12-24941287-T-C

Variant names:

• chr12-24941287-T-C
• rs10505955
• NM_005504.7:c.6+7640A>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.6+7640A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 152,112 control chromosomes in the GnomAD database, including 9,154 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 0.32 (9154 hom., cov: 33)
• Consequence: BCAT1 NM_005504.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.237
• Publications: 7 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.433 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.6+7640A>G		intron	N/A	NP_005495.2
	BCAT1	NM_001413094.1		c.6+7640A>G		intron	N/A	NP_001400023.1
	BCAT1	NM_001178091.2		c.6+7640A>G		intron	N/A	NP_001171562.1	P54687-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCAT1	ENST00000261192.12	TSL:1 MANE Select	c.6+7640A>G		intron	N/A	ENSP00000261192.7	P54687-1
	BCAT1	ENST00000905147.1		c.6+7640A>G		intron	N/A	ENSP00000575206.1
	BCAT1	ENST00000916642.1		c.6+7640A>G		intron	N/A	ENSP00000586701.1

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48767 AN: 151994 Hom.: 9158 Cov.: 33

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.321 AC: 48777 AN: 152112 Hom.: 9154 Cov.: 33 AF XY: 0.318 AC XY: 23615 AN XY: 74360

African (AFR) AF: 0.134 AC: 5562 AN: 41526

American (AMR) AF: 0.274 AC: 4191 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 1672 AN: 3464

East Asian (EAS) AF: 0.201 AC: 1043 AN: 5178

South Asian (SAS) AF: 0.273 AC: 1315 AN: 4824

European-Finnish (FIN) AF: 0.385 AC: 4073 AN: 10570

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29693 AN: 67954

Other (OTH) AF: 0.347 AC: 734 AN: 2114

Alfa AF: 0.386 Hom.: 6521

Bravo AF: 0.306

Asia WGS AF: 0.223 AC: 777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.57
PhyloP100		0.24
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: rs10505955; hg19: chr12-25094221;