chrX-152652703-C-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_018558.4(GABRQ):c.1321C>A(p.Gln441Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000129 in 1,210,215 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 72 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_018558.4 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 |
---|---|---|---|---|---|---|---|
GABRQ | NM_018558.4 | c.1321C>A | p.Gln441Lys | missense_variant | 9/9 | ENST00000598523.3 | |
MAGEA3-DT | XR_938525.3 | n.157-12909G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABRQ | ENST00000598523.3 | c.1321C>A | p.Gln441Lys | missense_variant | 9/9 | 1 | NM_018558.4 | P1 | |
MAGEA3-DT | ENST00000671457.1 | n.130-12909G>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000302 AC: 34AN: 112627Hom.: 0 Cov.: 24 AF XY: 0.000431 AC XY: 15AN XY: 34783
GnomAD3 exomes AF: 0.000354 AC: 65AN: 183362Hom.: 0 AF XY: 0.000472 AC XY: 32AN XY: 67808
GnomAD4 exome AF: 0.000111 AC: 122AN: 1097536Hom.: 0 Cov.: 31 AF XY: 0.000157 AC XY: 57AN XY: 362892
GnomAD4 genome ? AF: 0.000302 AC: 34AN: 112679Hom.: 0 Cov.: 24 AF XY: 0.000430 AC XY: 15AN XY: 34845
ClinVar
Submissions by phenotype
GABRQ-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 31, 2022 | 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