rs144022438
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_002063.4(GLRA2):c.1172C>T(p.Ala391Val) variant causes a missense change. The variant allele was found at a frequency of 0.000123 in 1,205,998 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 42 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_002063.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000677 AC: 75AN: 110854Hom.: 0 Cov.: 21 AF XY: 0.000636 AC XY: 21AN XY: 33030
GnomAD3 exomes AF: 0.000246 AC: 45AN: 183288Hom.: 0 AF XY: 0.000133 AC XY: 9AN XY: 67806
GnomAD4 exome AF: 0.0000667 AC: 73AN: 1095093Hom.: 0 Cov.: 31 AF XY: 0.0000610 AC XY: 22AN XY: 360537
GnomAD4 genome AF: 0.000676 AC: 75AN: 110905Hom.: 0 Cov.: 21 AF XY: 0.000604 AC XY: 20AN XY: 33091
ClinVar
Submissions by phenotype
GLRA2-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at