chr12-7818125-T-G

Position:

• chr12-7818125-T-G

Variant summary

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

The NM_001286234.2(SLC2A14):​c.1072-91A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 1,147,904 control chromosomes in the GnomAD database, including 184,365 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 0.51 (20545 hom., cov: 33)
  • Exomes 𝑓: 0.57 (163820 hom.)
• Consequence: SLC2A14 NM_001286234.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.485

Genes affected

SLC2A14 (HGNC:18301): (solute carrier family 2 member 14) Members of the glucose transporter (GLUT) family, including SLC2A14, are highly conserved integral membrane proteins that transport hexoses such as glucose and fructose into all mammalian cells. GLUTs show tissue and cell-type specific expression (Wu and Freeze, 2002 [PubMed 12504846]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A14	NM_001286234.2	c.1072-91A>C		intron_variant		ENST00000431042.7	NP_001273163.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A14	ENST00000431042.7	c.1072-91A>C		intron_variant		1	NM_001286234.2	ENSP00000407287.2

Frequencies

GnomAD3 genomes AF: 0.513 AC: 78041 AN: 151982 Hom.: 20540 Cov.: 33

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.530

GnomAD4 exome AF: 0.569 AC: 566421 AN: 995804 Hom.: 163820 AF XY: 0.564 AC XY: 281510 AN XY: 499322

Gnomad4 AFR exome AF: 0.399

Gnomad4 AMR exome AF: 0.418

Gnomad4 ASJ exome AF: 0.542

Gnomad4 EAS exome AF: 0.401

Gnomad4 SAS exome AF: 0.437

Gnomad4 FIN exome AF: 0.599

Gnomad4 NFE exome AF: 0.597

Gnomad4 OTH exome AF: 0.556

GnomAD4 genome AF: 0.513 AC: 78072 AN: 152100 Hom.: 20545 Cov.: 33 AF XY: 0.508 AC XY: 37784 AN XY: 74366

Gnomad4 AFR AF: 0.417

Gnomad4 AMR AF: 0.448

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.427

Gnomad4 FIN AF: 0.587

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.534

Alfa AF: 0.529 Hom.: 8593

Bravo AF: 0.500

Asia WGS AF: 0.497 AC: 1725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.64
DANN	Benign	0.39

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: rs10845990; hg19: chr12-7970721;