chr7-2538195-G-C
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP6
The NM_152743.4(BRAT1):c.2340C>G(p.Asp780Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000258 in 1,610,022 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D780H) has been classified as Uncertain significance.
Frequency
Consequence
NM_152743.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BRAT1 | NM_152743.4 | c.2340C>G | p.Asp780Glu | missense_variant | 14/14 | ENST00000340611.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BRAT1 | ENST00000340611.9 | c.2340C>G | p.Asp780Glu | missense_variant | 14/14 | 1 | NM_152743.4 | P1 | |
BRAT1 | ENST00000467558.5 | n.4126C>G | non_coding_transcript_exon_variant | 10/10 | 5 | ||||
BRAT1 | ENST00000469750.5 | n.4912C>G | non_coding_transcript_exon_variant | 11/11 | 2 | ||||
BRAT1 | ENST00000493232.5 | n.5046C>G | non_coding_transcript_exon_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000204 AC: 31AN: 152266Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000210 AC: 51AN: 242578Hom.: 0 AF XY: 0.000188 AC XY: 25AN XY: 132868
GnomAD4 exome AF: 0.000263 AC: 384AN: 1457638Hom.: 0 Cov.: 62 AF XY: 0.000235 AC XY: 170AN XY: 724698
GnomAD4 genome AF: 0.000203 AC: 31AN: 152384Hom.: 0 Cov.: 34 AF XY: 0.000188 AC XY: 14AN XY: 74524
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | May 04, 2023 | In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
BRAT1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 14, 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 | Dec 28, 2023 | - - |
Intellectual disability Benign:1
Likely benign, no assertion criteria provided | clinical testing | Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille | Jan 01, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at