rs192133446
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_152743.4(BRAT1):c.282+9G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000164 in 1,613,902 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_152743.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BRAT1 | ENST00000340611.9 | c.282+9G>A | intron_variant | Intron 3 of 13 | 1 | NM_152743.4 | ENSP00000339637.4 | |||
BRAT1 | ENST00000421712.1 | n.282+9G>A | intron_variant | Intron 2 of 4 | 3 | ENSP00000409209.2 | ||||
BRAT1 | ENST00000467558.5 | n.298+9G>A | intron_variant | Intron 2 of 9 | 5 | |||||
BRAT1 | ENST00000469750.5 | n.506+9G>A | intron_variant | Intron 3 of 10 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000913 AC: 139AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000275 AC: 69AN: 250680Hom.: 1 AF XY: 0.000199 AC XY: 27AN XY: 135690
GnomAD4 exome AF: 0.0000855 AC: 125AN: 1461592Hom.: 1 Cov.: 30 AF XY: 0.0000784 AC XY: 57AN XY: 727062
GnomAD4 genome AF: 0.000919 AC: 140AN: 152310Hom.: 0 Cov.: 32 AF XY: 0.000953 AC XY: 71AN XY: 74470
ClinVar
Submissions by phenotype
BRAT1-related disorder Benign:1
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
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at