Variant rs4658 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_006516.4(SLC2A1):c.*462G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 595,632 control chromosomes in the GnomAD database, including 24,313 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.34 ( 10919 hom., cov: 32)

Exomes 𝑓: 0.23 ( 13394 hom. )

Consequence

SLC2A1
NM_006516.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:2

Conservation

PhyloP100: -0.308

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BP6

Variant 1-42926579-C-G is Benign according to our data. Variant chr1-42926579-C-G is described in ClinVar as [Benign]. Clinvar id is 297374.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC2A1	NM_006516.4 linkuse as main transcript	c.*462G>C		3_prime_UTR_variant	10/10	ENST00000426263.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC2A1	ENST00000426263.10 linkuse as main transcript	c.*462G>C		3_prime_UTR_variant	10/10	1	NM_006516.4	P1

Frequencies

GnomAD3 genomes

AF:

0.341

AC:

51840

AN:

151984

Hom.:

10880

Cov.:

show subpopulations

Gnomad AFR

AF:

0.590

Gnomad AMI

AF:

0.104

Gnomad AMR

AF:

0.364

Gnomad ASJ

AF:

0.201

Gnomad EAS

AF:

0.313

Gnomad SAS

AF:

0.266

Gnomad FIN

AF:

0.246

Gnomad MID

AF:

0.266

Gnomad NFE

AF:

0.218

Gnomad OTH

AF:

0.308

GnomAD4 exome

AF:

0.235

AC:

104080

AN:

443528

Hom.:

13394

Cov.:

AF XY:

0.235

AC XY:

53402

AN XY:

227240

show subpopulations

Gnomad4 AFR exome

AF:

0.598

Gnomad4 AMR exome

AF:

0.370

Gnomad4 ASJ exome

AF:

0.191

Gnomad4 EAS exome

AF:

0.319

Gnomad4 SAS exome

AF:

0.257

Gnomad4 FIN exome

AF:

0.236

Gnomad4 NFE exome

AF:

0.212

Gnomad4 OTH exome

AF:

0.243

GnomAD4 genome

AF:

0.342

AC:

51949

AN:

152104

Hom.:

10919

Cov.:

AF XY:

0.342

AC XY:

25458

AN XY:

74340

show subpopulations

Gnomad4 AFR

AF:

0.591

Gnomad4 AMR

AF:

0.364

Gnomad4 ASJ

AF:

0.201

Gnomad4 EAS

AF:

0.313

Gnomad4 SAS

AF:

0.266

Gnomad4 FIN

AF:

0.246

Gnomad4 NFE

AF:

0.218

Gnomad4 OTH

AF:

0.307

Alfa

AF:

0.137

Hom.:

237

Bravo

AF:

0.359

Asia WGS

AF:

0.321

AC:

1117

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Dystonia 9

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Encephalopathy due to GLUT1 deficiency

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

Cadd

Benign

2.5

Dann

Benign

0.38

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