dbSNP rs41311266: ABAT:c.954+16C>T (chr16-8772933-C-T) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_020686.6(ABAT):c.954+16C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00752 in 1,612,984 control chromosomes in the GnomAD database, including 85 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0058 ( 7 hom., cov: 31)

Exomes 𝑓: 0.0077 ( 78 hom. )

Consequence

ABAT
NM_020686.6 intron

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -1.88

Publications

2 publications found

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 Gene-Disease associations (from GenCC):

GABA aminotransaminase deficiency
Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae), Orphanet
genetic developmental and epileptic encephalopathy
Inheritance: AR Classification: MODERATE Submitted by: ClinGen

ABAT links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 16-8772933-C-T is Benign according to our data. Variant chr16-8772933-C-T is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 445320.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.00576 (876/152122) while in subpopulation SAS AF = 0.0102 (49/4806). AF 95% confidence interval is 0.00792. There are 7 homozygotes in GnomAd4. There are 416 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 7 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020686.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ABAT	NM_020686.6	MANE Select	c.954+16C>T	intron	N/A	NP_065737.2
ABAT	NM_001386615.1		c.1050+16C>T	intron	N/A	NP_001373544.1
ABAT	NM_001386616.1		c.954+16C>T	intron	N/A	NP_001373545.1	H3BNQ7

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ABAT	ENST00000268251.13	TSL:1 MANE Select	c.954+16C>T	intron	N/A	ENSP00000268251.8	P80404
ABAT	ENST00000569156.5	TSL:1	c.954+16C>T	intron	N/A	ENSP00000454963.1	H3BNQ7
ABAT	ENST00000566590.5	TSL:1	n.*694+16C>T	intron	N/A	ENSP00000455198.1	H3BP84

Frequencies

GnomAD3 genomes

AF:

0.00575

AC:

874

AN:

152004

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00135

Gnomad AMI

AF:

0.0263

Gnomad AMR

AF:

0.00439

Gnomad ASJ

AF:

0.0383

Gnomad EAS

AF:

0.000386

Gnomad SAS

AF:

0.00998

Gnomad FIN

AF:

0.000662

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.00742

Gnomad OTH

AF:

0.0105

GnomAD2 exomes

AF:

0.00709

AC:

1782

AN:

251372

AF XY:

0.00771

show subpopulations

Gnomad AFR exome

AF:

0.00123

Gnomad AMR exome

AF:

0.00301

Gnomad ASJ exome

AF:

0.0393

Gnomad EAS exome

AF:

0.000163

Gnomad FIN exome

AF:

0.000231

Gnomad NFE exome

AF:

0.00754

Gnomad OTH exome

AF:

0.00978

GnomAD4 exome

AF:

0.00770

AC:

11251

AN:

1460862

Hom.:

Cov.:

AF XY:

0.00792

AC XY:

5758

AN XY:

726730

show subpopulations

African (AFR)

AF:

0.00152

AC:

AN:

33446

American (AMR)

AF:

0.00313

AC:

140

AN:

44718

Ashkenazi Jewish (ASJ)

AF:

0.0400

AC:

1046

AN:

26128

East Asian (EAS)

AF:

0.000101

AC:

AN:

39698

South Asian (SAS)

AF:

0.0111

AC:

955

AN:

86198

European-Finnish (FIN)

AF:

0.000562

AC:

AN:

53392

Middle Eastern (MID)

AF:

0.0256

AC:

130

AN:

5078

European-Non Finnish (NFE)

AF:

0.00749

AC:

8326

AN:

1111918

Other (OTH)

AF:

0.00944

AC:

569

AN:

60286

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.473

Heterozygous variant carriers

623

1246

1870

2493

3116

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

322

644

966

1288

1610

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00576

AC:

876

AN:

152122

Hom.:

Cov.:

AF XY:

0.00559

AC XY:

416

AN XY:

74366

show subpopulations

African (AFR)

AF:

0.00135

AC:

AN:

41482

American (AMR)

AF:

0.00439

AC:

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.0383

AC:

133

AN:

3472

East Asian (EAS)

AF:

0.000387

AC:

AN:

5168

South Asian (SAS)

AF:

0.0102

AC:

AN:

4806

European-Finnish (FIN)

AF:

0.000662

AC:

AN:

10582

Middle Eastern (MID)

AF:

0.0340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00744

AC:

506

AN:

68016

Other (OTH)

AF:

0.0104

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

137

183

229

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0109

Hom.:

Bravo

AF:

0.00611

Asia WGS

AF:

0.00520

AC:

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign/Likely benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

Gamma-aminobutyric acid transaminase deficiency (2)

not provided (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.083

(source)

DANN

Benign

0.66

PhyloP100

-1.9

RBP_binding_hub_radar

0.67

RBP_regulation_power_radar

1.8

Mutation Taster

=100/0

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over