1-153838088-C-T

Position:

• chr1-153838088-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.-1-9740G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 152,048 control chromosomes in the GnomAD database, including 6,106 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 0.27 (6106 hom., cov: 32)
• Consequence: GATAD2B NM_020699.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GATAD2B	NM_020699.4	c.-1-9740G>A		intron_variant		ENST00000368655.5	NP_065750.1
GATAD2B	XM_047426115.1	c.3-9740G>A		intron_variant			XP_047282071.1
GATAD2B	XM_047426117.1	c.-1-9740G>A		intron_variant			XP_047282073.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GATAD2B	ENST00000368655.5	c.-1-9740G>A		intron_variant		1	NM_020699.4	ENSP00000357644.4

Frequencies

GnomAD3 genomes AF: 0.270 AC: 41064 AN: 151930 Hom.: 6105 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.270 AC: 41092 AN: 152048 Hom.: 6106 Cov.: 32 AF XY: 0.275 AC XY: 20476 AN XY: 74326

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.384

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.283

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.292

Alfa AF: 0.241 Hom.: 1118

Bravo AF: 0.270

Asia WGS AF: 0.283 AC: 988 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.1
DANN	Benign	0.63

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: rs7512766; hg19: chr1-153810564;