rs148548421
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_152743.4(BRAT1):āc.166G>Cā(p.Val56Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000929 in 1,614,084 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V56M) has been classified as Likely benign.
Frequency
Consequence
NM_152743.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BRAT1 | NM_152743.4 | c.166G>C | p.Val56Leu | missense_variant | 3/14 | ENST00000340611.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BRAT1 | ENST00000340611.9 | c.166G>C | p.Val56Leu | missense_variant | 3/14 | 1 | NM_152743.4 | P1 | |
BRAT1 | ENST00000467558.5 | n.182G>C | non_coding_transcript_exon_variant | 2/10 | 5 | ||||
BRAT1 | ENST00000469750.5 | n.390G>C | non_coding_transcript_exon_variant | 3/11 | 2 | ||||
BRAT1 | ENST00000421712.1 | c.166G>C | p.Val56Leu | missense_variant, NMD_transcript_variant | 2/5 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000147 AC: 37AN: 250988Hom.: 1 AF XY: 0.000125 AC XY: 17AN XY: 135826
GnomAD4 exome AF: 0.0000958 AC: 140AN: 1461806Hom.: 2 Cov.: 30 AF XY: 0.000102 AC XY: 74AN XY: 727200
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152278Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74462
ClinVar
Submissions by phenotype
Neonatal-onset encephalopathy with rigidity and seizures Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 11, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at