chrX-152652830-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_018558.4(GABRQ):c.1448G>A(p.Arg483His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000422 in 1,209,065 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 15 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 (★).
Frequency
Consequence
NM_018558.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GABRQ | NM_018558.4 | c.1448G>A | p.Arg483His | missense_variant | 9/9 | ENST00000598523.3 | |
MAGEA3-DT | XR_938525.3 | n.157-13036C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABRQ | ENST00000598523.3 | c.1448G>A | p.Arg483His | missense_variant | 9/9 | 1 | NM_018558.4 | P1 | |
MAGEA3-DT | ENST00000671457.1 | n.130-13036C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000178 AC: 2AN: 112318Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34502
GnomAD3 exomes AF: 0.0000164 AC: 3AN: 183387Hom.: 0 AF XY: 0.0000295 AC XY: 2AN XY: 67835
GnomAD4 exome AF: 0.0000447 AC: 49AN: 1096747Hom.: 0 Cov.: 31 AF XY: 0.0000414 AC XY: 15AN XY: 362123
GnomAD4 genome ? AF: 0.0000178 AC: 2AN: 112318Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34502
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2021 | The c.1448G>A (p.R483H) 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 1448, causing the arginine (R) at amino acid position 483 to be replaced by a histidine (H). 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