rs3768043

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006516.4(SLC2A1):​c.18+4951G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 152,062 control chromosomes in the GnomAD database, including 32,907 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 0.63 ( 32907 hom., cov: 32)

Consequence

SLC2A1
NM_006516.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.77
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SLC2A1NM_006516.4 linkuse as main transcriptc.18+4951G>T intron_variant ENST00000426263.10 NP_006507.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SLC2A1ENST00000426263.10 linkuse as main transcriptc.18+4951G>T intron_variant 1 NM_006516.4 ENSP00000416293 P1

Frequencies

GnomAD3 genomes
AF:
0.629
AC:
95547
AN:
151944
Hom.:
32915
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.326
Gnomad AMI
AF:
0.832
Gnomad AMR
AF:
0.637
Gnomad ASJ
AF:
0.753
Gnomad EAS
AF:
0.662
Gnomad SAS
AF:
0.685
Gnomad FIN
AF:
0.750
Gnomad MID
AF:
0.669
Gnomad NFE
AF:
0.775
Gnomad OTH
AF:
0.665
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.628
AC:
95557
AN:
152062
Hom.:
32907
Cov.:
32
AF XY:
0.628
AC XY:
46647
AN XY:
74322
show subpopulations
Gnomad4 AFR
AF:
0.325
Gnomad4 AMR
AF:
0.637
Gnomad4 ASJ
AF:
0.753
Gnomad4 EAS
AF:
0.662
Gnomad4 SAS
AF:
0.684
Gnomad4 FIN
AF:
0.750
Gnomad4 NFE
AF:
0.775
Gnomad4 OTH
AF:
0.664
Alfa
AF:
0.722
Hom.:
15817
Bravo
AF:
0.611
Asia WGS
AF:
0.615
AC:
2140
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.68
CADD
Benign
10
DANN
Benign
0.65

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.

Other links and lift over

dbSNP: rs3768043; hg19: chr1-43419354; API