chr3-170997894-G-GT

Position:

• chr3-170997894-G-GT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_000340.2(SLC2A2):​c.*8dupA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0117 in 1,337,056 control chromosomes in the GnomAD database, including 5 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0041 (2 hom., cov: 32)
  • Exomes 𝑓: 0.013 (3 hom.)
• Consequence: SLC2A2 NM_000340.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.929

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]

ENSG00000286856 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00413 (611/148074) while in subpopulation SAS AF= 0.00667 (31/4646). AF 95% confidence interval is 0.00483. There are 2 homozygotes in gnomad4. There are 283 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A2	NM_000340.2	c.*8dupA		3_prime_UTR_variant	11/11	ENST00000314251.8	NP_000331.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A2	ENST00000314251	c.*8dupA		3_prime_UTR_variant	11/11	1	NM_000340.2	ENSP00000323568.3

Frequencies

GnomAD3 genomes AF: 0.00412 AC: 609 AN: 147984 Hom.: 2 Cov.: 32

Gnomad AFR AF: 0.00462

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00351

Gnomad ASJ AF: 0.00322

Gnomad EAS AF: 0.000588

Gnomad SAS AF: 0.00645

Gnomad FIN AF: 0.00101

Gnomad MID AF: 0.0162

Gnomad NFE AF: 0.00451

Gnomad OTH AF: 0.00544

GnomAD4 exome AF: 0.0126 AC: 15039 AN: 1188982 Hom.: 3 Cov.: 30 AF XY: 0.0122 AC XY: 7240 AN XY: 591782

Gnomad4 AFR exome AF: 0.0125

Gnomad4 AMR exome AF: 0.00884

Gnomad4 ASJ exome AF: 0.00743

Gnomad4 EAS exome AF: 0.00245

Gnomad4 SAS exome AF: 0.0132

Gnomad4 FIN exome AF: 0.00263

Gnomad4 NFE exome AF: 0.0138

Gnomad4 OTH exome AF: 0.0118

GnomAD4 genome AF: 0.00413 AC: 611 AN: 148074 Hom.: 2 Cov.: 32 AF XY: 0.00392 AC XY: 283 AN XY: 72176

Gnomad4 AFR AF: 0.00461

Gnomad4 AMR AF: 0.00351

Gnomad4 ASJ AF: 0.00322

Gnomad4 EAS AF: 0.000589

Gnomad4 SAS AF: 0.00667

Gnomad4 FIN AF: 0.00101

Gnomad4 NFE AF: 0.00451

Gnomad4 OTH AF: 0.00588

Bravo AF: 0.00404

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs573575421; hg19: chr3-170715683;