rs10513689

Positions:

• chr3-171009869-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The ENST00000314251.8(SLC2A2):​c.496+89C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 1,481,410 control chromosomes in the GnomAD database, including 18,467 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.21 (4521 hom., cov: 31)
  • Exomes 𝑓: 0.13 (13946 hom.)
• Consequence: SLC2A2 ENST00000314251.8 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.308

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BP6: Variant 3-171009869-G-A is Benign according to our data. Variant chr3-171009869-G-A is described in ClinVar as [Benign]. Clinvar id is 1264817.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A2	NM_000340.2	c.496+89C>T		intron_variant		ENST00000314251.8	NP_000331.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A2	ENST00000314251.8	c.496+89C>T		intron_variant		1	NM_000340.2	ENSP00000323568	P1
	ENST00000655926.1	n.291+14844G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31548 AN: 151148 Hom.: 4510 Cov.: 31

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.0758

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.00913

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.143

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.185

GnomAD4 exome AF: 0.128 AC: 170078 AN: 1330144 Hom.: 13946 AF XY: 0.128 AC XY: 84464 AN XY: 658284

Gnomad4 AFR exome AF: 0.419

Gnomad4 AMR exome AF: 0.123

Gnomad4 ASJ exome AF: 0.137

Gnomad4 EAS exome AF: 0.0150

Gnomad4 SAS exome AF: 0.148

Gnomad4 FIN exome AF: 0.132

Gnomad4 NFE exome AF: 0.121

Gnomad4 OTH exome AF: 0.139

GnomAD4 genome AF: 0.209 AC: 31588 AN: 151266 Hom.: 4521 Cov.: 31 AF XY: 0.207 AC XY: 15301 AN XY: 73862

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.172

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.00915

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.187

Alfa AF: 0.175 Hom.: 482

Bravo AF: 0.219

Asia WGS AF: 0.107 AC: 378 AN: 3474

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

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	GeneDx	Jun 23, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.63
DANN	Benign	0.28

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: rs10513689; hg19: chr3-170727658;