10-26217616-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001134366.2(GAD2):c.83C>T(p.Ala28Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000868 in 1,612,880 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001134366.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GAD2 | ENST00000376261.8 | c.83C>T | p.Ala28Val | missense_variant | Exon 2 of 16 | 1 | NM_001134366.2 | ENSP00000365437.3 | ||
GAD2 | ENST00000259271.7 | c.83C>T | p.Ala28Val | missense_variant | Exon 2 of 17 | 1 | ENSP00000259271.3 | |||
GAD2 | ENST00000428517.2 | n.83C>T | non_coding_transcript_exon_variant | Exon 2 of 4 | 1 | ENSP00000390434.2 | ||||
GAD2 | ENST00000648567 | c.-260C>T | 5_prime_UTR_variant | Exon 2 of 17 | ENSP00000498009.1 |
Frequencies
GnomAD3 genomes AF: 0.0000525 AC: 8AN: 152236Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000162 AC: 4AN: 247624Hom.: 0 AF XY: 0.0000224 AC XY: 3AN XY: 134200
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1460644Hom.: 0 Cov.: 32 AF XY: 0.00000551 AC XY: 4AN XY: 726538
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152236Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.83C>T (p.A28V) alteration is located in exon 2 (coding exon 2) of the GAD2 gene. This alteration results from a C to T substitution at nucleotide position 83, causing the alanine (A) at amino acid position 28 to be replaced by a valine (V). 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