Variant 19-48799813-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001190.4(BCAT2):c.557C>G(p.Thr186Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 1,558,204 control chromosomes in the GnomAD database, including 32,136 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.14 ( 2071 hom., cov: 32)

Exomes 𝑓: 0.20 ( 30065 hom. )

Consequence

BCAT2
NM_001190.4 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.38

Variant links:

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]

BCAT2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0057376027).

BP6

Variant 19-48799813-G-C is Benign according to our data. Variant chr19-48799813-G-C is described in ClinVar as [Benign]. Clinvar id is 1601520.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
BCAT2	NM_001190.4 linkuse as main transcript	c.557C>G	p.Thr186Arg	missense_variant	6/11	ENST00000316273.11
BCAT2	NM_001284325.2 linkuse as main transcript	c.437C>G	p.Thr146Arg	missense_variant	7/12
BCAT2	NM_001164773.2 linkuse as main transcript	c.281C>G	p.Thr94Arg	missense_variant	4/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCAT2	ENST00000316273.11 linkuse as main transcript	c.557C>G	p.Thr186Arg	missense_variant	6/11	1	NM_001190.4	P1	O15382-1

Frequencies

GnomAD3 genomes

AF:

0.143

AC:

21680

AN:

152104

Hom.:

2073

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0407

Gnomad AMI

AF:

0.238

Gnomad AMR

AF:

0.132

Gnomad ASJ

AF:

0.187

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.0741

Gnomad FIN

AF:

0.170

Gnomad MID

AF:

0.184

Gnomad NFE

AF:

0.214

Gnomad OTH

AF:

0.157

GnomAD3 exomes

AF:

0.143

AC:

23300

AN:

163330

Hom.:

2115

AF XY:

0.144

AC XY:

12508

AN XY:

86676

show subpopulations

Gnomad AFR exome

AF:

0.0337

Gnomad AMR exome

AF:

0.0958

Gnomad ASJ exome

AF:

0.165

Gnomad EAS exome

AF:

0.000500

Gnomad SAS exome

AF:

0.0831

Gnomad FIN exome

AF:

0.173

Gnomad NFE exome

AF:

0.213

Gnomad OTH exome

AF:

0.166

GnomAD4 exome

AF:

0.197

AC:

276976

AN:

1405982

Hom.:

30065

Cov.:

AF XY:

0.194

AC XY:

134382

AN XY:

694160

show subpopulations

Gnomad4 AFR exome

AF:

0.0315

Gnomad4 AMR exome

AF:

0.0986

Gnomad4 ASJ exome

AF:

0.170

Gnomad4 EAS exome

AF:

0.000438

Gnomad4 SAS exome

AF:

0.0843

Gnomad4 FIN exome

AF:

0.176

Gnomad4 NFE exome

AF:

0.223

Gnomad4 OTH exome

AF:

0.180

GnomAD4 genome

AF:

0.142

AC:

21677

AN:

152222

Hom.:

2071

Cov.:

AF XY:

0.139

AC XY:

10312

AN XY:

74432

show subpopulations

Gnomad4 AFR

AF:

0.0406

Gnomad4 AMR

AF:

0.132

Gnomad4 ASJ

AF:

0.187

Gnomad4 EAS

AF:

0.00135

Gnomad4 SAS

AF:

0.0746

Gnomad4 FIN

AF:

0.170

Gnomad4 NFE

AF:

0.214

Gnomad4 OTH

AF:

0.155

Alfa

AF:

0.188

Hom.:

977

Bravo

AF:

0.136

TwinsUK

AF:

0.213

AC:

790

ALSPAC

AF:

0.227

AC:

875

ESP6500AA

AF:

0.0438

AC:

187

ESP6500EA

AF:

0.197

AC:

1658

ExAC

AF:

0.0967

AC:

10685

Asia WGS

AF:

0.0350

AC:

123

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.084

BayesDel_addAF

Benign

-0.67

BayesDel_noAF

Benign

-0.60

CADD

Benign

DANN

Benign

0.73

Eigen

Benign

-0.90

Eigen_PC

Benign

-0.94

FATHMM_MKL

Benign

0.058

LIST_S2

Uncertain

0.95

D;.;D;D;D;D;D

MetaRNN

Benign

0.0057

T;T;T;T;T;T;T

MetaSVM

Benign

-0.97

MutationTaster

Benign

1.0

P;P;P

PrimateAI

Uncertain

0.53

PROVEAN

Benign

-1.7

N;N;N;.;.;.;.

REVEL

Benign

0.040

Sift

Benign

0.47

T;T;T;.;.;.;.

Sift4G

Benign

0.49

T;T;T;T;T;T;T

Polyphen

0.015

B;B;B;.;B;.;.

Vest4

0.25

MPC

0.50

ClinPred

0.015

GERP RS

2.0

Varity_R

0.18

gMVP

0.63

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over