chr1-42929202-AG-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS1
The NM_006516.4(SLC2A1):c.972+7delC variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000379 in 1,612,434 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_006516.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 152194Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000203 AC: 51AN: 250866Hom.: 0 AF XY: 0.000221 AC XY: 30AN XY: 135588
GnomAD4 exome AF: 0.000402 AC: 587AN: 1460122Hom.: 0 Cov.: 31 AF XY: 0.000384 AC XY: 279AN XY: 726456
GnomAD4 genome AF: 0.000158 AC: 24AN: 152312Hom.: 0 Cov.: 33 AF XY: 0.000201 AC XY: 15AN XY: 74472
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:3
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not specified Benign:2
The variant is found in EPILEPSY panel(s). -
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Dystonic disorder Uncertain:1
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GLUT1 deficiency syndrome Uncertain:1
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GLUT1 deficiency syndrome 1, autosomal recessive Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at