Variant 3-170996681-A-T 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 ENST00000314251.8(SLC2A2):c.*1222T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 397,614 control chromosomes in the GnomAD database, including 7,193 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.21 ( 4447 hom., cov: 32)

Exomes 𝑓: 0.13 ( 2746 hom. )

Consequence

SLC2A2
ENST00000314251.8 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.457

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:

(HGNC:):

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=-0.91).

BP6

Variant 3-170996681-A-T is Benign according to our data. Variant chr3-170996681-A-T is described in ClinVar as [Benign]. Clinvar id is 344138.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.399 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.*1222T>A		3_prime_UTR_variant	11/11	ENST00000314251.8	NP_000331.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A2	ENST00000314251.8 linkuse as main transcript	c.*1222T>A		3_prime_UTR_variant	11/11	1	NM_000340.2	ENSP00000323568	P1	P11168-1
	ENST00000655926.1 linkuse as main transcript	n.291+1656A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.207

AC:

31410

AN:

151976

Hom.:

4429

Cov.:

show subpopulations

Gnomad AFR

AF:

0.404

Gnomad AMI

AF:

0.0746

Gnomad AMR

AF:

0.171

Gnomad ASJ

AF:

0.143

Gnomad EAS

AF:

0.00943

Gnomad SAS

AF:

0.150

Gnomad FIN

AF:

0.129

Gnomad MID

AF:

0.146

Gnomad NFE

AF:

0.132

Gnomad OTH

AF:

0.192

GnomAD4 exome

AF:

0.134

AC:

32915

AN:

245520

Hom.:

2746

Cov.:

AF XY:

0.133

AC XY:

16527

AN XY:

124406

show subpopulations

Gnomad4 AFR exome

AF:

0.407

Gnomad4 AMR exome

AF:

0.149

Gnomad4 ASJ exome

AF:

0.140

Gnomad4 EAS exome

AF:

0.0205

Gnomad4 SAS exome

AF:

0.149

Gnomad4 FIN exome

AF:

0.135

Gnomad4 NFE exome

AF:

0.134

Gnomad4 OTH exome

AF:

0.156

GnomAD4 genome

AF:

0.207

AC:

31470

AN:

152094

Hom.:

4447

Cov.:

AF XY:

0.206

AC XY:

15298

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.404

Gnomad4 AMR

AF:

0.171

Gnomad4 ASJ

AF:

0.143

Gnomad4 EAS

AF:

0.00945

Gnomad4 SAS

AF:

0.150

Gnomad4 FIN

AF:

0.129

Gnomad4 NFE

AF:

0.132

Gnomad4 OTH

AF:

0.193

Alfa

AF:

0.174

Hom.:

387

Bravo

AF:

0.216

Asia WGS

AF:

0.109

AC:

383

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Fanconi-Bickel syndrome

Benign:1

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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

not provided

Benign:1

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

-0.91

CADD

Benign

2.6

DANN

Benign

0.47

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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