chrX-152652850-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_018558.4(GABRQ):c.1468G>A(p.Gly490Ser) 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 1,208,944 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. 11/16 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. G490D) 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.1468G>A | p.Gly490Ser | missense_variant | 9/9 | ENST00000598523.3 | |
MAGEA3-DT | XR_938525.3 | n.157-13056C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABRQ | ENST00000598523.3 | c.1468G>A | p.Gly490Ser | missense_variant | 9/9 | 1 | NM_018558.4 | P1 | |
MAGEA3-DT | ENST00000671457.1 | n.130-13056C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000355 AC: 4AN: 112574Hom.: 0 Cov.: 23 AF XY: 0.0000288 AC XY: 1AN XY: 34722
GnomAD3 exomes AF: 0.000109 AC: 20AN: 183405Hom.: 0 AF XY: 0.0000590 AC XY: 4AN XY: 67843
GnomAD4 exome AF: 0.0000100 AC: 11AN: 1096370Hom.: 0 Cov.: 31 AF XY: 0.00000553 AC XY: 2AN XY: 361956
GnomAD4 genome AF: 0.0000355 AC: 4AN: 112574Hom.: 0 Cov.: 23 AF XY: 0.0000288 AC XY: 1AN XY: 34722
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 06, 2023 | The c.1468G>A (p.G490S) 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 1468, causing the glycine (G) at amino acid position 490 to be replaced by a serine (S). 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