rs10513688

chr3-171009429-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000340.2(SLC2A2):c.496+529C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 151,958 control chromosomes in the GnomAD database, including 2,404 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 0.15 (2404 hom., cov: 32)
• Consequence: SLC2A2 NM_000340.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.269

Genes affected

SLC2A2 (HGNC:11006): (solute carrier family 2 member 2) This gene encodes an integral plasma membrane glycoprotein of the liver, islet beta cells, intestine, and kidney epithelium. The encoded protein mediates facilitated bidirectional glucose transport. Because of its low affinity for glucose, it has been suggested as a glucose sensor. Mutations in this gene are associated with susceptibility to diseases, including Fanconi-Bickel syndrome and noninsulin-dependent diabetes mellitus (NIDDM). Alternative splicing results in multiple transcript variants of this gene. [provided by RefSeq, Jul 2013]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A2	NM_000340.2	c.496+529C>T		intron_variant		ENST00000314251.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A2	ENST00000314251.8	c.496+529C>T		intron_variant		1	NM_000340.2	P1
	ENST00000655926.1	n.291+14404G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23127 AN: 151840 Hom.: 2399 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.00890

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.0929

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.144

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.152 AC: 23148 AN: 151958 Hom.: 2404 Cov.: 32 AF XY: 0.151 AC XY: 11192 AN XY: 74286

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.00892

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.0929

Gnomad4 NFE AF: 0.100

Gnomad4 OTH AF: 0.142

Alfa AF: 0.119 Hom.: 249

Bravo AF: 0.159

Asia WGS AF: 0.0750 AC: 266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	7.0
Dann	Benign	0.72

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: rs10513688; hg19: chr3-170727218;