chrX-152649258-A-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_018558.4(GABRQ):c.535A>G(p.Thr179Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000195 in 1,182,174 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 9 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 Likely benign (★).
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.535A>G | p.Thr179Ala | missense_variant | 5/9 | ENST00000598523.3 | |
MAGEA3-DT | XR_938525.3 | n.157-9464T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABRQ | ENST00000598523.3 | c.535A>G | p.Thr179Ala | missense_variant | 5/9 | 1 | NM_018558.4 | P1 | |
MAGEA3-DT | ENST00000671457.1 | n.130-9464T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000179 AC: 2AN: 111688Hom.: 0 Cov.: 23 AF XY: 0.0000590 AC XY: 2AN XY: 33898
GnomAD3 exomes AF: 0.0000109 AC: 2AN: 183509Hom.: 0 AF XY: 0.0000147 AC XY: 1AN XY: 67939
GnomAD4 exome AF: 0.0000196 AC: 21AN: 1070486Hom.: 0 Cov.: 25 AF XY: 0.0000206 AC XY: 7AN XY: 340304
GnomAD4 genome ? AF: 0.0000179 AC: 2AN: 111688Hom.: 0 Cov.: 23 AF XY: 0.0000590 AC XY: 2AN XY: 33898
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2022 | ENSG00000287394: BS2; GABRQ: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at