rs2242400

chr12-24945140-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005504.7(BCAT1):c.6+3787T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,222 control chromosomes in the GnomAD database, including 1,867 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.15 (1867 hom., cov: 32)
• Consequence: BCAT1 NM_005504.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.244

Genes affected

BCAT1 (HGNC:976): (branched chain amino acid transaminase 1) This gene encodes the cytosolic form of the enzyme branched-chain amino acid transaminase. This enzyme catalyzes the reversible transamination of branched-chain alpha-keto acids to branched-chain L-amino acids essential for cell growth. Two different clinical disorders have been attributed to a defect of branched-chain amino acid transamination: hypervalinemia and hyperleucine-isoleucinemia. As there is also a gene encoding a mitochondrial form of this enzyme, mutations in either gene may contribute to these disorders. Alternatively spliced transcript variants have been described. [provided by RefSeq, May 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BCAT1	NM_005504.7	c.6+3787T>C		intron_variant		ENST00000261192.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCAT1	ENST00000261192.12	c.6+3787T>C		intron_variant		1	NM_005504.7	P1
BCAT1	ENST00000342945.9	c.6+3787T>C		intron_variant		2
BCAT1	ENST00000539780.5	c.6+3787T>C		intron_variant		2
BCAT1	ENST00000546285.1	c.6+3787T>C		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22336 AN: 152102 Hom.: 1868 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.0614

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.153

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.147 AC: 22338 AN: 152222 Hom.: 1867 Cov.: 32 AF XY: 0.149 AC XY: 11120 AN XY: 74430

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.0608

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.152

Alfa AF: 0.119 Hom.: 1783

Bravo AF: 0.156

Asia WGS AF: 0.133 AC: 464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.9
Dann	Benign	0.64

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

Other links and lift over

dbSNP: rs2242400; hg19: chr12-25098074;