rs10494303

Positions:

• chr1-153920547-G-A
• chr1-153920547-G-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+2186C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 152,050 control chromosomes in the GnomAD database, including 16,000 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 0.45 (16000 hom., cov: 32)
• Consequence: GATAD2B NM_020699.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.754 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GATAD2B	NM_020699.4	c.-2+2186C>T		intron_variant		ENST00000368655.5	NP_065750.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GATAD2B	ENST00000368655.5	c.-2+2186C>T		intron_variant		1	NM_020699.4	ENSP00000357644	P1

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68654 AN: 151932 Hom.: 15978 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.452 AC: 68716 AN: 152050 Hom.: 16000 Cov.: 32 AF XY: 0.459 AC XY: 34117 AN XY: 74332

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.496

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.774

Gnomad4 SAS AF: 0.483

Gnomad4 FIN AF: 0.521

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.456

Alfa AF: 0.438 Hom.: 23771

Bravo AF: 0.455

Asia WGS AF: 0.577 AC: 2010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.4
DANN	Benign	0.53

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: rs10494303; hg19: chr1-153893023;