rs3931701

Positions:

• chr12-7924406-C-T

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The NM_006931.3(SLC2A3):​c.1068+4G>A variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.054 (552 hom., cov: 28)
  • Exomes 𝑓: 0.0060 (722 hom.)
  • Failed GnomAD Quality Control
• Consequence: SLC2A3 NM_006931.3 splice_donor_region, intron
• Scores: Splicing: ADA: 0.00006109
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.860

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 Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BP6: Variant 12-7924406-C-T is Benign according to our data. Variant chr12-7924406-C-T is described in ClinVar as [Benign]. Clinvar id is 771454.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A3	NM_006931.3	c.1068+4G>A		splice_donor_region_variant, intron_variant		ENST00000075120.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A3	ENST00000075120.12	c.1068+4G>A		splice_donor_region_variant, intron_variant		1	NM_006931.3	P1
SLC2A3	ENST00000486749.5	n.1809+4G>A		splice_donor_region_variant, intron_variant, non_coding_transcript_variant		1
SLC2A3	ENST00000707174.1	c.1068+4G>A		splice_donor_region_variant, intron_variant				P1
SLC2A3	ENST00000479059.3	n.579+4G>A		splice_donor_region_variant, intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.00 AC: 8042 AN: 150084 Hom.: 552 Cov.: 28 FAILED QC

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0542

Gnomad ASJ AF: 0.00289

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.0569

Gnomad FIN AF: 0.00179

Gnomad MID AF: 0.0160

Gnomad NFE AF: 0.00190

Gnomad OTH AF: 0.0421

GnomAD3 exomes AF: 0.0118 AC: 2906 AN: 245340 Hom.: 293 AF XY: 0.0105 AC XY: 1399 AN XY: 132946

Gnomad AFR exome AF: 0.0429

Gnomad AMR exome AF: 0.0166

Gnomad ASJ exome AF: 0.000298

Gnomad EAS exome AF: 0.0811

Gnomad SAS exome AF: 0.00920

Gnomad FIN exome AF: 0.000324

Gnomad NFE exome AF: 0.000335

Gnomad OTH exome AF: 0.00912

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00602 AC: 8714 AN: 1446656 Hom.: 722 Cov.: 31 AF XY: 0.00626 AC XY: 4506 AN XY: 719504

Gnomad4 AFR exome AF: 0.0502

Gnomad4 AMR exome AF: 0.0194

Gnomad4 ASJ exome AF: 0.00158

Gnomad4 EAS exome AF: 0.107

Gnomad4 SAS exome AF: 0.0152

Gnomad4 FIN exome AF: 0.000940

Gnomad4 NFE exome AF: 0.000392

Gnomad4 OTH exome AF: 0.0117

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0536 AC: 8049 AN: 150200 Hom.: 552 Cov.: 28 AF XY: 0.0537 AC XY: 3940 AN XY: 73384

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.0541

Gnomad4 ASJ AF: 0.00289

Gnomad4 EAS AF: 0.207

Gnomad4 SAS AF: 0.0559

Gnomad4 FIN AF: 0.00179

Gnomad4 NFE AF: 0.00190

Gnomad4 OTH AF: 0.0422

Alfa AF: 0.0246 Hom.: 46

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

Invitae

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	9.5
DANN	Benign	0.64

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000061
dbscSNV1_RF	Benign	0.086
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: rs3931701; hg19: chr12-8077002; COSMIC: COSV50008746; COSMIC: COSV50008746;