rs375938732
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 3P and 6B. PP2PP3_ModerateBP6_ModerateBS2
The NM_005458.8(GABBR2):c.1423C>T(p.Arg475Trp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000026 in 1,613,472 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. R475L) has been classified as Uncertain significance.
Frequency
Consequence
NM_005458.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GABBR2 | NM_005458.8 | c.1423C>T | p.Arg475Trp | missense_variant | 10/19 | ENST00000259455.4 | |
GABBR2 | XM_017015331.3 | c.1129C>T | p.Arg377Trp | missense_variant | 9/18 | ||
GABBR2 | XM_005252316.6 | c.649C>T | p.Arg217Trp | missense_variant | 8/17 | ||
GABBR2 | XM_017015332.3 | c.649C>T | p.Arg217Trp | missense_variant | 7/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABBR2 | ENST00000259455.4 | c.1423C>T | p.Arg475Trp | missense_variant | 10/19 | 1 | NM_005458.8 | P1 | |
GABBR2 | ENST00000637410.1 | n.1201C>T | non_coding_transcript_exon_variant | 10/19 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152142Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251090Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135724
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1461330Hom.: 0 Cov.: 30 AF XY: 0.0000261 AC XY: 19AN XY: 726974
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152142Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74308
ClinVar
Submissions by phenotype
Epileptic encephalopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 06, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at