Genetic Variant NM_014580.5:c.394C>T (chr9-127398079-C-T) – ACMG Classification: Benign (-9 pts)

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_014580.5(SLC2A8):c.394C>T(p.Leu132Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00582 in 1,587,392 control chromosomes in the GnomAD database, including 34 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0039 ( 1 hom., cov: 33)

Exomes 𝑓: 0.0060 ( 33 hom. )

Consequence

SLC2A8
NM_014580.5 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.713

Variant links:

Genes affected

SLC2A8 (HGNC:13812): (solute carrier family 2 member 8) This gene belongs to the solute carrier 2A family, which includes intracellular glucose transporters. Based on sequence comparison, the glucose transporters are grouped into three classes and this gene is a member of class II. The encoded protein, like other members of the family, contains several conserved residues and motifs and 12 transmembrane domains with both amino and carboxyl ends being on the cytosolic side of the membrane. Alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Nov 2012]

SLC2A8 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.29).

BP6

Variant 9-127398079-C-T is Benign according to our data. Variant chr9-127398079-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2659500.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.713 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 33 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A8	NM_014580.5 link	c.394C>T	p.Leu132Leu	synonymous_variant	Exon 3 of 10	ENST00000373371.8	NP_055395.2	Q9NY64Q8WZ05A0A024R871

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A8	ENST00000373371.8 link	c.394C>T	p.Leu132Leu	synonymous_variant	Exon 3 of 10	1	NM_014580.5	ENSP00000362469.3		Q9NY64

Frequencies

GnomAD3 genomes

AF:

0.00388

AC:

591

AN:

152216

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00133

Gnomad AMI

AF:

0.00440

Gnomad AMR

AF:

0.00366

Gnomad ASJ

AF:

0.000576

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00103

Gnomad FIN

AF:

0.000188

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00676

Gnomad OTH

AF:

0.00334

GnomAD3 exomes

AF:

0.00369

AC:

779

AN:

211140

Hom.:

AF XY:

0.00368

AC XY:

430

AN XY:

116796

show subpopulations

Gnomad AFR exome

AF:

0.00135

Gnomad AMR exome

AF:

0.00315

Gnomad ASJ exome

AF:

0.000441

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000797

Gnomad FIN exome

AF:

0.000164

Gnomad NFE exome

AF:

0.00635

Gnomad OTH exome

AF:

0.00466

GnomAD4 exome

AF:

0.00602

AC:

8644

AN:

1435058

Hom.:

Cov.:

AF XY:

0.00572

AC XY:

4075

AN XY:

712820

show subpopulations

Gnomad4 AFR exome

AF:

0.00118

Gnomad4 AMR exome

AF:

0.00329

Gnomad4 ASJ exome

AF:

0.000626

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000753

Gnomad4 FIN exome

AF:

0.000240

Gnomad4 NFE exome

AF:

0.00731

Gnomad4 OTH exome

AF:

0.00508

GnomAD4 genome

AF:

0.00388

AC:

591

AN:

152334

Hom.:

Cov.:

AF XY:

0.00324

AC XY:

241

AN XY:

74494

show subpopulations

Gnomad4 AFR

AF:

0.00132

Gnomad4 AMR

AF:

0.00366

Gnomad4 ASJ

AF:

0.000576

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00103

Gnomad4 FIN

AF:

0.000188

Gnomad4 NFE

AF:

0.00676

Gnomad4 OTH

AF:

0.00331

Alfa

AF:

0.00474

Hom.:

Bravo

AF:

0.00375

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Jul 01, 2022

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

SLC2A8: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.29

CADD

Benign

DANN

Benign

0.95

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