rs2839673
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001134366.2(GAD2):c.695G>A(p.Gly232Glu) variant causes a missense change. The variant allele was found at a frequency of 0.00782 in 1,613,388 control chromosomes in the GnomAD database, including 71 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001134366.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GAD2 | NM_001134366.2 | c.695G>A | p.Gly232Glu | missense_variant | 6/16 | ENST00000376261.8 | |
GAD2 | NM_000818.3 | c.695G>A | p.Gly232Glu | missense_variant | 6/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GAD2 | ENST00000376261.8 | c.695G>A | p.Gly232Glu | missense_variant | 6/16 | 1 | NM_001134366.2 | P1 | |
GAD2 | ENST00000259271.7 | c.695G>A | p.Gly232Glu | missense_variant | 6/17 | 1 | P1 | ||
GAD2 | ENST00000648567.1 | c.353G>A | p.Gly118Glu | missense_variant | 6/17 | ||||
GAD2 | ENST00000376248.1 | n.542G>A | non_coding_transcript_exon_variant | 4/4 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00590 AC: 898AN: 152148Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00646 AC: 1621AN: 251122Hom.: 11 AF XY: 0.00626 AC XY: 849AN XY: 135728
GnomAD4 exome AF: 0.00802 AC: 11719AN: 1461122Hom.: 69 Cov.: 29 AF XY: 0.00779 AC XY: 5663AN XY: 726902
GnomAD4 genome ? AF: 0.00590 AC: 898AN: 152266Hom.: 2 Cov.: 32 AF XY: 0.00602 AC XY: 448AN XY: 74444
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 22, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at