Variant rs3931701 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong

The NM_006931.3(SLC2A3):c.1068+4G>A variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.054 ( 552 hom., cov: 28)

Exomes 𝑓: 0.0060 ( 722 hom. )

Failed GnomAD Quality Control

Consequence

SLC2A3
NM_006931.3 splice_donor_region, intron

Scores

Splicing: ADA: 0.00006109

Clinical Significance

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

Conservation

PhyloP100: 0.860

Variant links:

Genes affected

SLC2A3 (HGNC:11007): (solute carrier family 2 member 3) Enables dehydroascorbic acid transmembrane transporter activity; glucose binding activity; and glucose transmembrane transporter activity. Involved in glucose import across plasma membrane and transport across blood-brain barrier. Is integral component of plasma membrane. Biomarker of Alzheimer's disease; acanthosis nigricans; diabetes mellitus; and type 2 diabetes mellitus. [provided by Alliance of Genome Resources, Apr 2022]

SLC2A3 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 (BayesDel_noAF=-0.53).

BP6

Variant 12-7924406-C-T is Benign according to our data. Variant chr12-7924406-C-T is described in ClinVar as [Benign]. Clinvar id is 771454.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A3	NM_006931.3 linkuse as main transcript	c.1068+4G>A		splice_donor_region_variant, intron_variant		ENST00000075120.12	NP_008862.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
SLC2A3	ENST00000075120.12 linkuse as main transcript	c.1068+4G>A	splice_donor_region_variant, intron_variant	1	NM_006931.3	ENSP00000075120	P1
SLC2A3	ENST00000486749.5 linkuse as main transcript	n.1809+4G>A	splice_donor_region_variant, intron_variant, non_coding_transcript_variant	1
SLC2A3	ENST00000707174.1 linkuse as main transcript	c.1068+4G>A	splice_donor_region_variant, intron_variant			ENSP00000516774	P1
SLC2A3	ENST00000479059.3 linkuse as main transcript	n.579+4G>A	splice_donor_region_variant, intron_variant, non_coding_transcript_variant	2

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

8042

AN:

150084

Hom.:

552

Cov.:

FAILED QC

Gnomad AFR

AF:

0.142

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0542

Gnomad ASJ

AF:

0.00289

Gnomad EAS

AF:

0.207

Gnomad SAS

AF:

0.0569

Gnomad FIN

AF:

0.00179

Gnomad MID

AF:

0.0160

Gnomad NFE

AF:

0.00190

Gnomad OTH

AF:

0.0421

GnomAD3 exomes

AF:

0.0118

AC:

2906

AN:

245340

Hom.:

293

AF XY:

0.0105

AC XY:

1399

AN XY:

132946

show subpopulations

Gnomad AFR exome

AF:

0.0429

Gnomad AMR exome

AF:

0.0166

Gnomad ASJ exome

AF:

0.000298

Gnomad EAS exome

AF:

0.0811

Gnomad SAS exome

AF:

0.00920

Gnomad FIN exome

AF:

0.000324

Gnomad NFE exome

AF:

0.000335

Gnomad OTH exome

AF:

0.00912

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00602

AC:

8714

AN:

1446656

Hom.:

722

Cov.:

AF XY:

0.00626

AC XY:

4506

AN XY:

719504

show subpopulations

Gnomad4 AFR exome

AF:

0.0502

Gnomad4 AMR exome

AF:

0.0194

Gnomad4 ASJ exome

AF:

0.00158

Gnomad4 EAS exome

AF:

0.107

Gnomad4 SAS exome

AF:

0.0152

Gnomad4 FIN exome

AF:

0.000940

Gnomad4 NFE exome

AF:

0.000392

Gnomad4 OTH exome

AF:

0.0117

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0536

AC:

8049

AN:

150200

Hom.:

552

Cov.:

AF XY:

0.0537

AC XY:

3940

AN XY:

73384

show subpopulations

Gnomad4 AFR

AF:

0.142

Gnomad4 AMR

AF:

0.0541

Gnomad4 ASJ

AF:

0.00289

Gnomad4 EAS

AF:

0.207

Gnomad4 SAS

AF:

0.0559

Gnomad4 FIN

AF:

0.00179

Gnomad4 NFE

AF:

0.00190

Gnomad4 OTH

AF:

0.0422

Alfa

AF:

0.0246

Hom.:

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	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

9.5

DANN

Benign

0.64

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000061

dbscSNV1_RF

Benign

0.086

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