chrX-152652851-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_018558.4(GABRQ):c.1469G>A(p.Gly490Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,209,051 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/16 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. G490S) has been classified as Uncertain significance.
Frequency
Consequence
NM_018558.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GABRQ | NM_018558.4 | c.1469G>A | p.Gly490Asp | missense_variant | 9/9 | ENST00000598523.3 | |
MAGEA3-DT | XR_938525.3 | n.157-13057C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABRQ | ENST00000598523.3 | c.1469G>A | p.Gly490Asp | missense_variant | 9/9 | 1 | NM_018558.4 | P1 | |
MAGEA3-DT | ENST00000671457.1 | n.130-13057C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000355 AC: 4AN: 112555Hom.: 0 Cov.: 24 AF XY: 0.0000288 AC XY: 1AN XY: 34715
GnomAD3 exomes AF: 0.000109 AC: 20AN: 183393Hom.: 0 AF XY: 0.0000590 AC XY: 4AN XY: 67837
GnomAD4 exome AF: 0.0000100 AC: 11AN: 1096496Hom.: 0 Cov.: 31 AF XY: 0.00000552 AC XY: 2AN XY: 362090
GnomAD4 genome ? AF: 0.0000355 AC: 4AN: 112555Hom.: 0 Cov.: 24 AF XY: 0.0000288 AC XY: 1AN XY: 34715
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 06, 2023 | The c.1469G>A (p.G490D) alteration is located in exon 9 (coding exon 9) of the GABRQ gene. This alteration results from a G to A substitution at nucleotide position 1469, causing the glycine (G) at amino acid position 490 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at