19-48796670-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001190.4(BCAT2):c.973C>T(p.Arg325Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000415 in 1,613,396 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar 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.973C>T | p.Arg325Trp | missense_variant | 9/11 | ENST00000316273.11 | |
BCAT2 | NM_001284325.2 | c.853C>T | p.Arg285Trp | missense_variant | 10/12 | ||
BCAT2 | NM_001164773.2 | c.697C>T | p.Arg233Trp | missense_variant | 7/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCAT2 | ENST00000316273.11 | c.973C>T | p.Arg325Trp | missense_variant | 9/11 | 1 | NM_001190.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152194Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000400 AC: 10AN: 250010Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135372
GnomAD4 exome AF: 0.0000370 AC: 54AN: 1461202Hom.: 0 Cov.: 34 AF XY: 0.0000413 AC XY: 30AN XY: 726968
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152194Hom.: 0 Cov.: 33 AF XY: 0.000108 AC XY: 8AN XY: 74352
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Nov 08, 2022 | This variant is present in population databases (rs143358538, gnomAD 0.008%). 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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt BCAT2 protein function. ClinVar contains an entry for this variant (Variation ID: 1477310). This variant has not been reported in the literature in individuals affected with BCAT2-related conditions. This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 325 of the BCAT2 protein (p.Arg325Trp). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at