chr7-2541709-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_152743.4(BRAT1):c.1134+9G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000343 in 1,602,598 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 Likely 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.1134+9G>A | intron_variant | Intron 8 of 13 | 1 | NM_152743.4 | ENSP00000339637.4 | |||
BRAT1 | ENST00000467558.5 | n.1416+9G>A | intron_variant | Intron 6 of 9 | 5 | |||||
BRAT1 | ENST00000469750.5 | n.2616+9G>A | intron_variant | Intron 6 of 10 | 2 | |||||
BRAT1 | ENST00000493232.5 | n.2535+9G>A | intron_variant | Intron 1 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000531 AC: 12AN: 225930Hom.: 0 AF XY: 0.0000323 AC XY: 4AN XY: 123988
GnomAD4 exome AF: 0.0000255 AC: 37AN: 1450396Hom.: 0 Cov.: 32 AF XY: 0.0000208 AC XY: 15AN XY: 720952
GnomAD4 genome AF: 0.000118 AC: 18AN: 152202Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74348
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