3-170999732-T-A

Position:

• chr3-170999732-T-A

Variant summary

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

The NM_000340.2(SLC2A2):​c.1069-566A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,022 control chromosomes in the GnomAD database, including 3,696 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 0.19 (3696 hom., cov: 32)
• Consequence: SLC2A2 NM_000340.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.133

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=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A2	NM_000340.2	c.1069-566A>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.1069-566A>T		intron_variant		1	NM_000340.2	ENSP00000323568	P1
SLC2A2	ENST00000497642.5	c.*536-566A>T		intron_variant, NMD_transcript_variant		1		ENSP00000418456
	ENST00000655926.1	n.291+4707T>A		intron_variant, non_coding_transcript_variant
SLC2A2	ENST00000469787.1	c.*536-566A>T		intron_variant, NMD_transcript_variant		2		ENSP00000417918

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29488 AN: 151904 Hom.: 3689 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.00928

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.194 AC: 29526 AN: 152022 Hom.: 3696 Cov.: 32 AF XY: 0.193 AC XY: 14359 AN XY: 74338

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.00931

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.183

Alfa AF: 0.136 Hom.: 906

Bravo AF: 0.202

Asia WGS AF: 0.105 AC: 369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.9
DANN	Benign	0.83

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: rs11920090; hg19: chr3-170717521;