19-48796448-T-C
Position:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_001190.4(BCAT2):āc.1120A>Gā(p.Lys374Glu) variant causes a missense change. The variant allele was found at a frequency of 0.000299 in 1,614,104 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.0017 ( 0 hom., cov: 33)
Exomes š: 0.00015 ( 1 hom. )
Consequence
BCAT2
NM_001190.4 missense
NM_001190.4 missense
Scores
2
14
Clinical Significance
Conservation
PhyloP100: 4.32
Genes affected
BCAT2 (HGNC:977): (branched chain amino acid transaminase 2) This gene encodes a branched chain aminotransferase found in mitochondria. The encoded protein forms a dimer that catalyzes the first step in the production of the branched chain amino acids leucine, isoleucine, and valine. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.0068501234).
BP6
Variant 19-48796448-T-C is Benign according to our data. Variant chr19-48796448-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 1637906.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCAT2 | NM_001190.4 | c.1120A>G | p.Lys374Glu | missense_variant | 10/11 | ENST00000316273.11 | |
BCAT2 | NM_001284325.2 | c.1000A>G | p.Lys334Glu | missense_variant | 11/12 | ||
BCAT2 | NM_001164773.2 | c.844A>G | p.Lys282Glu | missense_variant | 8/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCAT2 | ENST00000316273.11 | c.1120A>G | p.Lys374Glu | missense_variant | 10/11 | 1 | NM_001190.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00174 AC: 264AN: 152158Hom.: 0 Cov.: 33
GnomAD3 genomes
AF:
AC:
264
AN:
152158
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.000521 AC: 131AN: 251376Hom.: 1 AF XY: 0.000449 AC XY: 61AN XY: 135858
GnomAD3 exomes
AF:
AC:
131
AN:
251376
Hom.:
AF XY:
AC XY:
61
AN XY:
135858
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000148 AC: 217AN: 1461828Hom.: 1 Cov.: 33 AF XY: 0.000124 AC XY: 90AN XY: 727224
GnomAD4 exome
AF:
AC:
217
AN:
1461828
Hom.:
Cov.:
33
AF XY:
AC XY:
90
AN XY:
727224
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.00174 AC: 265AN: 152276Hom.: 0 Cov.: 33 AF XY: 0.00180 AC XY: 134AN XY: 74454
GnomAD4 genome
AF:
AC:
265
AN:
152276
Hom.:
Cov.:
33
AF XY:
AC XY:
134
AN XY:
74454
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ESP6500AA
AF:
AC:
23
ESP6500EA
AF:
AC:
1
ExAC
AF:
AC:
69
Asia WGS
AF:
AC:
1
AN:
3478
ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 19, 2023 | - - |
BCAT2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 06, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;.;T;T;T;T;T
MetaRNN
Benign
T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N;.;.;.;.
REVEL
Benign
Sift
Benign
T;T;T;.;.;.;.
Sift4G
Benign
T;T;T;T;T;T;T
Polyphen
B;B;B;.;B;.;.
Vest4
MVP
MPC
0.56
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at