rs10513686

Variant names:

• chr3-171007753-G-A
• rs10513686
• NM_000340.2:c.497-490C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-171007753-G-A
• chr3-171007753-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000340.2(SLC2A2):​c.497-490C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 151,862 control chromosomes in the GnomAD database, including 4,447 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 0.21 (4447 hom., cov: 32)
• Consequence: SLC2A2 NM_000340.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.940
• Publications: 20 publications found

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]

SLC2A2 Gene-Disease associations (from GenCC):

• glycogen storage disease due to GLUT2 deficiency

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae), Orphanet, PanelApp Australia, G2P
• neonatal diabetes mellitus

  Inheritance: AR Classification: STRONG Submitted by: Genomics England PanelApp
• permanent neonatal diabetes mellitus

  Inheritance: AR Classification: STRONG Submitted by: Genomics England PanelApp
• transient neonatal diabetes mellitus

  Inheritance: AR Classification: STRONG Submitted by: Genomics England PanelApp

ENSG00000286856 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000340.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A2	NM_000340.2	MANE Select	c.497-490C>T		intron	N/A	NP_000331.1
	SLC2A2	NM_001278658.2		c.140-490C>T		intron	N/A	NP_001265587.1
	SLC2A2	NM_001278659.2		c.-23-490C>T		intron	N/A	NP_001265588.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC2A2	ENST00000314251.8	TSL:1 MANE Select	c.497-490C>T		intron	N/A	ENSP00000323568.3
	SLC2A2	ENST00000497642.5	TSL:1	n.372-490C>T		intron	N/A	ENSP00000418456.1
	SLC2A2	ENST00000461867.1	TSL:3	c.-23-490C>T		intron	N/A	ENSP00000418888.1

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31470 AN: 151744 Hom.: 4437 Cov.: 32

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.00949

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.207 AC: 31509 AN: 151862 Hom.: 4447 Cov.: 32 AF XY: 0.206 AC XY: 15295 AN XY: 74258

African (AFR) AF: 0.406 AC: 16794 AN: 41390

American (AMR) AF: 0.171 AC: 2607 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 495 AN: 3462

East Asian (EAS) AF: 0.00951 AC: 49 AN: 5150

South Asian (SAS) AF: 0.150 AC: 722 AN: 4818

European-Finnish (FIN) AF: 0.129 AC: 1365 AN: 10576

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8968 AN: 67914

Other (OTH) AF: 0.189 AC: 399 AN: 2114

Alfa AF: 0.152 Hom.: 6687

Bravo AF: 0.217

Asia WGS AF: 0.109 AC: 383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.9
DANN	Benign	0.57
PhyloP100		0.94
Mutation Taster		=100/0	polymorphism (auto)

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: rs10513686; hg19: chr3-170725542;