1-153806760-C-T

Position:

• chr1-153806760-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.*3417G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 130,780 control chromosomes in the GnomAD database, including 1,615 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 0.14 (1607 hom., cov: 26)
  • Exomes 𝑓: 0.20 (8 hom.)
• Consequence: GATAD2B NM_020699.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GATAD2B	NM_020699.4	c.*3417G>A		3_prime_UTR_variant	11/11	ENST00000368655.5	NP_065750.1
GATAD2B	XM_047426115.1	c.*3417G>A		3_prime_UTR_variant	11/11		XP_047282071.1
GATAD2B	XM_047426117.1	c.*3417G>A		3_prime_UTR_variant	11/11		XP_047282073.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GATAD2B	ENST00000368655.5	c.*3417G>A		3_prime_UTR_variant	11/11	1	NM_020699.4	ENSP00000357644	P1
GATAD2B	ENST00000637918.1	c.135+4971G>A		intron_variant		5		ENSP00000490724

Frequencies

GnomAD3 genomes AF: 0.140 AC: 18296 AN: 130238 Hom.: 1609 Cov.: 26

Gnomad AFR AF: 0.0745

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.0994

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.126

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.141

GnomAD4 exome AF: 0.199 AC: 87 AN: 438 Hom.: 8 Cov.: 0 AF XY: 0.214 AC XY: 56 AN XY: 262

Gnomad4 FIN exome AF: 0.199

Gnomad4 NFE exome AF: 0.250

Gnomad4 OTH exome AF: 0.167

GnomAD4 genome AF: 0.140 AC: 18291 AN: 130342 Hom.: 1607 Cov.: 26 AF XY: 0.150 AC XY: 9342 AN XY: 62452

Gnomad4 AFR AF: 0.0745

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.0994

Gnomad4 EAS AF: 0.505

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.142

Alfa AF: 0.0811 Hom.: 157

Bravo AF: 0.115

Asia WGS AF: 0.268 AC: 929 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.66
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs1127092; hg19: chr1-153779236;