12-7935631-T-C

Position:

• chr12-7935631-T-C

Variant summary

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

The ENST00000075120.12(SLC2A3):​c.15+389A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 151,876 control chromosomes in the GnomAD database, including 6,757 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 0.30 (6757 hom., cov: 32)
• Consequence: SLC2A3 ENST00000075120.12 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.981

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A3	NM_006931.3	c.15+389A>G		intron_variant		ENST00000075120.12	NP_008862.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A3	ENST00000075120.12	c.15+389A>G		intron_variant		1	NM_006931.3	ENSP00000075120	P1

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44839 AN: 151756 Hom.: 6754 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.296 AC: 44892 AN: 151876 Hom.: 6757 Cov.: 32 AF XY: 0.300 AC XY: 22293 AN XY: 74234

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.524

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.278

Gnomad4 OTH AF: 0.302

Alfa AF: 0.270 Hom.: 2683

Bravo AF: 0.292

Asia WGS AF: 0.440 AC: 1527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.2
DANN	Benign	0.52

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		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: rs2244822; hg19: chr12-8088227;