chrX-152653216-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PP3_Strong
The NM_018558.4(GABRQ):c.1834C>T(p.Arg612Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000307 in 1,203,798 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 16 hemizygotes in GnomAD. In-silico tool predicts a pathogenic 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 Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GABRQ | NM_018558.4 | c.1834C>T | p.Arg612Trp | missense_variant | 9/9 | ENST00000598523.3 | |
MAGEA3-DT | XR_938525.3 | n.157-13422G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABRQ | ENST00000598523.3 | c.1834C>T | p.Arg612Trp | missense_variant | 9/9 | 1 | NM_018558.4 | P1 | |
MAGEA3-DT | ENST00000671457.1 | n.130-13422G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000179 AC: 2AN: 111575Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33759
GnomAD3 exomes AF: 0.0000109 AC: 2AN: 183402Hom.: 0 AF XY: 0.0000147 AC XY: 1AN XY: 67872
GnomAD4 exome AF: 0.0000320 AC: 35AN: 1092223Hom.: 0 Cov.: 29 AF XY: 0.0000447 AC XY: 16AN XY: 357743
GnomAD4 genome ? AF: 0.0000179 AC: 2AN: 111575Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33759
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 01, 2023 | The c.1834C>T (p.R612W) alteration is located in exon 9 (coding exon 9) of the GABRQ gene. This alteration results from a C to T substitution at nucleotide position 1834, causing the arginine (R) at amino acid position 612 to be replaced by a tryptophan (W). 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