19-48796422-GC-AT

Variant names:

• chr19-48796422-GC-AT
• ENST00000598162.5:c.1145_1146delGCinsAT
• BCAT2 p.Ser382Asn

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000598162.5(BCAT2):​c.1145_1146delGCinsAT​(p.Ser382Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: BCAT2 ENST00000598162.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.98
• Publications: 0 publications found

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 Gene-Disease associations (from GenCC):

• hypervalinemia and hyperleucine-isoleucinemia

  Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, ClinGen

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000598162.5. 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
	BCAT2	NM_001190.4	MANE Select	c.1140+5_1140+6delGCinsAT		splice_region intron	N/A	NP_001181.2	O15382-1
	BCAT2	NM_001284325.2		c.1020+5_1020+6delGCinsAT		splice_region intron	N/A	NP_001271254.1	B3KSI3
	BCAT2	NM_001164773.2		c.864+5_864+6delGCinsAT		splice_region intron	N/A	NP_001158245.1	O15382-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCAT2	ENST00000598162.5	TSL:1	c.1145_1146delGCinsAT	p.Ser382Asn	missense	N/A	ENSP00000470216.1	M0QZ10
	BCAT2	ENST00000599246.5	TSL:1	c.869_870delGCinsAT	p.Ser290Asn	missense	N/A	ENSP00000470680.1	M0QZP4
	BCAT2	ENST00000316273.11	TSL:1 MANE Select	c.1140+5_1140+6delGCinsAT		splice_region intron	N/A	ENSP00000322991.5	O15382-1

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr19-49299679;