rs3754219

chr1-42934015-A-Cchr1-42934015-A-T

Variant summary

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

The NM_006516.4(SLC2A1):c.115-2809T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 152,068 control chromosomes in the GnomAD database, including 10,828 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 0.34 (10828 hom., cov: 32)
• Consequence: SLC2A1 NM_006516.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300

Genes affected

SLC2A1 (HGNC:11005): (solute carrier family 2 member 1) This gene encodes a major glucose transporter in the mammalian blood-brain barrier. The encoded protein is found primarily in the cell membrane and on the cell surface, where it can also function as a receptor for human T-cell leukemia virus (HTLV) I and II. Mutations in this gene have been found in a family with paroxysmal exertion-induced dyskinesia. [provided by RefSeq, Apr 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A1	NM_006516.4	c.115-2809T>G		intron_variant		ENST00000426263.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A1	ENST00000426263.10	c.115-2809T>G		intron_variant		1	NM_006516.4	P1

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52191 AN: 151950 Hom.: 10827 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.343 AC: 52205 AN: 152068 Hom.: 10828 Cov.: 32 AF XY: 0.342 AC XY: 25392 AN XY: 74330

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.423

Gnomad4 EAS AF: 0.374

Gnomad4 SAS AF: 0.398

Gnomad4 FIN AF: 0.465

Gnomad4 NFE AF: 0.461

Gnomad4 OTH AF: 0.372

Alfa AF: 0.430 Hom.: 14348

Bravo AF: 0.325

Asia WGS AF: 0.328 AC: 1141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	4.9
Dann	Benign	0.74

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: rs3754219; hg19: chr1-43399686;