chrX-151955029-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004961.4(GABRE):c.1193C>T(p.Ala398Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000333 in 1,201,661 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004961.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GABRE | NM_004961.4 | c.1193C>T | p.Ala398Val | missense_variant | 9/9 | ENST00000370328.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABRE | ENST00000370328.4 | c.1193C>T | p.Ala398Val | missense_variant | 9/9 | 1 | NM_004961.4 | P1 | |
GABRE | ENST00000486255.1 | n.4272C>T | non_coding_transcript_exon_variant | 3/3 | 1 | ||||
GABRE | ENST00000483564.5 | n.843C>T | non_coding_transcript_exon_variant | 4/4 | 3 | ||||
GABRE | ENST00000495862.1 | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000894 AC: 1AN: 111815Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33989
GnomAD4 exome AF: 0.00000275 AC: 3AN: 1089792Hom.: 0 Cov.: 32 AF XY: 0.00000281 AC XY: 1AN XY: 356068
GnomAD4 genome AF: 0.00000894 AC: 1AN: 111869Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34053
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2023 | The c.1193C>T (p.A398V) alteration is located in exon 9 (coding exon 9) of the GABRE gene. This alteration results from a C to T substitution at nucleotide position 1193, causing the alanine (A) at amino acid position 398 to be replaced by a valine (V). 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