chrX-152652625-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_018558.4(GABRQ):c.1243G>A(p.Gly415Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000729 in 1,097,592 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. 11/16 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.1243G>A | p.Gly415Ser | missense_variant | 9/9 | ENST00000598523.3 | |
MAGEA3-DT | XR_938525.3 | n.157-12831C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABRQ | ENST00000598523.3 | c.1243G>A | p.Gly415Ser | missense_variant | 9/9 | 1 | NM_018558.4 | P1 | |
MAGEA3-DT | ENST00000671457.1 | n.130-12831C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? Cov.: 24
GnomAD3 exomes AF: 0.0000164 AC: 3AN: 183324Hom.: 0 AF XY: 0.0000295 AC XY: 2AN XY: 67778
GnomAD4 exome AF: 0.00000729 AC: 8AN: 1097592Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 4AN XY: 362970
GnomAD4 genome ? Cov.: 24
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 18, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at