7-2538673-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The ENST00000340611.9(BRAT1):c.1862G>A(p.Arg621Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00241 in 1,598,336 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R621P) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000340611.9 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BRAT1 | NM_152743.4 | c.1862G>A | p.Arg621Gln | missense_variant | 14/14 | ENST00000340611.9 | NP_689956.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BRAT1 | ENST00000340611.9 | c.1862G>A | p.Arg621Gln | missense_variant | 14/14 | 1 | NM_152743.4 | ENSP00000339637 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00185 AC: 282AN: 152188Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00205 AC: 472AN: 229856Hom.: 5 AF XY: 0.00232 AC XY: 295AN XY: 127172
GnomAD4 exome AF: 0.00247 AC: 3573AN: 1446030Hom.: 18 Cov.: 70 AF XY: 0.00263 AC XY: 1894AN XY: 719808
GnomAD4 genome AF: 0.00185 AC: 282AN: 152306Hom.: 0 Cov.: 34 AF XY: 0.00191 AC XY: 142AN XY: 74478
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 10, 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 | Athena Diagnostics | Apr 05, 2019 | - - |
BRAT1-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 13, 2019 | 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
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at