19-48796646-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001190.4(BCAT2):c.997C>T(p.Arg333Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000397 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 Likely benign (★). 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 Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCAT2 | NM_001190.4 | c.997C>T | p.Arg333Trp | missense_variant | 9/11 | ENST00000316273.11 | |
BCAT2 | NM_001284325.2 | c.877C>T | p.Arg293Trp | missense_variant | 10/12 | ||
BCAT2 | NM_001164773.2 | c.721C>T | p.Arg241Trp | missense_variant | 7/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCAT2 | ENST00000316273.11 | c.997C>T | p.Arg333Trp | missense_variant | 9/11 | 1 | NM_001190.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00206 AC: 313AN: 152042Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000619 AC: 155AN: 250360Hom.: 0 AF XY: 0.000494 AC XY: 67AN XY: 135548
GnomAD4 exome AF: 0.000223 AC: 326AN: 1461354Hom.: 0 Cov.: 34 AF XY: 0.000190 AC XY: 138AN XY: 727042
GnomAD4 genome AF: 0.00207 AC: 315AN: 152164Hom.: 0 Cov.: 33 AF XY: 0.00212 AC XY: 158AN XY: 74394
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 13, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at