rs7961152

Positions:

• chr12-24828677-A-C
• chr12-24828677-A-G
• chr12-24828677-A-T

Variant summary

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

The NM_005504.7(BCAT1):​c.1119+1146T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 152,102 control chromosomes in the GnomAD database, including 28,961 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 0.61 (28961 hom., cov: 33)
• Consequence: BCAT1 NM_005504.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

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]

LOC105369699 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BCAT1	NM_005504.7	c.1119+1146T>G		intron_variant		ENST00000261192.12
LOC105369699	XR_007063243.1	n.344-2024A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCAT1	ENST00000261192.12	c.1119+1146T>G		intron_variant		1	NM_005504.7	P1

Frequencies

GnomAD3 genomes AF: 0.609 AC: 92627 AN: 151982 Hom.: 28936 Cov.: 33

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.610 AC: 92716 AN: 152102 Hom.: 28961 Cov.: 33 AF XY: 0.612 AC XY: 45473 AN XY: 74362

Gnomad4 AFR AF: 0.701

Gnomad4 AMR AF: 0.654

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.827

Gnomad4 SAS AF: 0.673

Gnomad4 FIN AF: 0.482

Gnomad4 NFE AF: 0.549

Gnomad4 OTH AF: 0.598

Alfa AF: 0.575 Hom.: 10166

Bravo AF: 0.626

Asia WGS AF: 0.777 AC: 2703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.2
DANN	Benign	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

Other links and lift over

dbSNP: rs7961152; hg19: chr12-24981611;