rs8192675

chr3-171007094-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_000340.2(SLC2A2):c.612+54A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 954,848 control chromosomes in the GnomAD database, including 53,782 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.41 (15482 hom., cov: 31)
  • Exomes 𝑓: 0.30 (38300 hom.)
• Consequence: SLC2A2 NM_000340.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.90

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BP6: Variant 3-171007094-T-C is Benign according to our data. Variant chr3-171007094-T-C is described in ClinVar as [Benign]. Clinvar id is 1292088.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A2	NM_000340.2	c.612+54A>G		intron_variant		ENST00000314251.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A2	ENST00000314251.8	c.612+54A>G		intron_variant		1	NM_000340.2	P1
	ENST00000655926.1	n.291+12069T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62026 AN: 151588 Hom.: 15451 Cov.: 31

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.390

GnomAD4 exome AF: 0.299 AC: 240233 AN: 803142 Hom.: 38300 AF XY: 0.296 AC XY: 125535 AN XY: 424134

Gnomad4 AFR exome AF: 0.720

Gnomad4 AMR exome AF: 0.295

Gnomad4 ASJ exome AF: 0.315

Gnomad4 EAS exome AF: 0.220

Gnomad4 SAS exome AF: 0.278

Gnomad4 FIN exome AF: 0.262

Gnomad4 NFE exome AF: 0.292

Gnomad4 OTH exome AF: 0.332

GnomAD4 genome AF: 0.409 AC: 62105 AN: 151706 Hom.: 15482 Cov.: 31 AF XY: 0.404 AC XY: 29963 AN XY: 74120

Gnomad4 AFR AF: 0.712

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.227

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.388

Alfa AF: 0.328 Hom.: 4742

Bravo AF: 0.431

Asia WGS AF: 0.299 AC: 1043 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 23, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.47
Dann	Benign	0.19

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: rs8192675; hg19: chr3-170724883; COSMIC: COSV58586138;