NM_005504.7:c.1119+1146T>G

Variant names:

• chr12-24828677-A-C
• rs7961152
• NM_005504.7:c.1119+1146T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 22 publications found

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]

BCAT1-AS1 (HGNC:58192):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005504.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCAT1	NM_005504.7	MANE Select	c.1119+1146T>G		intron	N/A	NP_005495.2
	BCAT1	NM_001413086.1		c.1155+1146T>G		intron	N/A	NP_001400015.1
	BCAT1	NM_001413087.1		c.1191+1146T>G		intron	N/A	NP_001400016.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCAT1	ENST00000261192.12	TSL:1 MANE Select	c.1119+1146T>G		intron	N/A	ENSP00000261192.7	P54687-1
	BCAT1	ENST00000538118.5	TSL:1	c.1116+1146T>G		intron	N/A	ENSP00000440817.1	P54687-4
	BCAT1	ENST00000539282.5	TSL:2	c.1155+1146T>G		intron	N/A	ENSP00000443459.1	P54687-5

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

African (AFR) AF: 0.701 AC: 29084 AN: 41476

American (AMR) AF: 0.654 AC: 9993 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1663 AN: 3472

East Asian (EAS) AF: 0.827 AC: 4286 AN: 5182

South Asian (SAS) AF: 0.673 AC: 3247 AN: 4826

European-Finnish (FIN) AF: 0.482 AC: 5100 AN: 10570

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.549 AC: 37328 AN: 67966

Other (OTH) AF: 0.598 AC: 1266 AN: 2116

Alfa AF: 0.573 Hom.: 15733

Bravo AF: 0.626

Asia WGS AF: 0.777 AC: 2703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.2
DANN	Benign	0.63
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7961152; hg19: chr12-24981611;