rs140833277
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM1BP4_StrongBP6BS2
The NM_152743.4(BRAT1):c.434C>T(p.Ala145Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00112 in 1,566,410 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 Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. A145A) has been classified as Likely benign.
Frequency
Consequence
NM_152743.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BRAT1 | NM_152743.4 | c.434C>T | p.Ala145Val | missense_variant | 5/14 | ENST00000340611.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BRAT1 | ENST00000340611.9 | c.434C>T | p.Ala145Val | missense_variant | 5/14 | 1 | NM_152743.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000902 AC: 136AN: 150716Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000818 AC: 178AN: 217476Hom.: 0 AF XY: 0.000746 AC XY: 89AN XY: 119224
GnomAD4 exome AF: 0.00114 AC: 1620AN: 1415576Hom.: 2 Cov.: 33 AF XY: 0.00109 AC XY: 762AN XY: 697840
GnomAD4 genome AF: 0.000902 AC: 136AN: 150834Hom.: 0 Cov.: 31 AF XY: 0.00107 AC XY: 79AN XY: 73722
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 18, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 03, 2019 | - - |
BRAT1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 18, 2022 | 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 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at