rs768735440
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PP5
The NM_002063.4(GLRA2):c.1334G>A(p.Arg445Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000997 in 1,203,603 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely pathogenic (no stars).
Frequency
Consequence
NM_002063.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000275 AC: 3AN: 109251Hom.: 0 Cov.: 21 AF XY: 0.0000316 AC XY: 1AN XY: 31605
GnomAD3 exomes AF: 0.00000546 AC: 1AN: 183303Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67795
GnomAD4 exome AF: 0.00000822 AC: 9AN: 1094302Hom.: 0 Cov.: 30 AF XY: 0.00000278 AC XY: 1AN XY: 359810
GnomAD4 genome AF: 0.0000274 AC: 3AN: 109301Hom.: 0 Cov.: 21 AF XY: 0.0000316 AC XY: 1AN XY: 31665
ClinVar
Submissions by phenotype
See cases Pathogenic:1
Marcogliese et al., (2022) have identified 13 unrelated subjects with a variable neurodevelopmental disorder with or without autistic features. This variant (c.1134G>A) results in p.Arg445Gln. This change has a very low allele frequency in GnomAD (PM2) and in silico models predict pathogenicity (PP3). We classify this variant to be likely pathogenic based on our cohort of affected individuals with similar phenotypes. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at