Variant 16-8781189-TGATG-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_020686.6(ABAT):c.1382-95_1382-92delGATG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.636 in 1,429,434 control chromosomes in the GnomAD database, including 290,281 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.61 ( 28050 hom., cov: 0)

Exomes 𝑓: 0.64 ( 262231 hom. )

Consequence

ABAT
NM_020686.6 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.00100

Variant links:

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]

ABAT links:

TMEM186 (HGNC:24530): (transmembrane protein 186) This gene encodes a potential transmembrane protein. [provided by RefSeq, Dec 2012]

TMEM186 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 16-8781189-TGATG-T is Benign according to our data. Variant chr16-8781189-TGATG-T is described in ClinVar as [Benign]. Clinvar id is 1185367.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABAT	NM_020686.6 link	c.1382-95_1382-92delGATG		intron_variant		ENST00000268251.13	NP_065737.2	P80404X5D8S1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABAT	ENST00000268251.13 link	c.1382-119_1382-116delGATG		intron_variant		1	NM_020686.6	ENSP00000268251.8		P80404

Frequencies

GnomAD3 genomes

AF:

0.607

AC:

91327

AN:

150518

Hom.:

28049

Cov.:

show subpopulations

Gnomad AFR

AF:

0.497

Gnomad AMI

AF:

0.721

Gnomad AMR

AF:

0.569

Gnomad ASJ

AF:

0.709

Gnomad EAS

AF:

0.631

Gnomad SAS

AF:

0.604

Gnomad FIN

AF:

0.667

Gnomad MID

AF:

0.713

Gnomad NFE

AF:

0.663

Gnomad OTH

AF:

0.622

GnomAD4 exome

AF:

0.640

AC:

818481

AN:

1278800

Hom.:

262231

AF XY:

0.639

AC XY:

412509

AN XY:

645186

show subpopulations

Gnomad4 AFR exome

AF:

0.485

Gnomad4 AMR exome

AF:

0.576

Gnomad4 ASJ exome

AF:

0.695

Gnomad4 EAS exome

AF:

0.651

Gnomad4 SAS exome

AF:

0.592

Gnomad4 FIN exome

AF:

0.671

Gnomad4 NFE exome

AF:

0.649

Gnomad4 OTH exome

AF:

0.635

GnomAD4 genome

AF:

0.606

AC:

91352

AN:

150634

Hom.:

28050

Cov.:

AF XY:

0.603

AC XY:

44336

AN XY:

73534

show subpopulations

Gnomad4 AFR

AF:

0.497

Gnomad4 AMR

AF:

0.569

Gnomad4 ASJ

AF:

0.709

Gnomad4 EAS

AF:

0.631

Gnomad4 SAS

AF:

0.604

Gnomad4 FIN

AF:

0.667

Gnomad4 NFE

AF:

0.663

Gnomad4 OTH

AF:

0.620

Bravo

AF:

0.598

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Gamma-aminobutyric acid transaminase deficiency

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over