rs376653618
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong
The NM_006516.4(SLC2A1):c.19-5C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000739 in 1,610,160 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_006516.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000849 AC: 21AN: 247454Hom.: 0 AF XY: 0.0000671 AC XY: 9AN XY: 134066
GnomAD4 exome AF: 0.0000754 AC: 110AN: 1458000Hom.: 0 Cov.: 30 AF XY: 0.0000772 AC XY: 56AN XY: 725398
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152160Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74332
ClinVar
Submissions by phenotype
not specified Benign:2
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not provided Benign:2
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. -
SLC2A1: PM2, BP4, BP5, BS2 -
Epilepsy, idiopathic generalized, susceptibility to, 12 Benign:2
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This variant was classified as: Benign. The following ACMG criteria were applied in classifying this variant: BS1,BS2. -
Dystonia 9 Benign:1
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Encephalopathy due to GLUT1 deficiency Benign:1
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Childhood onset GLUT1 deficiency syndrome 2 Benign:1
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GLUT1 deficiency syndrome 1, autosomal recessive Benign:1
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Hereditary cryohydrocytosis with reduced stomatin Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at