rs11612319

chr12-7864329-G-Achr12-7864329-G-T

Variant summary

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

The NM_001286234.2(SLC2A14):c.18+5534C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 151,644 control chromosomes in the GnomAD database, including 5,676 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 0.26 (5676 hom., cov: 32)
• Consequence: SLC2A14 NM_001286234.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16

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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A14	NM_001286234.2	c.18+5534C>T		intron_variant		ENST00000431042.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A14	ENST00000431042.7	c.18+5534C>T		intron_variant		1	NM_001286234.2	P1

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39176 AN: 151526 Hom.: 5682 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.0736

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.258 AC: 39164 AN: 151644 Hom.: 5676 Cov.: 32 AF XY: 0.258 AC XY: 19087 AN XY: 74120

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.0728

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.374

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.289

Alfa AF: 0.200 Hom.: 603

Bravo AF: 0.240

Asia WGS AF: 0.197 AC: 686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.25
Dann	Benign	0.53

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11612319; hg19: chr12-8016925;