rs369808296
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_032569.4(GLYR1):c.596C>T(p.Ala199Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000211 in 1,613,626 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A199T) has been classified as Uncertain significance.
Frequency
Consequence
NM_032569.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLYR1 | NM_032569.4 | c.596C>T | p.Ala199Val | missense_variant | 6/16 | ENST00000321919.14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLYR1 | ENST00000321919.14 | c.596C>T | p.Ala199Val | missense_variant | 6/16 | 1 | NM_032569.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151778Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251476Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135912
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1461848Hom.: 0 Cov.: 32 AF XY: 0.0000248 AC XY: 18AN XY: 727222
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151778Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74068
ClinVar
Submissions by phenotype
GLYR1-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Undiagnosed Diseases Network, NIH | Mar 09, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at