rs11612319

Variant names:

• chr12-7864329-G-A
• rs11612319
• NM_001286234.2:c.18+5534C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-7864329-G-A
• chr12-7864329-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC2A14	NM_001286234.2	c.18+5534C>T		intron_variant	Intron 2 of 10	ENST00000431042.7	NP_001273163.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A14	ENST00000431042.7	c.18+5534C>T		intron_variant	Intron 2 of 10	1	NM_001286234.2	ENSP00000407287.2

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

African (AFR) AF: 0.142 AC: 5895 AN: 41398

American (AMR) AF: 0.211 AC: 3210 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1402 AN: 3462

East Asian (EAS) AF: 0.0728 AC: 373 AN: 5122

South Asian (SAS) AF: 0.279 AC: 1338 AN: 4794

European-Finnish (FIN) AF: 0.374 AC: 3936 AN: 10526

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 21983 AN: 67802

Other (OTH) AF: 0.289 AC: 606 AN: 2096

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
PhyloP100		-2.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs11612319; hg19: chr12-8016925;