rs1273394

Positions:

• chr16-8719430-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020686.6(ABAT):​c.-41-16269G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 151,980 control chromosomes in the GnomAD database, including 8,742 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 0.33 (8742 hom., cov: 32)
• Consequence: ABAT NM_020686.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.400

Genes affected

ABAT (HGNC:23): (4-aminobutyrate aminotransferase) 4-aminobutyrate aminotransferase (ABAT) is responsible for catabolism of gamma-aminobutyric acid (GABA), an important, mostly inhibitory neurotransmitter in the central nervous system, into succinic semialdehyde. The active enzyme is a homodimer of 50-kD subunits complexed to pyridoxal-5-phosphate. The protein sequence is over 95% similar to the pig protein. GABA is estimated to be present in nearly one-third of human synapses. ABAT in liver and brain is controlled by 2 codominant alleles with a frequency in a Caucasian population of 0.56 and 0.44. The ABAT deficiency phenotype includes psychomotor retardation, hypotonia, hyperreflexia, lethargy, refractory seizures, and EEG abnormalities. Multiple alternatively spliced transcript variants encoding the same protein isoform have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABAT	NM_020686.6	c.-41-16269G>T		intron_variant		ENST00000268251.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABAT	ENST00000268251.13	c.-41-16269G>T		intron_variant		1	NM_020686.6	P1

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50526 AN: 151862 Hom.: 8724 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.333 AC: 50571 AN: 151980 Hom.: 8742 Cov.: 32 AF XY: 0.334 AC XY: 24777 AN XY: 74276

Gnomad4 AFR AF: 0.407

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.319

Alfa AF: 0.315 Hom.: 10589

Bravo AF: 0.335

Asia WGS AF: 0.172 AC: 604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.37

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs1273394; hg19: chr16-8813287;