chr1-153823093-T-C

Position:

• chr1-153823093-T-C

Variant summary

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

The NM_020699.4(GATAD2B):​c.336-3358A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 152,146 control chromosomes in the GnomAD database, including 6,368 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 0.28 (6368 hom., cov: 33)
• Consequence: GATAD2B NM_020699.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GATAD2B	NM_020699.4	c.336-3358A>G		intron_variant		ENST00000368655.5
GATAD2B	XM_047426115.1	c.339-3358A>G		intron_variant
GATAD2B	XM_047426117.1	c.336-3358A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GATAD2B	ENST00000368655.5	c.336-3358A>G		intron_variant		1	NM_020699.4	P1

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42219 AN: 152028 Hom.: 6367 Cov.: 33

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.278 AC: 42247 AN: 152146 Hom.: 6368 Cov.: 33 AF XY: 0.282 AC XY: 21005 AN XY: 74382

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.287

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.302

Alfa AF: 0.316 Hom.: 1915

Bravo AF: 0.279

Asia WGS AF: 0.289 AC: 1009 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.58

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: rs10796956; hg19: chr1-153795569;