Variant rs4363451 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_020699.4(GATAD2B):c.729+15G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 1,579,648 control chromosomes in the GnomAD database, including 75,549 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.27 ( 6099 hom., cov: 32)

Exomes 𝑓: 0.31 ( 69450 hom. )

Consequence

GATAD2B
NM_020699.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.803

Variant links:

Genes affected

GATAD2B (HGNC:30778): (GATA zinc finger domain containing 2B) This gene encodes a zinc finger protein transcriptional repressor. The encoded protein is part of the methyl-CpG-binding protein-1 complex, which represses gene expression by deacetylating methylated nucleosomes. Mutations in this gene are linked to intellectual disability and dysmorphic features associated with cognitive disability. [provided by RefSeq, Jun 2016]

GATAD2B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.68).

BP6

Variant 1-153818025-C-T is Benign according to our data. Variant chr1-153818025-C-T is described in ClinVar as [Benign]. Clinvar id is 1285293.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-153818025-C-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
GATAD2B	NM_020699.4 linkuse as main transcript	c.729+15G>A	intron_variant	ENST00000368655.5	NP_065750.1	Q8WXI9
GATAD2B	XM_047426115.1 linkuse as main transcript	c.732+15G>A	intron_variant		XP_047282071.1
GATAD2B	XM_047426117.1 linkuse as main transcript	c.729+15G>A	intron_variant		XP_047282073.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
GATAD2B	ENST00000368655.5 linkuse as main transcript	c.729+15G>A	intron_variant	1	NM_020699.4	ENSP00000357644.4	Q8WXI9
GATAD2B	ENST00000634544.1 linkuse as main transcript	c.729+15G>A	intron_variant	5		ENSP00000489184.1	Q8WXI9
GATAD2B	ENST00000634408.1 linkuse as main transcript	c.729+15G>A	intron_variant	5		ENSP00000489595.1	A0A0U1RRM1
GATAD2B	ENST00000703630.1 linkuse as main transcript	c.306+15G>A	intron_variant			ENSP00000515408.1	A0A994J4D5

Frequencies

GnomAD3 genomes

AF:

0.268

AC:

40777

AN:

152012

Hom.:

6100

Cov.:

show subpopulations

Gnomad AFR

AF:

0.126

Gnomad AMI

AF:

0.224

Gnomad AMR

AF:

0.386

Gnomad ASJ

AF:

0.302

Gnomad EAS

AF:

0.285

Gnomad SAS

AF:

0.333

Gnomad FIN

AF:

0.343

Gnomad MID

AF:

0.326

Gnomad NFE

AF:

0.309

Gnomad OTH

AF:

0.295

GnomAD3 exomes

AF:

0.322

AC:

73044

AN:

226758

Hom.:

12506

AF XY:

0.325

AC XY:

40034

AN XY:

123150

show subpopulations

Gnomad AFR exome

AF:

0.118

Gnomad AMR exome

AF:

0.439

Gnomad ASJ exome

AF:

0.317

Gnomad EAS exome

AF:

0.273

Gnomad SAS exome

AF:

0.338

Gnomad FIN exome

AF:

0.340

Gnomad NFE exome

AF:

0.321

Gnomad OTH exome

AF:

0.337

GnomAD4 exome

AF:

0.309

AC:

440395

AN:

1427518

Hom.:

69450

Cov.:

AF XY:

0.310

AC XY:

219783

AN XY:

708702

show subpopulations

Gnomad4 AFR exome

AF:

0.117

Gnomad4 AMR exome

AF:

0.431

Gnomad4 ASJ exome

AF:

0.308

Gnomad4 EAS exome

AF:

0.302

Gnomad4 SAS exome

AF:

0.334

Gnomad4 FIN exome

AF:

0.344

Gnomad4 NFE exome

AF:

0.307

Gnomad4 OTH exome

AF:

0.300

GnomAD4 genome

AF:

0.268

AC:

40790

AN:

152130

Hom.:

6099

Cov.:

AF XY:

0.273

AC XY:

20311

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.126

Gnomad4 AMR

AF:

0.386

Gnomad4 ASJ

AF:

0.302

Gnomad4 EAS

AF:

0.286

Gnomad4 SAS

AF:

0.333

Gnomad4 FIN

AF:

0.343

Gnomad4 NFE

AF:

0.309

Gnomad4 OTH

AF:

0.292

Alfa

AF:

0.297

Hom.:

1879

Bravo

AF:

0.268

Asia WGS

AF:

0.285

AC:

994

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -

Severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Aug 10, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

1.7

DANN

Benign

0.79

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