rs12133923

Variant names:

• chr1-153800764-C-A
• rs12133923
• ENST00000637918.1:c.134-10688G>T

Variant summary

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

The ENST00000637918.1(GATAD2B):​c.134-10688G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 152,362 control chromosomes in the GnomAD database, including 14,563 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 0.42 (14498 hom., cov: 31)
  • Exomes 𝑓: 0.44 (65 hom.)
• Consequence: GATAD2B ENST00000637918.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133

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]

ENSG00000231827 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GATAD2B	ENST00000637918.1	c.134-10688G>T		intron_variant	Intron 2 of 3	5		ENSP00000490724.1
ENSG00000231827	ENST00000427283.1	n.1511+52C>A		intron_variant	Intron 7 of 10	6

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64129 AN: 151624 Hom.: 14489 Cov.: 31

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.446

GnomAD4 exome AF: 0.444 AC: 275 AN: 620 Hom.: 65 AF XY: 0.424 AC XY: 174 AN XY: 410

Gnomad4 AFR exome AF: 0.250

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 0.250

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.449

Gnomad4 NFE exome AF: 0.424

Gnomad4 OTH exome AF: 0.571

GnomAD4 genome AF: 0.423 AC: 64153 AN: 151742 Hom.: 14498 Cov.: 31 AF XY: 0.416 AC XY: 30849 AN XY: 74166

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.576

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.434

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.449

Alfa AF: 0.474 Hom.: 2645

Bravo AF: 0.414

Asia WGS AF: 0.279 AC: 971 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	0.29
DANN	Benign	0.79

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12133923; hg19: chr1-153773240;