19-48795352-G-A

Position:

• chr19-48795352-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000316273.11(BCAT2):​c.*74C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00267 in 1,593,248 control chromosomes in the GnomAD database, including 92 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 0.014 (49 hom., cov: 32)
  • Exomes 𝑓: 0.0015 (43 hom.)
• Consequence: BCAT2 ENST00000316273.11 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.83

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0141 (2140/152280) while in subpopulation AFR AF= 0.0479 (1989/41548). AF 95% confidence interval is 0.0461. There are 49 homozygotes in gnomad4. There are 999 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 49 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BCAT2	NM_001190.4	c.*74C>T		3_prime_UTR_variant	11/11	ENST00000316273.11	NP_001181.2
BCAT2	NM_001164773.2	c.*74C>T		3_prime_UTR_variant	9/9		NP_001158245.1
BCAT2	NM_001284325.2	c.*74C>T		3_prime_UTR_variant	12/12		NP_001271254.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BCAT2	ENST00000316273.11	c.*74C>T		3_prime_UTR_variant	11/11	1	NM_001190.4	ENSP00000322991	P1

Frequencies

GnomAD3 genomes AF: 0.0140 AC: 2136 AN: 152162 Hom.: 49 Cov.: 32

Gnomad AFR AF: 0.0479

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00662

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.000132

Gnomad OTH AF: 0.0115

GnomAD4 exome AF: 0.00147 AC: 2121 AN: 1440968 Hom.: 43 Cov.: 27 AF XY: 0.00131 AC XY: 942 AN XY: 717718

Gnomad4 AFR exome AF: 0.0479

Gnomad4 AMR exome AF: 0.00269

Gnomad4 ASJ exome AF: 0.000656

Gnomad4 EAS exome AF: 0.000507

Gnomad4 SAS exome AF: 0.000164

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000124

Gnomad4 OTH exome AF: 0.00378

GnomAD4 genome AF: 0.0141 AC: 2140 AN: 152280 Hom.: 49 Cov.: 32 AF XY: 0.0134 AC XY: 999 AN XY: 74462

Gnomad4 AFR AF: 0.0479

Gnomad4 AMR AF: 0.00654

Gnomad4 ASJ AF: 0.00144

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.000414

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000132

Gnomad4 OTH AF: 0.0123

Alfa AF: 0.000555 Hom.: 0

Bravo AF: 0.0159

Asia WGS AF: 0.0120 AC: 41 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	15
DANN	Benign	0.96
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs73587806; hg19: chr19-49298609;