chr1-42927667-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 3P and 10B. PM1PP2BP4_StrongBP6_ModerateBS1
The NM_006516.4(SLC2A1):c.1216G>A(p.Val406Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0000539 in 1,614,150 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V406F) has been classified as Uncertain significance.
Frequency
Consequence
NM_006516.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000269 AC: 41AN: 152162Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000796 AC: 20AN: 251262Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135826
GnomAD4 exome AF: 0.0000315 AC: 46AN: 1461870Hom.: 0 Cov.: 34 AF XY: 0.0000275 AC XY: 20AN XY: 727234
GnomAD4 genome AF: 0.000269 AC: 41AN: 152280Hom.: 0 Cov.: 33 AF XY: 0.000215 AC XY: 16AN XY: 74458
ClinVar
Submissions by phenotype
GLUT1 deficiency syndrome 1, autosomal recessive Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 03, 2025 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at