rs1139620

chr1-153805372-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.*4805G>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 0.41 in 151,972 control chromosomes in the GnomAD database, including 13,906 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 0.41 (13905 hom., cov: 30)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: GATAD2B NM_020699.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196

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=-0.85).
• 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/exons	MANE	UniProt
GATAD2B	NM_020699.4	c.*4805G>A		3_prime_UTR_variant	11/11	ENST00000368655.5
GATAD2B	XM_047426115.1	c.*4805G>A		3_prime_UTR_variant	11/11
GATAD2B	XM_047426117.1	c.*4805G>A		3_prime_UTR_variant	11/11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GATAD2B	ENST00000368655.5	c.*4805G>A		3_prime_UTR_variant	11/11	1	NM_020699.4	P1
GATAD2B	ENST00000637918.1	c.135+6359G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62304 AN: 151848 Hom.: 13901 Cov.: 30

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.0585

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.433

GnomAD4 exome AF: 0.500 AC: 3 AN: 6 Hom.: 1 Cov.: 0 AF XY: 0.750 AC XY: 3 AN XY: 4

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.410 AC: 62320 AN: 151966 Hom.: 13905 Cov.: 30 AF XY: 0.401 AC XY: 29777 AN XY: 74262

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.0582

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.436

Alfa AF: 0.488 Hom.: 20177

Bravo AF: 0.394

Asia WGS AF: 0.235 AC: 818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	8.8
Dann	Benign	0.54

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: rs1139620; hg19: chr1-153777848;