rs12043354

chr1-153881948-C-T

Variant summary

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

The NM_020699.4(GATAD2B):c.-2+40785G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 151,914 control chromosomes in the GnomAD database, including 1,756 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 0.13 (1756 hom., cov: 32)
• Consequence: GATAD2B NM_020699.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GATAD2B	NM_020699.4	c.-2+40785G>A		intron_variant		ENST00000368655.5
GATAD2B	XM_047426115.1	c.2+34504G>A		intron_variant
GATAD2B	XM_047426117.1	c.-2+16908G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GATAD2B	ENST00000368655.5	c.-2+40785G>A		intron_variant		1	NM_020699.4	P1

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19695 AN: 151796 Hom.: 1757 Cov.: 32

Gnomad AFR AF: 0.0732

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.130 AC: 19688 AN: 151914 Hom.: 1756 Cov.: 32 AF XY: 0.135 AC XY: 10017 AN XY: 74242

Gnomad4 AFR AF: 0.0731

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.488

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.134

Alfa AF: 0.123 Hom.: 228

Bravo AF: 0.123

Asia WGS AF: 0.263 AC: 912 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
Cadd	Benign	7.6
Dann	Benign	0.73

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

Other links and lift over

dbSNP: rs12043354; hg19: chr1-153854424;