19-48796646-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001190.4(BCAT2):āc.997C>Gā(p.Arg333Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,613,518 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 Uncertain significance (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R333Q) 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 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCAT2 | NM_001190.4 | c.997C>G | p.Arg333Gly | missense_variant | 9/11 | ENST00000316273.11 | |
BCAT2 | NM_001284325.2 | c.877C>G | p.Arg293Gly | missense_variant | 10/12 | ||
BCAT2 | NM_001164773.2 | c.721C>G | p.Arg241Gly | missense_variant | 7/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCAT2 | ENST00000316273.11 | c.997C>G | p.Arg333Gly | missense_variant | 9/11 | 1 | NM_001190.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152042Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000399 AC: 10AN: 250360Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135548
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461354Hom.: 0 Cov.: 34 AF XY: 0.0000110 AC XY: 8AN XY: 727042
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152164Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74394
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 30, 2024 | The c.997C>G (p.R333G) alteration is located in exon 9 (coding exon 9) of the BCAT2 gene. This alteration results from a C to G substitution at nucleotide position 997, causing the arginine (R) at amino acid position 333 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jan 17, 2022 | This sequence change replaces arginine, which is basic and polar, with glycine, which is neutral and non-polar, at codon 333 of the BCAT2 protein (p.Arg333Gly). This variant is present in population databases (rs149621078, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with BCAT2-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at