12-7847740-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.19-14926A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 151,802 control chromosomes in the GnomAD database, including 18,708 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 0.50 (18708 hom., cov: 32)
• Consequence: SLC2A14 NM_001286234.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.554

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A14	NM_001286234.2	c.19-14926A>C		intron_variant		ENST00000431042.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A14	ENST00000431042.7	c.19-14926A>C		intron_variant		1	NM_001286234.2	P1

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75341 AN: 151684 Hom.: 18691 Cov.: 32

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.497 AC: 75389 AN: 151802 Hom.: 18708 Cov.: 32 AF XY: 0.493 AC XY: 36542 AN XY: 74178

Gnomad4 AFR AF: 0.528

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.417

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.494

Gnomad4 NFE AF: 0.498

Gnomad4 OTH AF: 0.546

Alfa AF: 0.476 Hom.: 7429

Bravo AF: 0.491

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.6
Dann	Benign	0.70

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: rs7965203; hg19: chr12-8000336;