rs77015302
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_152743.4(BRAT1):c.1867G>A(p.Gly623Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00191 in 1,598,284 control chromosomes in the GnomAD database, including 40 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_152743.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BRAT1 | NM_152743.4 | c.1867G>A | p.Gly623Ser | missense_variant | 14/14 | ENST00000340611.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BRAT1 | ENST00000340611.9 | c.1867G>A | p.Gly623Ser | missense_variant | 14/14 | 1 | NM_152743.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00958 AC: 1458AN: 152208Hom.: 19 Cov.: 34
GnomAD3 exomes AF: 0.00236 AC: 539AN: 228442Hom.: 6 AF XY: 0.00184 AC XY: 233AN XY: 126662
GnomAD4 exome AF: 0.00110 AC: 1587AN: 1445958Hom.: 20 Cov.: 67 AF XY: 0.000959 AC XY: 690AN XY: 719792
GnomAD4 genome ? AF: 0.00960 AC: 1463AN: 152326Hom.: 20 Cov.: 34 AF XY: 0.00946 AC XY: 705AN XY: 74496
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 24, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Aug 31, 2017 | - - |
Neonatal-onset encephalopathy with rigidity and seizures Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at