rs45566933
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_ModerateBP6BS1
The NM_000817.3(GAD1):c.682A>C(p.Ile228Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000516 in 1,611,270 control chromosomes in the GnomAD database, including 1 homozygotes. 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000817.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GAD1 | NM_000817.3 | c.682A>C | p.Ile228Leu | missense_variant | Exon 7 of 17 | ENST00000358196.8 | NP_000808.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000388 AC: 59AN: 152234Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000322 AC: 81AN: 251304Hom.: 1 AF XY: 0.000302 AC XY: 41AN XY: 135830
GnomAD4 exome AF: 0.000529 AC: 772AN: 1458918Hom.: 1 Cov.: 28 AF XY: 0.000486 AC XY: 353AN XY: 726096
GnomAD4 genome AF: 0.000387 AC: 59AN: 152352Hom.: 0 Cov.: 32 AF XY: 0.000349 AC XY: 26AN XY: 74496
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
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GAD1: BS1 -
Neurodevelopmental disorder with progressive spasticity and brain white matter abnormalities Uncertain:1Benign:1
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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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -
Inborn genetic diseases Uncertain:1
The c.682A>C (p.I228L) alteration is located in exon 7 (coding exon 6) of the GAD1 gene. This alteration results from a A to C substitution at nucleotide position 682, causing the isoleucine (I) at amino acid position 228 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at