Genetic Variant BCAT2:c.1065+8G>A (chr19-48796570-C-T) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001190.4(BCAT2):c.1065+8G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0472 in 1,611,944 control chromosomes in the GnomAD database, including 1,965 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.048 ( 196 hom., cov: 33)

Exomes 𝑓: 0.047 ( 1769 hom. )

Consequence

BCAT2
NM_001190.4 splice_region, intron

Scores

Splicing: ADA: 0.0002320

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -2.76

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 19-48796570-C-T is Benign according to our data. Variant chr19-48796570-C-T is described in ClinVar as [Benign]. Clinvar id is 1666580.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.0691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
BCAT2	NM_001190.4 link	c.1065+8G>A	splice_region_variant, intron_variant	Intron 9 of 10	ENST00000316273.11	NP_001181.2	O15382-1
BCAT2	NM_001284325.2 link	c.945+8G>A	splice_region_variant, intron_variant	Intron 10 of 11		NP_001271254.1	O15382B3KSI3
BCAT2	NM_001164773.2 link	c.789+8G>A	splice_region_variant, intron_variant	Intron 7 of 8		NP_001158245.1	O15382-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCAT2	ENST00000316273.11 link	c.1065+8G>A		splice_region_variant, intron_variant	Intron 9 of 10	1	NM_001190.4	ENSP00000322991.5		O15382-1

Frequencies

GnomAD3 genomes

AF:

0.0474

AC:

7216

AN:

152138

Hom.:

191

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0505

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0392

Gnomad ASJ

AF:

0.0784

Gnomad EAS

AF:

0.0316

Gnomad SAS

AF:

0.0248

Gnomad FIN

AF:

0.0470

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.0491

Gnomad OTH

AF:

0.0522

GnomAD3 exomes

AF:

0.0441

AC:

10981

AN:

249064

Hom.:

271

AF XY:

0.0439

AC XY:

5909

AN XY:

134722

show subpopulations

Gnomad AFR exome

AF:

0.0513

Gnomad AMR exome

AF:

0.0269

Gnomad ASJ exome

AF:

0.0762

Gnomad EAS exome

AF:

0.0304

Gnomad SAS exome

AF:

0.0297

Gnomad FIN exome

AF:

0.0444

Gnomad NFE exome

AF:

0.0510

Gnomad OTH exome

AF:

0.0546

GnomAD4 exome

AF:

0.0472

AC:

68849

AN:

1459688

Hom.:

1769

Cov.:

AF XY:

0.0470

AC XY:

34097

AN XY:

726104

show subpopulations

Gnomad4 AFR exome

AF:

0.0528

Gnomad4 AMR exome

AF:

0.0283

Gnomad4 ASJ exome

AF:

0.0763

Gnomad4 EAS exome

AF:

0.0334

Gnomad4 SAS exome

AF:

0.0291

Gnomad4 FIN exome

AF:

0.0446

Gnomad4 NFE exome

AF:

0.0489

Gnomad4 OTH exome

AF:

0.0486

GnomAD4 genome

AF:

0.0475

AC:

7233

AN:

152256

Hom.:

196

Cov.:

AF XY:

0.0469

AC XY:

3494

AN XY:

74450

show subpopulations

Gnomad4 AFR

AF:

0.0506

Gnomad4 AMR

AF:

0.0391

Gnomad4 ASJ

AF:

0.0784

Gnomad4 EAS

AF:

0.0311

Gnomad4 SAS

AF:

0.0245

Gnomad4 FIN

AF:

0.0470

Gnomad4 NFE

AF:

0.0491

Gnomad4 OTH

AF:

0.0564

Alfa

AF:

0.0496

Hom.:

Bravo

AF:

0.0470

Asia WGS

AF:

0.0420

AC:

146

AN:

3478

EpiCase

AF:

0.0509

EpiControl

AF:

0.0535

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Feb 01, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.49

DANN

Benign

0.78

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00023

dbscSNV1_RF

Benign

0.016

SpliceAI score (max)

0.060

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