rs570576002
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_152743.4(BRAT1):c.2006C>T(p.Pro669Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000105 in 1,605,930 control chromosomes in the GnomAD database, including 5 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 (★). Synonymous variant affecting the same amino acid position (i.e. P669P) has been classified as Likely benign.
Frequency
Consequence
NM_152743.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BRAT1 | NM_152743.4 | c.2006C>T | p.Pro669Leu | missense_variant | 14/14 | ENST00000340611.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BRAT1 | ENST00000340611.9 | c.2006C>T | p.Pro669Leu | missense_variant | 14/14 | 1 | NM_152743.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152206Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000250 AC: 59AN: 235924Hom.: 1 AF XY: 0.000309 AC XY: 40AN XY: 129624
GnomAD4 exome AF: 0.000111 AC: 161AN: 1453606Hom.: 5 Cov.: 66 AF XY: 0.000149 AC XY: 108AN XY: 723246
GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152324Hom.: 0 Cov.: 34 AF XY: 0.0000806 AC XY: 6AN XY: 74486
ClinVar
Submissions by phenotype
Neonatal-onset encephalopathy with rigidity and seizures Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 23, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at