Variant 12-7819478-T-C 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_001286234.2(SLC2A14):c.1071+4A>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0047 ( 18 hom., cov: 27)

Exomes 𝑓: 0.0024 ( 127 hom. )

Failed GnomAD Quality Control

Consequence

SLC2A14
NM_001286234.2 splice_region, intron

Scores

Splicing: ADA: 0.2609

Clinical Significance

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

Conservation

PhyloP100: 1.73

Variant links:

Genes affected

SLC2A14 (HGNC:18301): (solute carrier family 2 member 14) Members of the glucose transporter (GLUT) family, including SLC2A14, are highly conserved integral membrane proteins that transport hexoses such as glucose and fructose into all mammalian cells. GLUTs show tissue and cell-type specific expression (Wu and Freeze, 2002 [PubMed 12504846]).[supplied by OMIM, Mar 2008]

SLC2A14 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=-0.56).

BP6

Variant 12-7819478-T-C is Benign according to our data. Variant chr12-7819478-T-C is described in ClinVar as [Benign]. Clinvar id is 789446.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
SLC2A14	NM_001286234.2 linkuse as main transcript	c.1071+4A>G		splice_region_variant, intron_variant		ENST00000431042.7	NP_001273163.1	Q8TDB8-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A14	ENST00000431042.7 linkuse as main transcript	c.1071+4A>G		splice_region_variant, intron_variant		1	NM_001286234.2	ENSP00000407287.2		Q8TDB8-2

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

718

AN:

151890

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00244

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000984

Gnomad ASJ

AF:

0.00433

Gnomad EAS

AF:

0.0563

Gnomad SAS

AF:

0.0462

Gnomad FIN

AF:

0.000283

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00103

Gnomad OTH

AF:

0.00288

GnomAD3 exomes

AF:

0.00220

AC:

550

AN:

249882

Hom.:

AF XY:

0.00226

AC XY:

305

AN XY:

134978

show subpopulations

Gnomad AFR exome

AF:

0.000862

Gnomad AMR exome

AF:

0.000203

Gnomad ASJ exome

AF:

0.000398

Gnomad EAS exome

AF:

0.0165

Gnomad SAS exome

AF:

0.00663

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000185

Gnomad OTH exome

AF:

0.00164

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00236

AC:

3432

AN:

1456514

Hom.:

127

Cov.:

AF XY:

0.00288

AC XY:

2089

AN XY:

724164

show subpopulations

Gnomad4 AFR exome

AF:

0.000809

Gnomad4 AMR exome

AF:

0.000381

Gnomad4 ASJ exome

AF:

0.00231

Gnomad4 EAS exome

AF:

0.0369

Gnomad4 SAS exome

AF:

0.0176

Gnomad4 FIN exome

AF:

0.000150

Gnomad4 NFE exome

AF:

0.000237

Gnomad4 OTH exome

AF:

0.00233

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00474

AC:

721

AN:

152008

Hom.:

Cov.:

AF XY:

0.00580

AC XY:

431

AN XY:

74278

show subpopulations

Gnomad4 AFR

AF:

0.00246

Gnomad4 AMR

AF:

0.000983

Gnomad4 ASJ

AF:

0.00433

Gnomad4 EAS

AF:

0.0558

Gnomad4 SAS

AF:

0.0471

Gnomad4 FIN

AF:

0.000283

Gnomad4 NFE

AF:

0.00103

Gnomad4 OTH

AF:

0.00332

Alfa

AF:

0.00170

Hom.:

EpiCase

AF:

0.00142

EpiControl

AF:

0.000237

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	Jan 05, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

DANN

Benign

0.68

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.26

dbscSNV1_RF

Benign

0.36

SpliceAI score (max)

0.020

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