7-2538326-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_152743.4(BRAT1):c.2209C>T(p.Arg737Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00435 in 1,613,002 control chromosomes in the GnomAD database, including 249 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as 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
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BRAT1 | ENST00000340611.9 | c.2209C>T | p.Arg737Trp | missense_variant | 14/14 | 1 | NM_152743.4 | ENSP00000339637.4 | ||
BRAT1 | ENST00000467558.5 | n.3995C>T | non_coding_transcript_exon_variant | 10/10 | 5 | |||||
BRAT1 | ENST00000469750.5 | n.4781C>T | non_coding_transcript_exon_variant | 11/11 | 2 | |||||
BRAT1 | ENST00000493232.5 | n.4915C>T | non_coding_transcript_exon_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0230 AC: 3495AN: 152196Hom.: 122 Cov.: 34
GnomAD3 exomes AF: 0.00594 AC: 1475AN: 248252Hom.: 52 AF XY: 0.00438 AC XY: 591AN XY: 134812
GnomAD4 exome AF: 0.00241 AC: 3515AN: 1460688Hom.: 128 Cov.: 65 AF XY: 0.00211 AC XY: 1533AN XY: 726670
GnomAD4 genome AF: 0.0230 AC: 3499AN: 152314Hom.: 121 Cov.: 34 AF XY: 0.0222 AC XY: 1652AN XY: 74480
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jun 28, 2017 | - - |
Neonatal-onset encephalopathy with rigidity and seizures Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 15, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at