chrX-152652835-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_018558.4(GABRQ):c.1453C>T(p.Arg485Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000108 in 1,208,797 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 (★).
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.1453C>T | p.Arg485Cys | missense_variant | 9/9 | ENST00000598523.3 | |
MAGEA3-DT | XR_938525.3 | n.157-13041G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABRQ | ENST00000598523.3 | c.1453C>T | p.Arg485Cys | missense_variant | 9/9 | 1 | NM_018558.4 | P1 | |
MAGEA3-DT | ENST00000671457.1 | n.130-13041G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000267 AC: 3AN: 112417Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34575
GnomAD3 exomes AF: 0.0000327 AC: 6AN: 183406Hom.: 0 AF XY: 0.0000295 AC XY: 2AN XY: 67850
GnomAD4 exome AF: 0.00000912 AC: 10AN: 1096380Hom.: 0 Cov.: 31 AF XY: 0.00000829 AC XY: 3AN XY: 361768
GnomAD4 genome ? AF: 0.0000267 AC: 3AN: 112417Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34575
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.1453C>T (p.R485C) 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 1453, causing the arginine (R) at amino acid position 485 to be replaced by a cysteine (C). 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