19-48796645-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001190.4(BCAT2):c.998G>A(p.Arg333Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000186 in 1,613,678 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R333G) has been classified as Uncertain significance.
Frequency
Consequence
NM_001190.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCAT2 | NM_001190.4 | c.998G>A | p.Arg333Gln | missense_variant | 9/11 | ENST00000316273.11 | |
BCAT2 | NM_001284325.2 | c.878G>A | p.Arg293Gln | missense_variant | 10/12 | ||
BCAT2 | NM_001164773.2 | c.722G>A | p.Arg241Gln | missense_variant | 7/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCAT2 | ENST00000316273.11 | c.998G>A | p.Arg333Gln | missense_variant | 9/11 | 1 | NM_001190.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152158Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 250418Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135570
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461402Hom.: 0 Cov.: 34 AF XY: 0.0000110 AC XY: 8AN XY: 727050
GnomAD4 genome AF: 0.0000919 AC: 14AN: 152276Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74444
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 11, 2023 | The c.998G>A (p.R333Q) alteration is located in exon 9 (coding exon 9) of the BCAT2 gene. This alteration results from a G to A substitution at nucleotide position 998, causing the arginine (R) at amino acid position 333 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at