chrX-152652764-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_018558.4(GABRQ):c.1382G>A(p.Arg461Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,210,423 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 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 (★).
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.1382G>A | p.Arg461Gln | missense_variant | 9/9 | ENST00000598523.3 | |
MAGEA3-DT | XR_938525.3 | n.157-12970C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABRQ | ENST00000598523.3 | c.1382G>A | p.Arg461Gln | missense_variant | 9/9 | 1 | NM_018558.4 | P1 | |
MAGEA3-DT | ENST00000671457.1 | n.130-12970C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000622 AC: 7AN: 112514Hom.: 0 Cov.: 24 AF XY: 0.0000577 AC XY: 2AN XY: 34664
GnomAD3 exomes AF: 0.0000164 AC: 3AN: 183242Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67716
GnomAD4 exome AF: 0.0000155 AC: 17AN: 1097856Hom.: 0 Cov.: 31 AF XY: 0.00000551 AC XY: 2AN XY: 363212
GnomAD4 genome ? AF: 0.0000622 AC: 7AN: 112567Hom.: 0 Cov.: 24 AF XY: 0.0000576 AC XY: 2AN XY: 34727
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 26, 2022 | The c.1382G>A (p.R461Q) 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 1382, causing the arginine (R) at amino acid position 461 to be replaced by a glutamine (Q). 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