF XY:

0.296

AC XY:

125535

AN XY:

424134

show subpopulations

Gnomad4 AFR exome

AF:

0.720

Gnomad4 AMR exome

AF:

0.295

Gnomad4 ASJ exome

AF:

0.315

Gnomad4 EAS exome

AF:

0.220

Gnomad4 SAS exome

AF:

0.278

Gnomad4 FIN exome

AF:

0.262

Gnomad4 NFE exome

AF:

0.292

Gnomad4 OTH exome

AF:

0.332

GnomAD4 genome

AF:

0.409

AC:

62105

AN:

151706

Hom.:

15482

Cov.:

AF XY:

0.404

AC XY:

29963

AN XY:

74120

show subpopulations

Gnomad4 AFR

AF:

0.712

Gnomad4 AMR

AF:

0.351

Gnomad4 ASJ

AF:

0.330

Gnomad4 EAS

AF:

0.227

Gnomad4 SAS

AF:

0.274

Gnomad4 FIN

AF:

0.245

Gnomad4 NFE

AF:

0.294

Gnomad4 OTH

AF:

0.388

Alfa

AF:

0.328

Hom.:

4742

Bravo

AF:

0.431

Asia WGS

AF:

0.299

AC:

1043

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 23, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.47

DANN

Benign

0.19

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