chr7-2542173-A-C
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_152743.4(BRAT1):āc.962T>Gā(p.Leu321Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00838 in 1,571,350 control chromosomes in the GnomAD database, including 65 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. L321L) 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 -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BRAT1 | NM_152743.4 | c.962T>G | p.Leu321Arg | missense_variant | 7/14 | ENST00000340611.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BRAT1 | ENST00000340611.9 | c.962T>G | p.Leu321Arg | missense_variant | 7/14 | 1 | NM_152743.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00660 AC: 1003AN: 151992Hom.: 5 Cov.: 32
GnomAD3 exomes AF: 0.00598 AC: 1104AN: 184708Hom.: 7 AF XY: 0.00611 AC XY: 603AN XY: 98702
GnomAD4 exome AF: 0.00857 AC: 12165AN: 1419238Hom.: 60 Cov.: 32 AF XY: 0.00857 AC XY: 6018AN XY: 702068
GnomAD4 genome AF: 0.00659 AC: 1002AN: 152112Hom.: 5 Cov.: 32 AF XY: 0.00629 AC XY: 468AN XY: 74364
ClinVar
Submissions by phenotype
not provided Benign:4
Likely benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Nov 14, 2018 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2024 | BRAT1: BP4, BS2 - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 23, 2020 | This variant is associated with the following publications: (PMID: 29375859) - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Sep 12, 2016 | - - |
BRAT1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 13, 2023 | This variant is classified as 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
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Neonatal-onset encephalopathy with rigidity and seizures;C4748032:Neurodevelopmental disorder with cerebellar atrophy and with or without seizures Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Apr 01, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at