chr7-2539800-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_152743.4(BRAT1):c.1484C>T(p.Pro495Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000136 in 1,611,806 control chromosomes in the GnomAD database, including 3 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). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P495S) has been classified as Uncertain significance.
Frequency
Consequence
NM_152743.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BRAT1 | NM_152743.4 | c.1484C>T | p.Pro495Leu | missense_variant | 11/14 | ENST00000340611.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BRAT1 | ENST00000340611.9 | c.1484C>T | p.Pro495Leu | missense_variant | 11/14 | 1 | NM_152743.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152210Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000231 AC: 56AN: 242724Hom.: 0 AF XY: 0.000333 AC XY: 44AN XY: 131972
GnomAD4 exome AF: 0.000136 AC: 199AN: 1459478Hom.: 3 Cov.: 32 AF XY: 0.000190 AC XY: 138AN XY: 725884
GnomAD4 genome AF: 0.000138 AC: 21AN: 152328Hom.: 0 Cov.: 33 AF XY: 0.000188 AC XY: 14AN XY: 74488
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 30, 2019 | - - |
Neonatal-onset encephalopathy with rigidity and seizures Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 17, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at