rs113005748

Variant names:

• chr9-127398079-C-T
• rs113005748
• NM_014580.5:c.394C>T

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_Moderate BP6_Moderate BP7 BS2

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
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.713
• Publications: 1 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014580.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A8	NM_014580.5	MANE Select	c.394C>T	p.Leu132Leu	synonymous	Exon 3 of 10	NP_055395.2
	SLC2A8	NM_001271711.2		c.394C>T	p.Leu132Leu	synonymous	Exon 3 of 9	NP_001258640.1	Q5VVV9
	SLC2A8	NM_001271712.2		c.-64+793C>T		intron	N/A	NP_001258641.1	A0A087WT42

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A8	ENST00000373371.8	TSL:1 MANE Select	c.394C>T	p.Leu132Leu	synonymous	Exon 3 of 10	ENSP00000362469.3	Q9NY64
	SLC2A8	ENST00000373360.7	TSL:1	c.394C>T	p.Leu132Leu	synonymous	Exon 3 of 9	ENSP00000362458.3	Q5VVV9
	SLC2A8	ENST00000954537.1		c.394C>T	p.Leu132Leu	synonymous	Exon 3 of 10	ENSP00000624596.1

Frequencies

GnomAD3 genomes AF: 0.00388 AC: 591 AN: 152216 Hom.: 1 Cov.: 33

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

GnomAD2 exomes AF: 0.00369 AC: 779 AN: 211140 AF XY: 0.00368

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 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.: 33 Cov.: 31 AF XY: 0.00572 AC XY: 4075 AN XY: 712820

African (AFR) AF: 0.00118 AC: 39 AN: 33064

American (AMR) AF: 0.00329 AC: 142 AN: 43110

Ashkenazi Jewish (ASJ) AF: 0.000626 AC: 16 AN: 25554

East Asian (EAS) AF: 0.00 AC: 0 AN: 38814

South Asian (SAS) AF: 0.000753 AC: 63 AN: 83692

European-Finnish (FIN) AF: 0.000240 AC: 10 AN: 41600

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5594

European-Non Finnish (NFE) AF: 0.00731 AC: 8072 AN: 1104158

Other (OTH) AF: 0.00508 AC: 302 AN: 59472

GnomAD4 genome AF: 0.00388 AC: 591 AN: 152334 Hom.: 1 Cov.: 33 AF XY: 0.00324 AC XY: 241 AN XY: 74494

African (AFR) AF: 0.00132 AC: 55 AN: 41576

American (AMR) AF: 0.00366 AC: 56 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.000576 AC: 2 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5176

South Asian (SAS) AF: 0.00103 AC: 5 AN: 4834

European-Finnish (FIN) AF: 0.000188 AC: 2 AN: 10626

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00676 AC: 460 AN: 68020

Other (OTH) AF: 0.00331 AC: 7 AN: 2116

Alfa AF: 0.00474 Hom.: 1

Bravo AF: 0.00375

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	11
DANN	Benign	0.95
PhyloP100		-0.71
PromoterAI		-0.047	Neutral
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs113005748; hg19: chr9-130160358;