rs841853

Positions:

• chr1-42935767-A-C

Variant summary

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

The NM_006516.4(SLC2A1):​c.115-4561T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.659 in 151,988 control chromosomes in the GnomAD database, including 33,399 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 0.66 (33399 hom., cov: 31)
• Consequence: SLC2A1 NM_006516.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.446

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]

SLC2A1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC2A1	NM_006516.4	c.115-4561T>G		intron_variant		ENST00000426263.10	NP_006507.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC2A1	ENST00000426263.10	c.115-4561T>G		intron_variant		1	NM_006516.4	ENSP00000416293.2

Frequencies

GnomAD3 genomes AF: 0.659 AC: 100148 AN: 151870 Hom.: 33370 Cov.: 31

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.740

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.767

Gnomad FIN AF: 0.712

Gnomad MID AF: 0.729

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.659 AC: 100226 AN: 151988 Hom.: 33399 Cov.: 31 AF XY: 0.661 AC XY: 49082 AN XY: 74302

Gnomad4 AFR AF: 0.561

Gnomad4 AMR AF: 0.632

Gnomad4 ASJ AF: 0.686

Gnomad4 EAS AF: 0.775

Gnomad4 SAS AF: 0.768

Gnomad4 FIN AF: 0.712

Gnomad4 NFE AF: 0.698

Gnomad4 OTH AF: 0.664

Alfa AF: 0.683 Hom.: 52386

Bravo AF: 0.647

Asia WGS AF: 0.747 AC: 2598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.50

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: rs841853; hg19: chr1-43401438;