17-7283804-T-C

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_001042.3(SLC2A4):c.390T>C(p.Asn130=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.637 in 1,613,772 control chromosomes in the GnomAD database, including 329,905 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.70 (37714 hom., cov: 32)
  • Exomes 𝑓: 0.63 (292191 hom.)
• Consequence: SLC2A4 NM_001042.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.48

Genes affected

SLC2A4 (HGNC:11009): (solute carrier family 2 member 4) This gene is a member of the solute carrier family 2 (facilitated glucose transporter) family and encodes a protein that functions as an insulin-regulated facilitative glucose transporter. In the absence of insulin, this integral membrane protein is sequestered within the cells of muscle and adipose tissue. Within minutes of insulin stimulation, the protein moves to the cell surface and begins to transport glucose across the cell membrane. Mutations in this gene have been associated with noninsulin-dependent diabetes mellitus (NIDDM). [provided by RefSeq, Jul 2008]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BP7: Synonymous conserved (PhyloP=-3.48 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.846 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A4	NM_001042.3	c.390T>C	p.Asn130=	synonymous_variant	4/11	ENST00000317370.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A4	ENST00000317370.13	c.390T>C	p.Asn130=	synonymous_variant	4/11	1	NM_001042.3	P1
	ENST00000576271.1	n.45+223A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.696 AC: 105825 AN: 151940 Hom.: 37644 Cov.: 32

Gnomad AFR AF: 0.853

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.648

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.708

GnomAD3 exomes AF: 0.647 AC: 162129 AN: 250728 Hom.: 53201 AF XY: 0.646 AC XY: 87507 AN XY: 135552

Gnomad AFR exome AF: 0.858

Gnomad AMR exome AF: 0.595

Gnomad ASJ exome AF: 0.636

Gnomad EAS exome AF: 0.643

Gnomad SAS exome AF: 0.658

Gnomad FIN exome AF: 0.627

Gnomad NFE exome AF: 0.634

Gnomad OTH exome AF: 0.648

GnomAD4 exome AF: 0.630 AC: 921529 AN: 1461714 Hom.: 292191 Cov.: 59 AF XY: 0.631 AC XY: 459101 AN XY: 727158

Gnomad4 AFR exome AF: 0.863

Gnomad4 AMR exome AF: 0.605

Gnomad4 ASJ exome AF: 0.644

Gnomad4 EAS exome AF: 0.639

Gnomad4 SAS exome AF: 0.653

Gnomad4 FIN exome AF: 0.624

Gnomad4 NFE exome AF: 0.621

Gnomad4 OTH exome AF: 0.646

GnomAD4 genome AF: 0.697 AC: 105960 AN: 152058 Hom.: 37714 Cov.: 32 AF XY: 0.696 AC XY: 51772 AN XY: 74336

Gnomad4 AFR AF: 0.854

Gnomad4 AMR AF: 0.664

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.647

Gnomad4 SAS AF: 0.653

Gnomad4 FIN AF: 0.640

Gnomad4 NFE AF: 0.628

Gnomad4 OTH AF: 0.712

Alfa AF: 0.645 Hom.: 45668

Bravo AF: 0.704

Asia WGS AF: 0.687 AC: 2391 AN: 3478

EpiCase AF: 0.648

EpiControl AF: 0.649

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.027
Dann	Benign	0.45

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

Other links and lift over

dbSNP: rs5435; hg19: chr17-7187123; COSMIC: COSV50300952; COSMIC: COSV50300952;