rs7976243

Positions:

• chr12-7933487-C-A
• chr12-7933487-C-T

Variant summary

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

The NM_006931.3(SLC2A3):​c.108+323G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 456,834 control chromosomes in the GnomAD database, including 22,329 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 0.29 (6753 hom., cov: 32)
  • Exomes 𝑓: 0.31 (15576 hom.)
• Consequence: SLC2A3 NM_006931.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730

Genes affected

SLC2A3 (HGNC:11007): (solute carrier family 2 member 3) Enables dehydroascorbic acid transmembrane transporter activity; glucose binding activity; and glucose transmembrane transporter activity. Involved in glucose import across plasma membrane and transport across blood-brain barrier. Is integral component of plasma membrane. Biomarker of Alzheimer's disease; acanthosis nigricans; diabetes mellitus; and type 2 diabetes mellitus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A3	NM_006931.3	c.108+323G>T		intron_variant		ENST00000075120.12	NP_008862.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A3	ENST00000075120.12	c.108+323G>T		intron_variant		1	NM_006931.3	ENSP00000075120.7

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44744 AN: 151764 Hom.: 6753 Cov.: 32

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.303

GnomAD4 exome AF: 0.312 AC: 95214 AN: 304950 Hom.: 15576 Cov.: 3 AF XY: 0.318 AC XY: 51012 AN XY: 160324

Gnomad4 AFR exome AF: 0.283

Gnomad4 AMR exome AF: 0.282

Gnomad4 ASJ exome AF: 0.341

Gnomad4 EAS exome AF: 0.520

Gnomad4 SAS exome AF: 0.405

Gnomad4 FIN exome AF: 0.298

Gnomad4 NFE exome AF: 0.278

Gnomad4 OTH exome AF: 0.305

GnomAD4 genome AF: 0.295 AC: 44789 AN: 151884 Hom.: 6753 Cov.: 32 AF XY: 0.299 AC XY: 22211 AN XY: 74208

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.527

Gnomad4 SAS AF: 0.409

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.304

Alfa AF: 0.276 Hom.: 11383

Bravo AF: 0.292

Asia WGS AF: 0.439 AC: 1527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.73
DANN	Benign	0.53

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: rs7976243; hg19: chr12-8086083;