chr7-2539577-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 4P and 3B. PM1PM2BP4_ModerateBP6
The NM_152743.4(BRAT1):āc.1564G>Cā(p.Glu522Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000986 in 1,581,582 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E522K) has been classified as Uncertain significance.
Frequency
Consequence
NM_152743.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BRAT1 | NM_152743.4 | c.1564G>C | p.Glu522Gln | missense_variant | 12/14 | ENST00000340611.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BRAT1 | ENST00000340611.9 | c.1564G>C | p.Glu522Gln | missense_variant | 12/14 | 1 | NM_152743.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000513 AC: 78AN: 152164Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000140 AC: 28AN: 200214Hom.: 0 AF XY: 0.000111 AC XY: 12AN XY: 107708
GnomAD4 exome AF: 0.0000553 AC: 79AN: 1429300Hom.: 0 Cov.: 32 AF XY: 0.0000565 AC XY: 40AN XY: 708078
GnomAD4 genome AF: 0.000506 AC: 77AN: 152282Hom.: 0 Cov.: 33 AF XY: 0.000430 AC XY: 32AN XY: 74456
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jul 10, 2023 | In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 26947546, 32211283) - |
BRAT1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 07, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Neonatal-onset encephalopathy with rigidity and seizures Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 15, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at