dbSNP rs28365848: SLC2A1:c.-390delA (chr1-42959040-CT-C) – ACMG Classification: Benign (-16 pts)

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_006516.4(SLC2A1):c.-390delA variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 220,588 control chromosomes in the GnomAD database, including 5,620 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.23 ( 4176 hom., cov: 26)

Exomes 𝑓: 0.19 ( 1444 hom. )

Consequence

SLC2A1
NM_006516.4 upstream_gene

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: 0.718

Variant links:

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 links:

SLC2A1-DT (HGNC:44187): (SLC2A1 divergent transcript)

SLC2A1-DT links:

ENSG00000283973 (HGNC:):

ENSG00000283973 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 1-42959040-CT-C is Benign according to our data. Variant chr1-42959040-CT-C is described in ClinVar as [Benign]. Clinvar id is 297392.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A1	NM_006516.4 link	c.-390delA		upstream_gene_variant		ENST00000426263.10	NP_006507.2	P11166Q59GX2
SLC2A1-DT	NR_033967.1 link	n.-8delT		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A1	ENST00000426263.10 link	c.-390delA		upstream_gene_variant		1	NM_006516.4	ENSP00000416293.2		P11166

Frequencies

GnomAD3 genomes

AF:

0.231

AC:

35091

AN:

151988

Hom.:

4175

Cov.:

show subpopulations

Gnomad AFR

AF:

0.258

Gnomad AMI

AF:

0.162

Gnomad AMR

AF:

0.249

Gnomad ASJ

AF:

0.230

Gnomad EAS

AF:

0.229

Gnomad SAS

AF:

0.208

Gnomad FIN

AF:

0.247

Gnomad MID

AF:

0.275

Gnomad NFE

AF:

0.210

Gnomad OTH

AF:

0.223

GnomAD4 exome

AF:

0.190

AC:

13033

AN:

68482

Hom.:

1444

Cov.:

AF XY:

0.191

AC XY:

7055

AN XY:

36914

show subpopulations

Gnomad4 AFR exome

AF:

0.227

Gnomad4 AMR exome

AF:

0.204

Gnomad4 ASJ exome

AF:

0.195

Gnomad4 EAS exome

AF:

0.180

Gnomad4 SAS exome

AF:

0.202

Gnomad4 FIN exome

AF:

0.208

Gnomad4 NFE exome

AF:

0.185

Gnomad4 OTH exome

AF:

0.191

GnomAD4 genome

AF:

0.231

AC:

35119

AN:

152106

Hom.:

4176

Cov.:

AF XY:

0.234

AC XY:

17403

AN XY:

74350

show subpopulations

Gnomad4 AFR

AF:

0.258

Gnomad4 AMR

AF:

0.249

Gnomad4 ASJ

AF:

0.230

Gnomad4 EAS

AF:

0.228

Gnomad4 SAS

AF:

0.209

Gnomad4 FIN

AF:

0.247

Gnomad4 NFE

AF:

0.210

Gnomad4 OTH

AF:

0.225

Alfa

AF:

0.0646

Hom.:

138

Bravo

AF:

0.230

Asia WGS

AF:

0.243

AC:

845

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:8

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Dystonia 9

Benign:1

Apr 11, 2023

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Encephalopathy due to GLUT1 deficiency

Benign:1

Apr 11, 2023

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Childhood onset GLUT1 deficiency syndrome 2

Benign:1

Apr 11, 2023

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:1

Jun 18, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

GLUT1 deficiency syndrome

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Dystonic disorder

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hereditary cryohydrocytosis with reduced stomatin

Benign:1

Apr 11, 2023

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Epilepsy, idiopathic generalized, susceptibility to, 12

Benign:1

Apr 11, 2023

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over