rs73587806

Variant names:

• chr19-48795352-G-A
• rs73587806
• NM_001190.4:c.*74C>T

Your query was ambiguous. Multiple possible variants found:

• chr19-48795352-G-A
• chr19-48795352-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001190.4(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 NM_001190.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.83
• Publications: 3 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: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 49 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001190.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCAT2	NM_001190.4	MANE Select	c.*74C>T		3_prime_UTR	Exon 11 of 11	NP_001181.2
	BCAT2	NM_001284325.2		c.*74C>T		3_prime_UTR	Exon 12 of 12	NP_001271254.1
	BCAT2	NM_001164773.2		c.*74C>T		3_prime_UTR	Exon 9 of 9	NP_001158245.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCAT2	ENST00000316273.11	TSL:1 MANE Select	c.*74C>T		3_prime_UTR	Exon 11 of 11	ENSP00000322991.5
	BCAT2	ENST00000545387.6	TSL:1	c.*74C>T		3_prime_UTR	Exon 9 of 9	ENSP00000440973.1
	BCAT2	ENST00000593515.5	TSL:5	c.*74C>T		3_prime_UTR	Exon 11 of 11	ENSP00000469139.1

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

African (AFR) AF: 0.0479 AC: 1582 AN: 33012

American (AMR) AF: 0.00269 AC: 119 AN: 44272

Ashkenazi Jewish (ASJ) AF: 0.000656 AC: 17 AN: 25910

East Asian (EAS) AF: 0.000507 AC: 20 AN: 39454

South Asian (SAS) AF: 0.000164 AC: 14 AN: 85386

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 52192

Middle Eastern (MID) AF: 0.00122 AC: 7 AN: 5730

European-Non Finnish (NFE) AF: 0.000124 AC: 136 AN: 1095266

Other (OTH) AF: 0.00378 AC: 226 AN: 59746

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

African (AFR) AF: 0.0479 AC: 1989 AN: 41548

American (AMR) AF: 0.00654 AC: 100 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.00144 AC: 5 AN: 3470

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5180

South Asian (SAS) AF: 0.000414 AC: 2 AN: 4826

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10624

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.000132 AC: 9 AN: 68030

Other (OTH) AF: 0.0123 AC: 26 AN: 2110

Alfa AF: 0.00452 Hom.: 2

Bravo AF: 0.0159

Asia WGS AF: 0.0120 AC: 41 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	15
DANN	Benign	0.96
PhyloP100		1.8
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism

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: rs73587806; hg19: chr19-49298609;